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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgtttggattttcttatgctttgagctatctatgtactatgaattttgggttcctcatgttgatggaactaaataaagaaatgttttgcagGCTTTTGATGGGAAAAAATGGGAGAAGTTTAATAGTGAAAAAGTAGCCTCACTTGCCTATGCCCGAATTCAAGGAAAAGGTTCTCTTATTGCTCATTTCC

Basic information

species Glycine max
transcript GLYMA08G01040.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G01040.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G459746_T01 (Zea mays), 3'ss of exon 13
----------------------------------------------------------gttgtttggattttcttatgctttgagctatctatgtact-atgaattttgggttcctcatgttgatggaa----ctaaataaa---gaaatgttttgcagGCTTTTGATGGGAAAAAATGGGAGAAGTTTAATAGTGAAAAAGTAGCCTCACTTGCCTATGCCCGAATTCAAGGAAAAGGTTCTCTTATTGCTCATTTCC
                                                          |   || |     |  ||||| |||    || | |    | || || | |  |      |  | || |       || |   |    |  || |||| ||| ||||| |||| ||||| |||||||||||||| ||||| || || || |||||||| |||||  |||| ||||| |||    |||| |||||||||||||
gtcagaaaattattccaattgacgaagtgctactgcattgatgtaaagttgtaaactagcctttggtcaacttatatgccttgccaaatttgtactttgataaaatatccggcttgaacatcgacgtgctatcctgagccattttgtcatctttttcagACTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAAACAGCTCTGATTGCTCATTTCC

upper sequence: GLYMA08G01040.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G451716_T01 (Zea mays), 3'ss of exon 13
---------gttgtttggattttcttatgctttgagctatctatgtactatgaattttgggttcctcatgttgatggaactaaataaagaaatgttttgcagGCTTTTGATGGGAAAAAATGGGAGAAGTTTAATAGTGAAAAAGTAGCCTCACTTGCCTATGCCCGAATTCAAGGAAAAGGTTCTCTTATTGCTCATTTCC
         |  |  |  || |||  |||| | |  |  |  ||  | ||  |||    ||    | |   ||| | |  | || | |    | | |||||| | ||| |||||||||  |||||||| || || ||||| ||||| ||||||||||| |||||  |||| |||||||||    ||||  ||||||||||||
aaagattatgaaggctaaatcttcgaatgcat-gcacgcttcataaa-tagaaatggaaggagtataaaaatgaagaactttaacacatctgtctcttgcagACATTTCATGGGAAAAGGTGGGAGAAATTCAACAGTGAGAAAGTGGCCTCACTTGCTTATGCTAGAATCCAAGGAAAATCAGCTCTAGTTGCTCATTTCC

upper sequence: GLYMA08G01040.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM5G814700_T01 (Zea mays), 3'ss of exon 3
-----------------------------------------------gttgtttggatttt-------cttatgctttgagctatctatgtact---atgaattttgggttcctcatgttgatg-gaactaaataaagaaat---------gttttgcagGCTTTTGATGGGAAAAAATGGGAGAAGTTTAATAGTGAAAAAGTAGCCTCACTTGCCTATGCCCGAATTCAAGGAAAAGGTTCTCTTATTGCTCATTTCC
                                               | | ||| || |||       |||||       || |  | ||||||   || || | |   |     |  | |||| |  |||     ||  ||         ||||| |||  |||| |||| ||||| |||||||||||||| ||||| || || || |||||||| |||||| |||| ||||| |||    | || |||||||||||||
gtgagaattattcaattaaataagtgctactgtatcgtgcagttatggctattttgacttttgatcaacttatatggcttgccaaatttgtacttcgataaaatatccatctggaacatggatgtgtgctatcctgagctattttttcatcgtttttcagAGTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCCAGAATCCAAGGGAAAACAGCCCTGATTGCTCATTTCC

upper sequence: GLYMA08G01040.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G156956_T01 (Zea mays), 3'ss of exon 12
---------------gttgtttggattttcttatgctttgagctatctatgtactatgaattttgggttcctcatgttgatgg-aactaaataaagaaatgttttgcagGCTTTTGATGGGAAAAAATGGGAGAAGTTTAATAGTGAAAAAGTAGCCTCACTTGCCTATGCCCGAATTCAAGGAAAAGGTTCTCTTATTGCTCATTTCC
                 |   | |||        |    |    || ||| || | | | |   |  ||     ||   |    ||||| |      | |  | ||||| | ||  | || || |||||||||||||| |||||||| ||||| || |||||||| || ||| |||| || ||||      || | |||||||||||||
gtatgttcctgtgcccataccttgatacctgacagtaagggaaaatatatctagtttaactccagaattggatgtgagaagattaactatagctgatacttctgtgcagACATTCAACGGCAAGAAATGGGAGAAGTTCAATAGTGAGAAAGTGGCATCACTTGCGTACGCCAGAATCCAGGGAAGGAACGCTTTGATTGCTCATTTCC

upper sequence: GLYMA08G01040.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 13
----------------------------gttgtttggattttcttatgcttt-------gagctatctatgtactatgaattttgggttc-----ctcatgttgatggaa-----ctaaataaag------aaatgttttgcagGCTTTTGATGGGAAAAAATGGGAGAAGTTTAATAGTGAAAAAGTAGCCTCACTTGCCTATGCCCGAATTCAAGGAAAAGGTTCTCTTATTGCTCATTTCC
                             |  ||   | ||| ||  |||||        ||||   | | |||      |  |  | ||     || || | ||  ||      ||||  | |       | || |||  ||||| ||  |||| ||||| ||||||||||| || ||||| || || || || ||||| ||||| |||||||||||||||  | ||||||||||||||||||
gttagaatccatgcattgtaatataattatacttaatacttttttcggctttcaaaggaaagcttcttgtctacagaatttcataaggtctgcaactgatatggactgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGTAAAAAGTGGGAGAAGTTCAACAGTGAGAAGGTGGCATCTCTTGCATATGCTCGAATTCAAGGAAAAACTGCTCTTATTGCTCATTTCC

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|13480999|gb|BG510342.1|BG510342
EST:     ATGATTGATCCTGGTCAAATTATTCCTTTCCATCAG                         GCTTTTGATGGGAAAAAATGGGAGAAGTTTAATAGTGAAAAAGTAGCCTCA
genomic: ATGATTGATCCTGGTCAAATTATTCCTTTCCATCAGgttgtttgga ... tgttttgcagGCTTTTGATGGGAAAAAATGGGAGAAGTTTAATAGTGAAAAAGTAGCCTCA
EST: gi|16106132|gb|BI893872.1|BI893872
EST:     ATGCATTCATAAACATGATTGATCCTGGNCAAATTATTCCTTTCCATCAG                         GCTTTTGATGGGAAAAAATGGGAGAAGTTTAATAGTGAAAAAGTAGCCTCA
genomic: ATGCATTCATAAACATGATTGATCCTGGTCAAATTATTCCTTTCCATCAGgttgtttgga ... tgttttgcagGCTTTTGATGGGAAAAAATGGGAGAAGTTTAATAGTGAAAAAGTAGCCTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatgaattttgggttcctcatgttgatggaactaaataaagaaatgttttgcagGCTTTTGATGGGAAAAAATGGGAGAAGTTTAATAGTGAAAAAGTAGCCTCACTTGCCTATGCCCGAATTCAAGGAAAAGGTTCTCTTATTGCTCATTTCC
                              aactaaa  putative branch site (score: 2)
                              aactaaataaagaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgtttggattttcttatgctttgagctatctatgtactatgaattttgggttcctcatgttgatggaactaaataaagaaatgttttgcagGCTTTTGATGGGAAAAAATGGGAGAAGTTTAATAGTGAAAAAGTAGCCTCACTTGCCTATGCCCGAATTCAAGGAAAAGGTTCTCTTATTGCTCATTTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA