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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagaccaatatcacttggaccaaccgaccccttgttggtgtttaagagcctctttgatcattgtttgtttgttgttgtttttgtttttgttttttggcagTGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCGTCAAT

Basic information

species Glycine max
transcript GLYMA06G15890.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G15890.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G133844_T01 (Zea mays), 3'ss of exon 1
--aagac--caatatcacttggaccaaccgaccccttgttggtgtttaagagcctctttgatcattgtt-tgtttgt-tgttgtttttgtttttgttttttggcagTGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCGTCAAT--------------------------------------------
  |||||  | | |  ||     ||  ||  ||||               |||      |  |   |   ||  ||  || ||    ||  |  | |||   |||||||||||||| ||||||||| | |||||||||||||| || || || ||| |||||                                            
gtaagacgacgacaagacccccccccccccccccccctacttctccctctagctctcgcgcgcgcggccatgcatgcatgatgaaactggctgagcttt---gcagTGAAGAAAGGGCAGATTGTGCGCGTGGACAAGGAGAAGTACCTGAACAGCATCAATTATCTGTCAGTGGGACACCCGCCCTTCTACAAGGGGCTGGACTA

upper sequence: GLYMA06G15890.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0044g01310.t01 (Vitis vinifera), 3'ss of exon 1
aagaccaatatcacttggaccaaccgaccccttgttggtgtttaagagcctctttgatcattgtttgtttgttgttgtttttgtttttgttttttggcagTGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCGTCAAT
      | |||| || ||     | |     || ||||| ||||| |       ||    | | || ||  || |   ||||| |||    | | ||||||||||||||| || || |||||||||||||||||||| ||||| |||||  |||||
---gtgagtatctctgggctt--ctgtttttttcttggt-tttaaaattgatggtggg-gtgggttcttatttttcagttttgatttgtgatatgggcagTGAAGAAAGGCCAAATAGTGAGGGTGGACAAGGAGAAGTATCTTAATAGTATCAAT

upper sequence: GLYMA06G15890.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S230_32V6.1 (Physcomitrella patens), 3'ss of exon 2
------------------------aagaccaatatcacttggaccaaccgaccccttgttggtgtttaagagcctctttgatcatt---gtttgtttgttgttgtt---tttgtt---tttgtttttt---ggcagTGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCGTCAAT
                        ||  || |    | ||     |    |||  | ||   | |||||     || ||    |||   || ||||||    |      | || |   ||||| |  |   ||||||||||||||| ||||||||||| || |||||||| |||||||| || || ||  | 
gtacgatcatcatctttctcggggaatgcctaatcaatttttgtta--taacctttcgtatatatttaattatgtcgtttgcaattcgagtctgtttgcctcttcgaaatctgatcaatttgtctcgtcgtggcagTGAAGAAAGGACAGATTGTGAGAGTTGACAAGGAAAAATATCTGAACAGTGTAGAG

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|209708698|gb|BW678879.1|BW678879
EST:     TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCT                         TGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
genomic: TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCTgtgagttaag ... tttttggcagTGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
EST: gi|192316855|gb|FK006082.1|FK006082
EST:     TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCT                         TGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
genomic: TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCTgtgagttaag ... tttttggcagTGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
EST: gi|151403156|gb|EV272966.1|EV272966
EST:     TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCT                         TGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
genomic: TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCTgtgagttaag ... tttttggcagTGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
EST: gi|213600560|gb|DB960108.1|DB960108
EST:     TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCT                         TGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
genomic: TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCTgtgagttaag ... tttttggcagTGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
EST: gi|192317603|gb|FK008999.1|FK008999
EST:     TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCT                         TGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
genomic: TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCTgtgagttaag ... tttttggcagTGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
EST: gi|209706472|gb|BW670831.1|BW670831
EST:     TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCT                         TGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
genomic: TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCTgtgagttaag ... tttttggcagTGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
EST: gi|19345850|gb|BM890730.1|BM890730
EST:     TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCT                         TGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
genomic: TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCTgtgagttaag ... tttttggcagTGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
EST: gi|298178035|gb|HO023884.1|HO023884
EST:     TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCT                         TGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
genomic: TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCTgtgagttaag ... tttttggcagTGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
EST: gi|213603478|gb|DB966629.1|DB966629
EST:     TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCT                         TGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
genomic: TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCTgtgagttaag ... tttttggcagTGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
EST: gi|31306990|gb|CD392193.1|CD392193
EST:     CCGTCTATTCCT                         TGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
genomic: CCGTCTATTCCTgtgagttaag ... tttttggcagTGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
EST: gi|209712066|gb|BW674213.1|BW674213
EST:     TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCT                         TGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
genomic: TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCTgtgagttaag ... tttttggcagTGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
EST: gi|209708699|gb|BW678880.1|BW678880
EST:     TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCT                         TGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
genomic: TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCTgtgagttaag ... tttttggcagTGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
EST: gi|120530396|gb|EH258529.1|EH258529
EST:     TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCT                         TGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
genomic: TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCTgtgagttaag ... tttttggcagTGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
EST: gi|151401315|gb|EV271129.1|EV271129
EST:     TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCT                         TGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
genomic: TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCTgtgagttaag ... tttttggcagTGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
EST: gi|298177637|gb|HO027304.1|HO027304
EST:     TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCT                         TGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
genomic: TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCTgtgagttaag ... tttttggcagTGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
EST: gi|151403653|gb|EV273463.1|EV273463
EST:     TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCT                         TGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
genomic: TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCTgtgagttaag ... tttttggcagTGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
EST: gi|209711472|gb|BW665224.1|BW665224
EST:     TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCT                         TGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
genomic: TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCTgtgagttaag ... tttttggcagTGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
EST: gi|213617933|gb|DB957386.1|DB957386
EST:     TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCT                         TGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
genomic: TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCTgtgagttaag ... tttttggcagTGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
EST: gi|213611375|gb|DB983967.1|DB983967
EST:     TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCGATTCCT                         TGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
genomic: TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCTgtgagttaag ... tttttggcagTGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
EST: gi|192319047|gb|FK009071.1|FK009071
EST:     TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCT                         TGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
genomic: TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCTgtgagttaag ... tttttggcagTGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
EST: gi|209711473|gb|BW665225.1|BW665225
EST:     TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCT                         TGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
genomic: TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCTgtgagttaag ... tttttggcagTGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
EST: gi|209706473|gb|BW670832.1|BW670832
EST:     TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCT                         TGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
genomic: TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCTgtgagttaag ... tttttggcagTGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
EST: gi|151404681|gb|EV274495.1|EV274495
EST:     TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCT                         TGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG
genomic: TCAGTCTTCAAGTGCTGCTGCTCCTAAACCCAAGAAACCCGTCTATTCCTgtgagttaag ... tttttggcagTGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagcctctttgatcattgtttgtttgttgttgtttttgtttttgttttttggcagTGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCGTCAAT
      ctttgat  putative branch site (score: 5)
                             ttgtttttgtttttgt  putative PPT
                             ttgtttttgtttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagaccaatatcacttggaccaaccgaccccttgttggtgtttaagagcctctttgatcattgtttgtttgttgttgtttttgtttttgttttttggcagTGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCGTCAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - -cacttgg
- - - - - - - - - -ccaaccg
- - - - - - - - - - - - - acccctt
- - - - - - - - - - - - - - - - -gttggtg
- - - - - - - - - - - - - - - - - - - - - - - agcctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgt