Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atacatataaaatttttttttttccttctgaaaggtaatctaagttaaacatgcaactgtttcaattaaatttttttagttttaacctcctctaccccagGTCCTCACTTCAATCCGTTCAAGAAGGATCATGGGGCTCCTTCAGATGATAAGCGCCATGCTGGTGATTTGGGCAACATTGCTGCAGGCCCTGATG

Basic information

species Glycine max
transcript GLYMA16G27020.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G27020.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0007g07280.t01 (Vitis vinifera), 3'ss of exon 2
atacatataaaatttttttttttccttctgaaaggtaatctaagttaaacatgcaact--gtttcaattaaatttttttagttt-taacctcctctaccccagGTCCTCACTTCAATCCGTTCAAGAAGGATCATGGGGCTCCTTCAGATGATAAGCGCCATGCTGGTGATTTGGGCAACATTGCTGCAGGCCCTGATG
     |||  | |||| |||  | | | |       || | ||   ||   |   | |  | | |  ||  || || | |||   |    |    ||    ||| || || || |||||  | ||||| |||||||| |||||| ||||| |  |||||||||||||||||||||| ||||| | ||| || || ||||
---gttatttacttttgtttcattcattttctctacaaccaaacagaatagtagcattttgctcctgtttgatcttctaagtgggttttgtatcttattttagGACCCCATTTTAATCCACTGAAGAAAGATCATGGCGCTCCTACAGATAAAGAGCGCCATGCTGGTGATTTGGGAAACATCGTTGCCGGTCCAGATG
















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|23058846|gb|BU578339.1|BU578339
EST:     TCCATATTCATG-TTCTCNGTTGACACCACCAATGGCTGCAACTCCACTG                         GTCCTCACTTCAATCCGTTCAAGAAGGATCATGGGGCTCCTTCAGATGATA
genomic: TCCATATTCATGCTT-T-TGGTGACACCACCAATGGCTGCAACTCCACTGgttctctctt ... tctaccccagGTCCTCACTTCAATCCGTTCAAGAAGGATCATGGGGCTCCTTCAGATGATA
EST: gi|31470014|gb|CD412042.1|CD412042
EST:     GTTCCATATTCATGCTTTTGGTGACACCACCAATGGCTGCAACTCCACTG                         GTCCTCACTTCAATCCGTTCAAGAAGGATCATGGGGCTCCTTCAGATGATA
genomic: GTTCCATATTCATGCTTTTGGTGACACCACCAATGGCTGCAACTCCACTGgttctctctt ... tctaccccagGTCCTCACTTCAATCCGTTCAAGAAGGATCATGGGGCTCCTTCAGATGATA
EST: gi|31470725|gb|CD412753.1|CD412753
EST:     GTTCCATATTCATGCTTTTGGTGACACCACCAATGGCTGCAACTCCACTG                         GTCCTCACTTCAATCCGTTCAAGAAGGATCATGGGGCTCCTTCAGATGATA
genomic: GTTCCATATTCATGCTTTTGGTGACACCACCAATGGCTGCAACTCCACTGgttctctctt ... tctaccccagGTCCTCACTTCAATCCGTTCAAGAAGGATCATGGGGCTCCTTCAGATGATA
EST: gi|7146773|gb|AW508695.1|AW508695
EST:     GTTCCATATTCATGCTTTTGGTGACACCACCAATGGCTGCAACTCCACTG                         GTCCTCACTTCAATCCGTTCAAGAAGGATCATGGGGCTCCTTCAGATGATA
genomic: GTTCCATATTCATGCTTTTGGTGACACCACCAATGGCTGCAACTCCACTGgttctctctt ... tctaccccagGTCCTCACTTCAATCCGTTCAAGAAGGATCATGGGGCTCCTTCAGATGATA
EST: gi|209702151|gb|BW677951.1|BW677951
EST:     GTTCCATATTCATGCTTTTGGTGACACCACCAATGGCTGCAACTCCACTG                         GTCCTCACTTCAATCCGTTCAAGAAGGATCATGGGGCTCCTTCAGATGATA
genomic: GTTCCATATTCATGCTTTTGGTGACACCACCAATGGCTGCAACTCCACTGgttctctctt ... tctaccccagGTCCTCACTTCAATCCGTTCAAGAAGGATCATGGGGCTCCTTCAGATGATA
EST: gi|192334422|gb|FK024115.1|FK024115
EST:     GTTCCATATTCATGCTTTTGGTGACACCACCAATGGCTGCAACTCCACTG                         GTCCTCACTTCAATCCGTTCAAGAAGGATCATGGGGCTCCTTCAGATGATA
genomic: GTTCCATATTCATGCTTTTGGTGACACCACCAATGGCTGCAACTCCACTGgttctctctt ... tctaccccagGTCCTCACTTCAATCCGTTCAAGAAGGATCATGGGGCTCCTTCAGATGATA
EST: gi|6747004|gb|AW317460.1|AW317460
EST:     GTTCCATATTCATGCTTTTGGTGACACCACCAATGGCTGCAACTCCACTG                         GTCCTCACTTCAATCCGTTCAAGAAGGATCATGGGGCTCCTTCAGATGATA
genomic: GTTCCATATTCATGCTTTTGGTGACACCACCAATGGCTGCAACTCCACTGgttctctctt ... tctaccccagGTCCTCACTTCAATCCGTTCAAGAAGGATCATGGGGCTCCTTCAGATGATA
EST: gi|31472202|gb|CD414230.1|CD414230
EST:     GTTCCATATTCATGCTTTTGGTGACACCACCAATGGCTGCAACTCCACTG                         GTCCTCACTTCAATCCGTTCAAGAAGGATCATGGGGCTCCTTCAGATGATA
genomic: GTTCCATATTCATGCTTTTGGTGACACCACCAATGGCTGCAACTCCACTGgttctctctt ... tctaccccagGTCCTCACTTCAATCCGTTCAAGAAGGATCATGGGGCTCCTTCAGATGATA
EST: gi|209702150|gb|BW677950.1|BW677950
EST:     GTTCCATATTCATGCTTTTGGTGACACCACCAATGGCTGCAACTCCACTG                         GTCCTCACTTCAATCCGTTCAAGAAGGATCATGGGGCTCCTTCAGATGATA
genomic: GTTCCATATTCATGCTTTTGGTGACACCACCAATGGCTGCAACTCCACTGgttctctctt ... tctaccccagGTCCTCACTTCAATCCGTTCAAGAAGGATCATGGGGCTCCTTCAGATGATA
EST: gi|298171130|gb|HO016162.1|HO016162
EST:     GTTCCATATTCATGCTTTTGGTGACACCACCAATGGCTGCAACTCCACTG                         GTCCTCACTTCAATCCGCTCAAGAAGGATCATGGGGCTCCTTCAGATGATA
genomic: GTTCCATATTCATGCTTTTGGTGACACCACCAATGGCTGCAACTCCACTGgttctctctt ... tctaccccagGTCCTCACTTCAATCCGTTCAAGAAGGATCATGGGGCTCCTTCAGATGATA
EST: gi|10255867|gb|BE823633.1|BE823633
EST:     GTTCCATATTCATGCTTTTGGTGACACCACCAATGGCTGCAACTCCACTG                         GTCCTCACTTCAATCCGTTCAAGAAGGATCATGGGGCTCCTTCAGATGATA
genomic: GTTCCATATTCATGCTTTTGGTGACACCACCAATGGCTGCAACTCCACTGgttctctctt ... tctaccccagGTCCTCACTTCAATCCGTTCAAGAAGGATCATGGGGCTCCTTCAGATGATA
EST: gi|298197096|gb|HO041839.1|HO041839
EST:     GTTCCATATTCATGCTTTTGGTGACACCACCAATGGCTGCAACTCCACTG                         GTCCTCACTTCAATCCGTTCAAGAAGGATCATGGGGCTCCTTCAGATGATA
genomic: GTTCCATATTCATGCTTTTGGTGACACCACCAATGGCTGCAACTCCACTGgttctctctt ... tctaccccagGTCCTCACTTCAATCCGTTCAAGAAGGATCATGGGGCTCCTTCAGATGATA
EST: gi|15200962|gb|BI424621.1|BI424621
EST:     GTTCCATATTCATGCTTTTGGTGACACCACCAATGGCTGCAACTCCACTG                         GTCCTCACTTCAATCCGTTCAAGAAGGATCATGGGGCTCCTTCAGATGATA
genomic: GTTCCATATTCATGCTTTTGGTGACACCACCAATGGCTGCAACTCCACTGgttctctctt ... tctaccccagGTCCTCACTTCAATCCGTTCAAGAAGGATCATGGGGCTCCTTCAGATGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaacatgcaactgtttcaattaaatttttttagttttaacctcctctaccccagGTCCTCACTTCAATCCGTTCAAGAAGGATCATGGGGCTCCTTCAGATGATAAGCGCCATGCTGGTGATTTGGGCAACATTGCTGCAGGCCCTGATG
                                  ttttaac  putative branch site (score: 2)
                                        cctcctctacccc  CT-rich tract
         aactgtttcaattaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atacatataaaatttttttttttccttctgaaaggtaatctaagttaaacatgcaactgtttcaattaaatttttttagttttaacctcctctaccccagGTCCTCACTTCAATCCGTTCAAGAAGGATCATGGGGCTCCTTCAGATGATAAGCGCCATGCTGGTGATTTGGGCAACATTGCTGCAGGCCCTGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - -ccttctg
- - - - - - - - - - - - - - - - - - - - - - - - acatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgtttc