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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttattgtgctagtgtcttcttcatgcttgtgtttattatgctacagttgaatttgatgcaatgctagccaaaaatgttaatttcatttccttattttagGACATTGAGAAAGAAGTCAGAAAAGAAGTTGACGAAGCCATTGCTAAAGCAAAG

Basic information

species Glycine max
transcript GLYMA02G03080.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G03080.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g50620.1 (Oryza sativa), 3'ss of exon 5
------------------------cttattgtgctagtgtcttcttcatgcttgtgtttattat-gctacagttgaatttgatgcaatgctagccaaa-----aatgttaatt---tcatttccttattttagGACATTGAGAAAGAAGTCAGAAAAGAAGTTGACGAAGCCATTGCTAAAGCAAAG
                         ||| |||   ||||   | |  |||   ||  | | ||  | | || ||  ||||  ||  ||  |  |   |     |   || |||   |  ||   || | | ||||||| ||||||||| ||||||||||||| || || |||||||| |||||||||
gtatcatatcatatgtcaaatatgtttaatgtttaagtgatgtata-atgacagtcgtgactagagatgcaatttcatttagtggtatattctctgtattattatgattcattaacttgttcttttgtctcagGACATGGAGAAAGAAATCAGAAAAGAAGTCGATGATGCCATTGCGAAAGCAAAG
















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|9820676|gb|BE556186.1|BE556186
EST:     TGCTGCTGAAAAGGAGCTAAAG                         GACATTGAGAAAGAAGTCATAAGAGAAGTTGACGAAGCCATTGCTAAAGCA
genomic: TGCTGCTGAAAAGGAGCTAAAGgtgattaaat ... cttattttagGACATTGAGAAAGAAGTCAGAAAAGAAGTTGACGAAGCCATTGCTAAAGCA
EST: gi|51338002|gb|CO981868.1|CO981868
EST:     TAAGAAAGCTGGTATTGTCTCATGATATTGCTGCTGAAAAGGAGCTAAAG                         GACATTGAGAAAGAAGTCAGAAAAGAAGTTGACGAAGCCATTGCTAAAGCA
genomic: TAAGAAAGCTGGTATTGTCTCATGATATTGCTGCTGAAAAGGAGCTAAAGgtgattaaat ... cttattttagGACATTGAGAAAGAAGTCAGAAAAGAAGTTGACGAAGCCATTGCTAAAGCA
EST: gi|15664218|gb|BI701589.1|BI701589
EST:     TAAGAAAGCTGGTATTGTCTCATGATATTGCTGCTGAAAAGGAGCTAAAG                         GACATTGAGAAAGAAGTCAGAAAAGAAGTTGACGAAGCCATTGCTAAAGCA
genomic: TAAGAAAGCTGGTATTGTCTCATGATATTGCTGCTGAAAAGGAGCTAAAGgtgattaaat ... cttattttagGACATTGAGAAAGAAGTCAGAAAAGAAGTTGACGAAGCCATTGCTAAAGCA
EST: gi|151406873|gb|EV276688.1|EV276688
EST:     GCTGCTGAAAAGGAGCTAAAG                         GACATTGAGAAAGAAGTCAGAAAAGAAGTTGACGAAGCCATTGCTAAAGCA
genomic: GCTGCTGAAAAGGAGCTAAAGgtgattaaat ... cttattttagGACATTGAGAAAGAAGTCAGAAAAGAAGTTGACGAAGCCATTGCTAAAGCA
EST: gi|9819785|gb|BE555298.1|BE555298
EST:     ATGATATTGCTGCTGAAAAGGAGCTAAAG                         GACATTGAGAAAGAAGTCAGAAAAGAAGTTGACGAAGCCATTGCTAAAGCA
genomic: ATGATATTGCTGCTGAAAAGGAGCTAAAGgtgattaaat ... cttattttagGACATTGAGAAAGAAGTCAGAAAAGAAGTTGACGAAGCCATTGCTAAAGCA
EST: gi|58016185|gb|CX702927.1|CX702927
EST:     TAAGAAAGCTGGTATTGTCTCATGATATTGCTGCTGAAAAGGAGCTAAAG                         GACATTGAGAAAGAAGTCAGAAAAGAAGTTGACGAAGCCATTGCTAAAGCA
genomic: TAAGAAAGCTGGTATTGTCTCATGATATTGCTGCTGAAAAGGAGCTAAAGgtgattaaat ... cttattttagGACATTGAGAAAGAAGTCAGAAAAGAAGTTGACGAAGCCATTGCTAAAGCA
EST: gi|15199292|gb|BI423757.1|BI423757
EST:     TAAGAAAGCTGGTATTGTCTCATGATATTGCTGCTGAAAAGGAGCTAAAG                         GACATTGAGAAAGAAGTCAGAAAAGAAGTTGACGAAGCCATTGCTAAAGCA
genomic: TAAGAAAGCTGGTATTGTCTCATGATATTGCTGCTGAAAAGGAGCTAAAGgtgattaaat ... cttattttagGACATTGAGAAAGAAGTCAGAAAAGAAGTTGACGAAGCCATTGCTAAAGCA
EST: gi|13787399|gb|BG649991.1|BG649991
EST:     CTCATGATATTGCTGCTGAAAAGGAGCTAAAG                         GACATTGAGAAAGAAGTCAGAAAAGAAGTTGACGAAGCCATTGCTAAAGCA
genomic: CTCATGATATTGCTGCTGAAAAGGAGCTAAAGgtgattaaat ... cttattttagGACATTGAGAAAGAAGTCAGAAAAGAAGTTGACGAAGCCATTGCTAAAGCA
EST: gi|58019317|gb|CX706059.1|CX706059
EST:     TAAGAAAGCTGGTATTGTCTCATGATATTGCTGCTGAAAAGGAGCTAAAG                         GACATTGAGAAAGAAGTCAGAAAAGAAGTTGACGAAGCCATTGCTAAAGCA
genomic: TAAGAAAGCTGGTATTGTCTCATGATATTGCTGCTGAAAAGGAGCTAAAGgtgattaaat ... cttattttagGACATTGAGAAAGAAGTCAGAAAAGAAGTTGACGAAGCCATTGCTAAAGCA
EST: gi|151406023|gb|EV275838.1|EV275838
EST:     TAAGAAAGCTGGTATTGTCTCATGATATTGCTGCTGAAAAGGAGCTAAAG                         GACATTGAGAAAGAAGTCAGAAAAGAAGTTGACGAAGCCATTGCTAAAGCA
genomic: TAAGAAAGCTGGTATTGTCTCATGATATTGCTGCTGAAAAGGAGCTAAAGgtgattaaat ... cttattttagGACATTGAGAAAGAAGTCAGAAAAGAAGTTGACGAAGCCATTGCTAAAGCA
EST: gi|19054086|gb|BM732753.1|BM732753
EST:     TAAGAAAGCTGGTATTGTCTCATGATATTGCTGCTGAAAAGGAGCTAAAG                         GACATTGAGAAAGAAGTCA
genomic: TAAGAAAGCTGGTATTGTCTCATGATATTGCTGCTGAAAAGGAGCTAAAGgtgattaaat ... cttattttagGACATTGAGAAAGAAGTCA
EST: gi|6666275|gb|AW277734.1|AW277734
EST:     ATTGCTGCTGAAAAGGAGCTAAAG                         GACATTGAGAAAGAAGTCAGAAAAGAAGTTGACGAAGCCATTGCTAAAGCA
genomic: ATTGCTGCTGAAAAGGAGCTAAAGgtgattaaat ... cttattttagGACATTGAGAAAGAAGTCAGAAAAGAAGTTGACGAAGCCATTGCTAAAGCA
EST: gi|27427278|gb|CA938798.1|CA938798
EST:     TAAGAAAGCTGGTATTGTCTCATGATATTGCTGCTGAAAAGGAGCTAAAG                         GACATTGAGAAAGAAGTCAGAAAAGAAGTTGACGAAGCCATTGCTAAAGCA
genomic: TAAGAAAGCTGGTATTGTCTCATGATATTGCTGCTGAAAAGGAGCTAAAGgtgattaaat ... cttattttagGACATTGAGAAAGAAGTCAGAAAAGAAGTTGACGAAGCCATTGCTAAAGCA
EST: gi|58016174|gb|CX702916.1|CX702916
EST:     TAAGAAAGCTGGTATTGTCTCATGATATTGCTGCTGAAAAGGAGCTAAAG                         GACATTGAGAAAGAAGTCAGAAAAGAAGTTGACGAAGCCATTGCTAAAGCA
genomic: TAAGAAAGCTGGTATTGTCTCATGATATTGCTGCTGAAAAGGAGCTAAAGgtgattaaat ... cttattttagGACATTGAGAAAGAAGTCAGAAAAGAAGTTGACGAAGCCATTGCTAAAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttgaatttgatgcaatgctagccaaaaatgttaatttcatttccttattttagGACATTGAGAAAGAAGTCAGAAAAGAAGTTGACGAAGCCATTGCTAAAGCAAAG
                              tgttaat  putative branch site (score: 3)
                                    tttcatttccttattt  CT-rich tract
                         aaaaatgttaatttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttattgtgctagtgtcttcttcatgcttgtgtttattatgctacagttgaatttgatgcaatgctagccaaaaatgttaatttcatttccttattttagGACATTGAGAAAGAAGTCAGAAAAGAAGTTGACGAAGCCATTGCTAAAGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - gctagtg
- - - - - - - - - - -tcatgct
- - - - - - - - - - - - - - - - - - - -tgctaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gccaaaa