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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatacataagacgtgccttctagcttttgatcgttgtttccatgaaattcaatcatttgactaaaattttatctcttgtagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGAGGTGCACGATTTGATGATGGTGTTGGTGGTGACAATGAGGTTC

Basic information

species Glycine max
transcript GLYMA16G01810.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 7
----------------gtaaatacataaga-cgtgcc---ttctagcttttgatcgttgtttccatgaaattcaatcatttgactaaaat----tttatctcttgtagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGAGGTGCACGATTTGATGATGGTGTTGGTGGTGACAATGAGGTTC
                | |||  || |||| | |  |   ||   ||  || |      | |   ||| |  ||    | |||  ||||     || |  |  | |||||||| || || ||||| ||||||||||| || |||||||| |||||||| ||||||||||| || || |||||||| ||||| ||||| ||||||||||
gtatgtgcaacattgtgaaaactcacaagaacttatcaattttctgcacttaaagtgcttctgtttgacaagcatgtttctgaaaaaaaaaatgttgacttggtttagATGGCCCGCTCGAAGAAAGCATGCATTGTCTTCTTTGATGAGGTTGATGCTATTGGAGGTGCTCGCTTCGATGATGGGGTTGGGGGTGATAATGAGGTTC

upper sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G110185_T03 (Zea mays), 3'ss of exon 7
----gtaaatacataagacgtgccttctagcttttgatcgttgtttccatgaaattcaatcatttgactaaaattttatctcttgtagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGAGGTGCACGATTTGATGATGGTGTTGGTGGTGACAATGAGGTTC
    || ||| | ||| | ||  | || || ||||  |   ||    ||||  | |  ||   |  |  ||||| ||  || ||||||||||| || |||||||||||||||||||| || ||||||||||||||||||||||| ||||| || ||||||||||| |||||||||||||||||||| |
ggctgtgaatccgtaaaaggt-tcatccagttttt--ttcctgcacacatgttaat--atttctgaaacaaaatatt--ctattgtagATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCAATTGGTGGTGCTCGTTTTGATGATGGGGTTGGTGGTGACAATGAGGTGC

upper sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 7
--------------gtaaatacataagacgtgccttctagcttttgatcgttgtttccatgaaattcaatcatttgactaaaattttatctcttgtagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGAGGTGCACGATTTGATGATGGTGTTGGTGGTGACAATGAGGTTC
              || ||| | ||| | ||  | || || ||||  |   ||    ||||  | |  ||   |  |  ||||| ||  || ||||||||||| || |||||||||||||||||||| || ||||||||||||||||||||||| ||||| || ||||||||||| |||||||||||||||||||| |
gtatatctagggctgtgaatccgtaaaaggt-tcatccagttttt--ttcctgcacacatgttaat--atttctgaaacaaaatatt--ctattgtagATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCAATTGGTGGTGCTCGTTTTGATGATGGGGTTGGTGGTGACAATGAGGTGC

upper sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 7
gtaaatacataag-acgtgccttctagcttttgatcgttgtttccatgaa-----attcaatcatttgactaaaat---tttatctcttgtagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGAGGTGCACGATTTGATGATGGTGTTGGTGGTGACAATGAGGTTC
||| ||| ||      |   ||   |   ||    |  | ||| |||| |      ||||| ||| |  || ||||   ||  ||| | ||||||||| || |||||||| || |||||||| || || |||||||||||||| ||||| ||||| || ||||||||||| || ||||| ||||||||||| |
gtatatatatggctgtgaatctgtaaatattatcccagtcttttcatgtacgtgtgttcaa-catatttctgaaatgaattcttctatggtagATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCTATTGGTGGTGCTCGTTTTGATGATGGGGTGGGTGGCGACAATGAGGTGC

upper sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 7
-----------gtaaatacataagacgtgccttctagcttttgatcgttgtttccatgaaattcaatcatttgactaaaattttatctc-ttgtagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGAGGTGCACGATTTGATGATGGTGTTGGTGGTGACAATGAGGTTC
             | ||   ||     || ||||     ||| || |||  ||         |  ||  |  ||||   |  || | |   || ||||||| || || || || || || |||||||||||||||||||| ||||| || || ||||| || |||||||||||||||||||| ||||||||||| |
gtcacaagctgccacatgtttacagtttgtcttcatttattttattgtt-cttgatcattgctatattgtccgactgctacctttttttgctgcagATGGCACGCTCCAAAAAAGCGTGTATTGTGTTTTTTGATGAAGTAGATGCCATAGGGGGTGCGCGTTTTGATGATGGTGTTGGTGGGGACAATGAGGTCC

upper sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 7
-------------gtaaatacata-agacgtgccttctagcttttgatcgttgtttccatgaaattcaatcatttgactaaa--attttatctctt-gtagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGAGGTGCACGATTTGATGATGGTGTTGGTGGTGACAATGAGGTTC
             ||  ||   |  ||| |  | ||     |  ||     | |||  ||||   ||| |  |   ||      || |||  | |  | |||||||||||||||||||||| |||||||| ||||||||||| || ||||| ||||||||||| || ||||| |||||  | || ||||| ||||||||||
gtgctaatttattgtttatttgtttagatgaacattagttttcatgtgacgtattttgatgattctca-tggtgcaacctgtccatgttacttgtgagcagATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCTATTGGAGGTGCTCGGTTTGACGATGGATTGGGGGGTGATAATGAGGTTC

upper sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S49_256V6.1 (Physcomitrella patens), 3'ss of exon 7
-----------gtaaatacataagacgtgccttctagcttttgatcgttgtttccatgaaattcaatcatttgactaaaattttatct--cttgt----agATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGAGGTGCACGATTTGATGATGGTGTTGGTGGTGACAATGAGGTTC
            |   |||  ||    |   | ||   | || | ||| |  | | |  |     ||| |    | |    |||||    |||||    ||||||| ||||||||||| || |||||||||||||||||||| || ||||| ||||||||||| || || || |||||  | || ||||| || |||||||
ccgccagtgtattgtttactcaaacgctaagtactgtgtattca-cgtggcctacttcgatgcttatcgtggtgcgatttgtttatggaacttgtgagcagATGGCCCGTTCAAAGAAAGCGTGCATTGTGTTTTTTGATGAGGTAGATGCCATTGGAGGTGCTCGTTTCGACGATGGGTTGGGAGGTGATAACGAGGTTC

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|208167903|gb|GD966017.1|GD966017
EST:     TTCAGAAATATGTCGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAG                         ATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
genomic: TTCAGAAATATGTCGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtaaatacat ... tctcttgtagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
EST: gi|18039872|gb|BM308166.1|BM308166
EST:     TTCAGAAATATGTCGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAG                         ATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
genomic: TTCAGAAATATGTCGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtaaatacat ... tctcttgtagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
EST: gi|19268833|gb|BM885089.1|BM885089
EST:     TTCAGAAATATGTTGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAG                         ATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
genomic: TTCAGAAATATGTCGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtaaatacat ... tctcttgtagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
EST: gi|207816388|gb|GD787915.1|GD787915
EST:     TTCAGAAATATGTTGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAG                         ATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
genomic: TTCAGAAATATGTCGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtaaatacat ... tctcttgtagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
EST: gi|17963522|gb|BM270270.1|BM270270
EST:     TTCAGAAATATGTCGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAG                         ATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
genomic: TTCAGAAATATGTCGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtaaatacat ... tctcttgtagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
EST: gi|298174191|gb|HO017527.1|HO017527
EST:     TATGTCGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAG                         ATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
genomic: TATGTCGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtaaatacat ... tctcttgtagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
EST: gi|193479172|gb|FK446645.1|FK446645
EST:     TTCAGAAATATGTCGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAG                         ATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGA
genomic: TTCAGAAATATGTCGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtaaatacat ... tctcttgtagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGA
EST: gi|254319386|gb|GR829006.1|GR829006
EST:     TTCAGAAATATGTCGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAG                         ATGGCTCGTTCAA-GA-GGCATGCATTGGTGTTTTTTGATGAAGTTGATGC
genomic: TTCAGAAATATGTCGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtaaatacat ... tctcttgtagATGGCTCGTTCAAAGAAGGCATGCATTG-TGTTTTTTGATGAAGTTGATGC
EST: gi|298171740|gb|HO021332.1|HO021332
EST:     TTCAGAAATATGTCGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAG                         ATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
genomic: TTCAGAAATATGTCGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtaaatacat ... tctcttgtagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
EST: gi|193590240|gb|FK545268.1|FK545268
EST:     TAGGATGGTTCGTGAACTGTTTCAG                         ATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
genomic: TAGGATGGTTCGTGAACTATTTCAGgtaaatacat ... tctcttgtagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatcgttgtttccatgaaattcaatcatttgactaaaattttatctcttgtagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGAGGTGCACGATTTGATGATGGTGTTGGTGGTGACAATGAGGTTC
                                gactaaa  putative branch site (score: 2)
                                        ttttatctctt  CT-rich tract
                  aaattcaatcatttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatacataagacgtgccttctagcttttgatcgttgtttccatgaaattcaatcatttgactaaaattttatctcttgtagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGAGGTGCACGATTTGATGATGGTGTTGGTGGTGACAATGAGGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG