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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttcatttgtgattggtttggttgtaattatagcttgtaaataataaatcatgtcttctttgtcataggctcactttgatctttcctctgttcttttagGTGGGCGATTGTATATCTGGCACAGATGAAACCACTCATTGTGCCTATACTGAACGAGGGTGAATAAGTCTCTGAACAGATGTAACTCCTTGTAAGTTAG

Basic information

species Glycine max
transcript GLYMA08G43510.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G43510.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv00s0187g00310.t01 (Vitis vinifera), 3'ss of exon 3
----ttttcatttgtgattggtttggttgtaattatagcttgtaaataataaatcatgtcttctttgtcataggctcactttgatctttcctctgttcttttagGTGGGCGATTGTATATCTGGCACAGATGAAACCACTCATTGTGCCTATACTGAACGAGGGTGAATAAG-TCTCTGAACAGATGTAACTCCTTGTAAGTTAG
    |||   ||| |  ||    ||    | | |  ||   | | || || |  ||| | || | ||     |  | |||   |||  | |||   | | |||||||||| ||||||||||||||||||||||| ||||||||||| || || || || || |  || | || |   |  ||| |     |     | |  ||  
gcattttatttttatttttatagtgaacttgaatgcagtaggaatatcattatgcatattttatatggt---gatttactaaaatcccttctccact-tgttagGTGGGCAATTGTATATCTGGCACAGATGAACCCACTCATTGTCCCAATCCTCAATGAAGTGGAGTGAGATGATTCTACAAAGAGTGCATGCGGAAGATTG-

upper sequence: GLYMA08G43510.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv00s0187g00270.t01 (Vitis vinifera), 3'ss of exon 3
ttttcatttgtgattggtttggttgtaa--ttatagcttgtaaataataaatcatgtcttctttgt-cataggctcactttgatctttcctctgttcttttagGTGGGCGATTGTATATCTGGCACAGATGAAACCACTCATTGTGCCTATACTGAACGAGGGTGAATAAG-TCTCTGAACAGATGTAACTCCTTGTAAGTTAG
  | ||||| | |    |||  | || |  ||  |    |||   |    || |||  |  ||| |     |  | |||   |||  | |||   | | |||||||||| ||||||||||||||||||||||| ||||||||||| || || || || || |  || | || |   |  ||| |     |     | |  ||  
--tgcattttttaaaatttttatagtgaacttgaatgcagtaggaatgtcattatgcatattttatatggtgatttactaaaatcccttctccact-tgttagGTGGGCAATTGTATATCTGGCACAGATGAATCCACTCATTGTCCCAATCCTCAATGAAGTGGAGTGAGATGATTCTACAAAGAGTGCATGCGGAAGATTG-
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|58020284|gb|CX707026.1|CX707026
EST:     ATTTCACCTTACTTTGGTAATTACTGCAACAATTTGCTGCTGGATGAT                         GTGGGCGATTGTATATCTGGCACAGATGAAACCACTCATTGTGCCTATACT
genomic: ATTTCACCTTACTTTGGTAATTACTGCAACAATTTGCTGCTGGATGATgtaagtgttg ... gttcttttagGTGGGCGATTGTATATCTGGCACAGATGAAACCACTCATTGTGCCTATACT
EST: gi|5688382|gb|AI941397.1|AI941397
EST:     ATTTCACCTTACTTTGGTAATTACTGCAACAATTTGCTGCTGGATGAT                         GTGGGCGATTGTATATCTGGCACAGATGAAACCACTCATTGTGCCTATACT
genomic: ATTTCACCTTACTTTGGTAATTACTGCAACAATTTGCTGCTGGATGATgtaagtgttg ... gttcttttagGTGGGCGATTGTATATCTGGCACAGATGAAACCACTCATTGTGCCTATACT
EST: gi|192308067|gb|FK000395.1|FK000395
EST:     ATTTCACCTTACTTTGGTAATTACTGCAACAATTTGCTGCTGGATGAT                         GTGGGCGATTGTATATCTGGCACAGATGAAACCACTCATTGTGCCTATACT
genomic: ATTTCACCTTACTTTGGTAATTACTGCAACAATTTGCTGCTGGATGATgtaagtgttg ... gttcttttagGTGGGCGATTGTATATCTGGCACAGATGAAACCACTCATTGTGCCTATACT
EST: gi|19936520|gb|BQ080902.1|BQ080902
EST:     ATTTCACCTTACTTTGGTAATTACTGCAACAATTTGCTGCTGGATGAT                         GTGGGCGATTGTATATCTGGCACAGATGAAACCACTCATTGTGCCTATACT
genomic: ATTTCACCTTACTTTGGTAATTACTGCAACAATTTGCTGCTGGATGATgtaagtgttg ... gttcttttagGTGGGCGATTGTATATCTGGCACAGATGAAACCACTCATTGTGCCTATACT
EST: gi|151412736|gb|EV282548.1|EV282548
EST:     ATTTCACCTTACTTTGGTAATTACTGCAACAATTTGCTGCTGGATGAT                         GTGGGCGATTGTATATCTGGCACAGATGAAACCACTCATTGTGCCTATACT
genomic: ATTTCACCTTACTTTGGTAATTACTGCAACAATTTGCTGCTGGATGATgtaagtgttg ... gttcttttagGTGGGCGATTGTATATCTGGCACAGATGAAACCACTCATTGTGCCTATACT
EST: gi|10253951|gb|BE821766.1|BE821766
EST:     ATTTCACCTTACTTTGGTAATTACTGCAACAATTTGCTGCTGGATGAT                         GTGGGCGATTGTATATCTGGCACAGATGAAACCACTCATTGTGCCTATACT
genomic: ATTTCACCTTACTTTGGTAATTACTGCAACAATTTGCTGCTGGATGATgtaagtgttg ... gttcttttagGTGGGCGATTGTATATCTGGCACAGATGAAACCACTCATTGTGCCTATACT
EST: gi|298193950|gb|HO040598.1|HO040598
EST:     ATTTCACCTTACTTTGGTAATTACTGCAACAATTTGCTGCTGGATGAT                         GTGGGCGATTGTATATCTGGCACA
genomic: ATTTCACCTTACTTTGGTAATTACTGCAACAATTTGCTGCTGGATGATgtaagtgttg ... gttcttttagGTGGGCGATTGTATATCTGGCACA
EST: gi|192331111|gb|FK020331.1|FK020331
EST:     ATTTCACCTTACTTTGGTAATTACTGCAACAATTTGCTGCTGGATGAT                         GTGGGCGATTGTATATCTGGCACAGATGAAACCACTCATTGTGCCTATACT
genomic: ATTTCACCTTACTTTGGTAATTACTGCAACAATTTGCTGCTGGATGATgtaagtgttg ... gttcttttagGTGGGCGATTGTATATCTGGCACAGATGAAACCACTCATTGTGCCTATACT
EST: gi|213588897|gb|DB969544.1|DB969544
EST:     ATTTCACCTTACTTTGGTAATTACTGCAACAATTTGCTGCTGGATGAT                         GTGGGCGATTGTATATCTGGCACAGATGAAACCACTCATTGTGCCTATACT
genomic: ATTTCACCTTACTTTGGTAATTACTGCAACAATTTGCTGCTGGATGATgtaagtgttg ... gttcttttagGTGGGCGATTGTATATCTGGCACAGATGAAACCACTCATTGTGCCTATACT
EST: gi|192334376|gb|FK024097.1|FK024097
EST:     ATTTCACCTTACTTTGGTAATTACTGCAACAATTTGCTGCTGGATGAT                         GTGGGCGATTGTATATCTGGCACAGATGAAACCACTCATTGTGCCTATACT
genomic: ATTTCACCTTACTTTGGTAATTACTGCAACAATTTGCTGCTGGATGATgtaagtgttg ... gttcttttagGTGGGCGATTGTATATCTGGCACAGATGAAACCACTCATTGTGCCTATACT
EST: gi|192313404|gb|FK005498.1|FK005498
EST:     ATTTCACCTTACTTTGGTAATTACTGCAACAATTTGCTGCTGGATGAT                         GTGGGCGATTGTATATCTGGCACAGATGAAGCCACTCATTGTGCCTATACT
genomic: ATTTCACCTTACTTTGGTAATTACTGCAACAATTTGCTGCTGGATGATgtaagtgttg ... gttcttttagGTGGGCGATTGTATATCTGGCACAGATGAAACCACTCATTGTGCCTATACT
EST: gi|58016702|gb|CX703444.1|CX703444
EST:     ATTTCACCTTACTTTGGTAATTACTGCAACAATTTGCTGCTGGATGAT                         GTGGGCGATTGTATATCTGGCACAGATGAAACCACTCATTGTGCCTATACT
genomic: ATTTCACCTTACTTTGGTAATTACTGCAACAATTTGCTGCTGGATGATgtaagtgttg ... gttcttttagGTGGGCGATTGTATATCTGGCACAGATGAAACCACTCATTGTGCCTATACT
EST: gi|5770380|gb|AI973554.1|AI973554
EST:     ATTTCACCTTACTTTGGTAATTACTGCAACAATTTGCTGCTGGATGAT                         GTGGGCGATTGTATATCTGGCACAGATGAAACCACTCATTGTGCCTATACT
genomic: ATTTCACCTTACTTTGGTAATTACTGCAACAATTTGCTGCTGGATGATgtaagtgttg ... gttcttttagGTGGGCGATTGTATATCTGGCACAGATGAAACCACTCATTGTGCCTATACT
EST: gi|18717556|gb|BM522959.1|BM522959
EST:     ATTTCACCTTACTTTGGTAATTACTGCAACAATTTGCTGCTGGATGAT                         GTGGGCGATTGTATATCTGGCACAGATGAAACCACTCATTGTGCCTATACT
genomic: ATTTCACCTTACTTTGGTAATTACTGCAACAATTTGCTGCTGGATGATgtaagtgttg ... gttcttttagGTGGGCGATTGTATATCTGGCACAGATGAAACCACTCATTGTGCCTATACT
EST: gi|37996659|gb|CF808248.1|CF808248
EST:     ATTTCACCTTACTTTGGTAATTACTGCAACAATTTGCTGCTGGATGAT                         GTGGGCGATTGTATATCTGGCACAGATGAAACCACTCATTGTGCCTATACT
genomic: ATTTCACCTTACTTTGGTAATTACTGCAACAATTTGCTGCTGGATGATgtaagtgttg ... gttcttttagGTGGGCGATTGTATATCTGGCACAGATGAAACCACTCATTGTGCCTATACT
EST: gi|58015787|gb|CX702529.1|CX702529
EST:     ATTTCACCTTACTTTGGTAATTACTGCAACAATTTGCTGCTGGATGAT                         GTGGGCGATTGTATATCTGGCACAGATGAAACCACTCATTGTGCCTATACT
genomic: ATTTCACCTTACTTTGGTAATTACTGCAACAATTTGCTGCTGGATGATgtaagtgttg ... gttcttttagGTGGGCGATTGTATATCTGGCACAGATGAAACCACTCATTGTGCCTATACT
EST: gi|192334377|gb|FK024098.1|FK024098
EST:     TTTCACCTTACTTTGGTAATTACTGCAACAATTTGCTGCTGGATGAT                         GTGGGCGATTGTATATCTGGCACAGATGAAACCACTCATTGTGCCTATACT
genomic: TTTCACCTTACTTTGGTAATTACTGCAACAATTTGCTGCTGGATGATgtaagtgttg ... gttcttttagGTGGGCGATTGTATATCTGGCACAGATGAAACCACTCATTGTGCCTATACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaatcatgtcttctttgtcataggctcactttgatctttcctctgttcttttagGTGGGCGATTGTATATCTGGCACAGATGAAACCACTCATTGTGCCTATACTGAACGAGGGTGAATAAGTCTCTGAACAGATGTAACTCCTTGTAAGTTAG
                         ctcactttgatctttc  CT-rich tract
                                              ttctttta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttcatttgtgattggtttggttgtaattatagcttgtaaataataaatcatgtcttctttgtcataggctcactttgatctttcctctgttcttttagGTGGGCGATTGTATATCTGGCACAGATGAAACCACTCATTGTGCCTATACTGAACGAGGGTGAATAAGTCTCTGAACAGATGTAACTCCTTGTAAGTTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - -ggtttgg
- - - - - - - - - - - - - - - - -gcttgta
- - - - - - - - - - - - - - - - - - - - - - - - -tcatgtc