Human ALU Subfamilies

Summary

Re-analysis of the Human ALU subfamily structure using coseg an extended version of the Price et al algorithim ( Whole-genome analysis of Alu repeat elements reveals complex evolutionary history, Alkes L. Price, Eleazar Eskin, and Pavel Pevzner, 2004 Genome Research ). The new analysis was based on 562,843 Alu sequences collected from human and aligned against AluSx. New subfamilies ( highlighted with red in the tree ) and existing subfamilies were then re-aligned to AluJo to create the multiple alignment.

Alignments

structure : <<<<------------------------------- L E F T M O N O M E R ---------------------------------------------------------------<<<<>>>>---------------------------------- R I G H T M O N O M E R -------------------------------------------------------------------------------------->>>> structure [1] : <------A BOX----> <--B BOX--*> Reference ( alu-canonical ) : GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGAGGATCGCTTGAGCCCAGGAGTTCGAGACCAGCCTGGGCAACATAGCGAGACCCCGTCTCTACAAAAAATACAAAAA-TTAGCCGGGCGTGGTGGCGCGCGCCTGTAGTCCCAGCTACTCGG-GAGGCTGAGGCAGGAGGATCGCTTGAGCCCAGGAGTTC-GAGGCTGCAGTGAGCTATGATCGCGCC-----------ACTGCACTCCA-------GCCTGGGCGACA-GAGCGAGACCCTGTCTC 7SLRNA#SINE/Alu 187bp deletion at ^ : ...............G.ii.......i.......TAi.i.......i....i................i..........^^^^........i........................TA......A.A..... 7SLRNA#SINE/Alu 157bp deletion at ^ : ........i.........i...................... ..........ii...............i.......... Ti.....i....C......^^^^^... ........... .....i..i... T..........i..... FAM#SINE/Alu : ........i................................ ...........i.......................... .......i....C..............TGTGAATAGCC........... .....i..i... T..........i..... FRAM#SINE/Alu : ........i................................ ...........i.......................... ........................... ........... ............ ...........i..... FLAM_A#SINE/Alu : ...............G.i........i.......TAi.i.......i......................................................................A......A.A..... FLAM_C#SINE/Alu : ......................................................................................................................A......A.A.....

AluJo#SINE/Alu RepbaseID: ALU : R.................................................................................................................................... ............................................ ...................................... ........................... ........... ............ ................. AluJr#SINE/Alu : R....................................................................G.........................................................i..... ............................................ ...........i.......................... ........................... ........... ............ ................. AluJr4#SINE/Alu : R....................................................................G........................................................Ni..... .................................i.......... ...................................... ....i.i.................... ........... ............ ................. AluJb#SINE/Alu : R.............................................................i.....................................i.i..i........................... ............................................ ..............................i....G.. ...............ii.......... ........... ............ .................

AluSz#SINE/Alu : R.......................................................C.....i......Gi......................C......i.i..i.............T............. .............................i.............. ................i.........i...i....GiG ....i..........iiA......... ........... ............ .........i.i..... AluSz6#SINE/Alu : R.......................................................C.....i......G.......................C......i..i.i.............T............. .............................i.............. ............C...i.........i...i....GiG ....i..........iiA......... ........... ............ .........i....... AluSx#SINE/Alu : R.......................................................C.....i.i....Gi......................C......i.i..i.............T............. .............................i.............. ................i.........i...i....GiG ....i..........iiA......... ........... ............ .........i.i..... AluSx1#SINE/Alu : R.......................................................C.....i.i....Gi......................C......i.i..i.............T............. ...................G.........i.............. ................i.........i...i....GiG ....i..........iiA......... ........... ............ .........i.i..... AluSx3#SINE/Alu : R.......................................................C.....i.--...Gi......................C......i.i..i.............T.............A............................................ ................i.........i...i....GiG ....i..........iiA......... ........... ............ .........i.i..... AluSx4#SINE/Alu : R.......................................................C.....i..-...Gi......................C...i..i.i..i.............T............. ............................................ .............i..i.........i...i....GiG ....i..........iiA......... ........... ............ .........i.i..... AluSg#SINE/Alu : R.......................................................C.....i.--...Gi......................C......i.i..i.............T............. .............................i.............. ................i.........i...i....GiG ....i..........iiA......... ........... ............ .........i.i..... AluSg4#SINE/Alu : R.......................................................T.....i.--...Gi......................C...G..i.i..i.............T............. ...........i.......G.........i.............. ................i.........i...i....GiG ....i..........iiA......... ........... ............ .........i.i..... AluSg7#SINE/Alu [2] : R.......................................................T.....i.--...Gi.........i............C...G..i.i..i.............T............. ...................G.........i.............. .............-..i..i......i...i....GiG ....i..........iiA......... ........... ............ .........i.i..... AluSq#SINE/Alu : R.......................................................C.....i.i....Gi......................C......i.i..i.............T............. ...................G.........i.............. ................i.........i...i....GiG ....i..........iiA......... ........... ........i...A......i..i.i..... AluSq2#SINE/Alu : R.......................................................C.....i.i....Gi......................C......i.i..i.............T............. ...................G.........i.............. ................i.........i...i....GiG ....i..........iiA......... .i......... ............A......i..i.i..... AluSq4#SINE/Alu : R.......................................................C.....i..-...Gi......................C......i.i..i.............T............. ...................G.........i.............. ................i.........iA..i.i..GiG ....i..........iiA......... ........... ........i...A......i..i.i..... AluSq10#SINE/Alu : R.......................................................T.....i.i....Gi.........T............C......i.i..i.............T............. ..................iG.........i.............. .i...i..........i.........i...i....GiG ....i..........iiA......... .ii........ .......G....A.........iii..... AluSp#SINE/Alu : R.......................................................C.....i.i....Gi.i...................iC......i.A..i.............T............. .............................i.............. ................i.........i...i....GiG ....i...i......iiA......... .i......... ........i...A......i..i.i.....

AluSc8#SINE/Alu [3] : R.......................................................C.....i.--...Gi......A.........T.....Ci....ii.i..i.............T.............A..................i......................... ................i.........i...i....GiG ....i..........iiA......... ........... ............ .........i.i..... AluSc#SINE/Alu : R.......................................................C.....i.--...Gi..i...A.........T.....C......i.i..i.............T............. ............................................ ................i.........i...i....GiG ....i..........iiA......... ........... ......-..... .........i.i..... AluSc5#SINE/Alu : R.......................................................C.....i.--...Gi......A.........T.....C......i.i..i.............T............. .....i...............i.......i.............. ................i.........i..Ai.....iG ....i..........iiA......... ........... ......-..... .........i.i..... AluY#SINE/Alu : R.......................................................C.....i.--...Gi......A.........T.....Ci....ii.i..i.............T.............A...................G........................ ................i..G..G...i...i....GiG ...Ci..........iiA......... ........... ............ .........i.i..... AluYb8#SINE/Alu : ........................................................T.....i--....Gi......A.........T.....Ci....Ai.i..i.............T.............A...........ii......G........................ ................i..G..G...i...i...iGiG ...Ci..........iiA...i..... ......G...iCAGTCCG............ .........i.i..... AluYb9#SINE/Alu : ........................................................T.....i--....Gi......A.........T.....Ci....Ai.i..i.............T.............A...........i.......G.....................G.. ................i..G..G...i...i...iGiG ...Ci..........iiA...i..... ......G...iCAGTCCG............ .........i.i..... AluYh9#SINE/Alu : ...............................................A........C.....i--....Gi......A.........T.....Ci...iii.i..i......i......T.............A...................G........i.....i......... ................i..G..G...i...i....GiG ...Ci...........iA.i....... .......i... ............ .........i.i..... AluYg6#SINE/Alu : ...................................................i....C.....i.--...Gi......A.........T.....Ci....ii.i..i.............T.............A..........i.............................A... ................i..G..G...i...i....GiG ...Ci.........iiiA......... ........... ............ ......i..i.i..... AluYa5#SINE/Alu : ........................................................C.....i.--...Gi......A.........T..i..Ci..A.ii.i..i.............T.............A............i......G.....................i.. ................i..G..G...i...i....GiG ...Ci..........iiA....C.... ........... ............ .........i.i..... AluYa8#SINE/Alu : ........................................................C.....i.--...Gi......A.........T..i..Ci..A.ii.i..i.............T....C........ A...........i......G.............i.......i.. ................i..G..G...i...i....GiG ...Ci..........iiA....C.... ........... ............ .........i.i..... AluYe5#SINE/Alu [4] : R.......................................................C.....i.--...Gi......A.........T.....Ci....ii.i..i.............T.............A...........A.......G........................ ................i..G..G...i...C..i.GG.G...C...........iiA......... ........... ............ .--......i.i..... AluYe6#SINE/Alu [5] : R.......................................................C.....i.--...Gi......A.........T.....Ci....ii.i..i.............T.............A...........A.......G....................G... ................i..G..G...i...C..i.GG.G...C...........iiA......... ........... ............ .--......i.i..... AluYk4#SINE/Alu : R.......................................................C.....i.--...Gi......A.........T.....Ci....ii.i..i.............T.............A...........i.......G........................ ................i..G..G...i...i....GiG ...Ci..........iiA...A..... ......G...i ..........A. .........i.i..... AluYk12#SINE/Alu : R.......................................................C.....i.--...Gi......A.........T.....Ci....ii.i..i.............T.............A.................i.G.........i.............. ................i..G..A...i....i...GiG ...Ci..........iiG...A..... ......G.... ..i.......A. ...i.....i.i..... AluYk11#SINE/Alu : R..i....................................................C.....i.--i..Gi......A.........T.i...Ci....ii.i..i.............T.............A...........i.......G........................ ................i..G..G...i..ii....GiG ...Ci..........iiA...i..... ......A...i ........T.A. .....i...i.i..... AluYc#SINE/Alu : R.......................................................C.....i.--...Gi......A.........------------ii.i..i.............T.............A...........i.......G........................ ................i..G..G...i...i....GiG ...Ci..........iiA......... ........... ............ .........i.i..... AluYc3#SINE/Alu RepbaseID: AluYd3a1 : R.....................i.................................C.....i.--...Gi......A.........------------ii.i..i.............T.............A...........i.......G........................A................i..G..G...i...i....GiG ...Ci..........iiA......... ........... ............ .........i.i..... AluYc5#SINE/Alu : R.......................................................C.....i.--...Gi......A.........------------ii.i..i.............T.............A...........ii......G........................ ................i..G..G...i...i.i..GiG ...Ci..........GiA......... ..A.......C ............ .........i.i..... AluYd8#SINE/Alu : ........................................................C.....i.--...Gi......A.........------------ii.i..i.............T.............A...........ii......G........................ ................i..G..G...i...i.i..GiG ...Ci..........GiA......... ..A.......C ............ ..i......i.i.....

KEY

pink columns = CpG sites
"." = Matched base to AluJo canonical sequence
A-T = Transversion
i   = Transition
-   = Gap
^   = Chained alignments

[1] A/B Box Locations: Ludwig and Brosius et al. 2005. The asterisk in the B-Box indicates the location of the deleted 7SL S-domain.
[2] Perfect match to AluSg_4 defined by Alkes Price ( Price et al 2004 ). However we renamed to AluSg7 to follow the defacto nomenclature.
[3] Perfect match to AluSc_8 defined by Alkes Price ( Price et al 2004 ).
[4] Previously known as AluYf4
[5] Previously known as AluYf5

Tree

Zoomable PDF: alu-tree.pdf


Institute for Systems Biology This server is made possible by funding from the National Human Genome Research Institute (NHGRI grant # RO1 HG002939-01) 2003.