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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcattaattaacagatctgaaggcttgcagttttggtttaagttttaatttgtgtattttgactcttttcttattgtcctattgaacagACTGATAATGTTGAAGAAATAGCTTTAAAGATTTCTCAATTGCCAAAAGCATCAGAAAAACATAAAAGGATTACTGTTATCACCCAAGGTGCAGATCCTG

Basic information

species Glycine max
transcript GLYMA10G06580.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G06580.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv13s0019g04480.t01 (Vitis vinifera), 3'ss of exon 10
---gtaatcattaattaacagatctg-----aaggcttgcagttttggtttaagttttaatttgtgtattttgactcttttcttattgtcctat-tgaacagACTGATAATGTTGAAGAAATAGCTTTAAAGATTTCTCAATTGCCAAAAGCATCAGAAAAACATAAAAGGATTACTGTTATCACCCAAGGTGCAGATCCTG
   |  || | |   |    ||| ||      | | |||  |                ||    || | |||    ||  | |   |||| | | ||| ||||||||||| ||||| || || ||  |||| || ||||||| ||||||||||||||  | ||| || || |||||||| ||||| ||||||||||||||||
gtagggattacttggtgttggatttgtttttgatgattgttgccccctacaggaaggaaaaaaatggaattt---cctcatttggctgtcttttgtgatcagACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCATCAGGGACACACAAGAGAATTACTGTGATCACTCAAGGTGCAGATCCTG

upper sequence: GLYMA10G06580.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv13s0019g04470.t01 (Vitis vinifera), 3'ss of exon 10
---gtaatcattaattaacagatctgaaggcttgcagttttggtttaagttttaatttgtgtattttgactcttttctt--attgtcctat-tgaacagACTGATAATGTTGAAGAAATAGCTTTAAAGATTTCTCAATTGCCAAAAGCATCAGAAAAACATAAAAGGATTACTGTTATCACCCAAGGTGCAGATCCTG
   |  || | |   |    ||||||         | | ||||          ||       |     | |   |  ||    |||| | | ||| ||||||||||||||||| || || ||  |||| || ||||||| ||||||||||||||  | ||| || || |||||||| ||||| ||||||||||||||||
gtagggattacttggtgttggatctgtttttgatgattgttggcccctacaagaaggaaaaaaaaggaatttcctcatttggctgtcttttgtgatcagACTGATAATGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCATCAGGGACACACAAGAGAATTACTGTGATCACTCAAGGTGCAGATCCTG
















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|58024551|gb|CX711292.1|CX711292
EST:     TTGGAAATGAAACTGAAGCAAGAACATTTTCTAAAGCTCAAGGCTGGGAG                         ACTGATAATGTTGAAGAAATAGCTTTAAAGATTTCTCAATTGCCAAAAGCA
genomic: TTGGAAATGAAACTGAAGCAAGAACATTTTCTAAAGCTCAAGGCTGGGAGgtaatcatta ... tattgaacagACTGATAATGTTGAAGAAATAGCTTTAAAGATTTCTCAATTGCCAAAAGCA
EST: gi|298169113|gb|HO020473.1|HO020473
EST:     TTGGAAATGAAACTGAAGCAAAAACATTTTCTAAAGCTCAAGGCTGGGAG                         ACTGATAATGTTGAAGAAATAGCTTCAAAGATTTCTCAATTGCCAAAAGCA
genomic: TTGGAAATGAAACTGAAGCAAGAACATTTTCTAAAGCTCAAGGCTGGGAGgtaatcatta ... tattgaacagACTGATAATGTTGAAGAAATAGCTTTAAAGATTTCTCAATTGCCAAAAGCA
EST: gi|12689938|gb|BG156274.1|BG156274
EST:     TTGGAAATGAAACTGAAGCAAGAACATTTTCTAAAGCTCAAGGCTGGGAG                         ACTGATAATGTTGAAGAAATAGCTTTAAAGATTTCTCAATTGCCAAAAGCA
genomic: TTGGAAATGAAACTGAAGCAAGAACATTTTCTAAAGCTCAAGGCTGGGAGgtaatcatta ... tattgaacagACTGATAATGTTGAAGAAATAGCTTTAAAGATTTCTCAATTGCCAAAAGCA
EST: gi|12772068|gb|BG236995.1|BG236995
EST:     GAAACTGAAGCAAGAACATTTTCTAAAGCTCAAGGCTGGGAG                         ACTGATAATGTTGAAGAAATAGCTTTAAAGATTTCTCAATTGCCAAAAGCA
genomic: GAAACTGAAGCAAGAACATTTTCTAAAGCTCAAGGCTGGGAGgtaatcatta ... tattgaacagACTGATAATGTTGAAGAAATAGCTTTAAAGATTTCTCAATTGCCAAAAGCA
EST: gi|22525420|gb|BU084231.1|BU084231
EST:     TTGGAAATGAAACTGAAGCAAGAACATTTTCTAAAGCTCAAGGCTGGGAG                         ACTGATAATGTTGAAGAAATAGCTTTAAAGATTTCTCAATTGCCAAAAGCA
genomic: TTGGAAATGAAACTGAAGCAAGAACATTTTCTAAAGCTCAAGGCTGGGAGgtaatcatta ... tattgaacagACTGATAATGTTGAAGAAATAGCTTTAAAGATTTCTCAATTGCCAAAAGCA
EST: gi|120531830|gb|EH259963.1|EH259963
EST:     TGGAAATGAAACTGAAGCAAGAACCATTT-CTAAAGCTCAAG-CTGGGAG                         ACTGATAATGTTGAAGAA-TAG-TTTAAAGATT
genomic: TGGAAATGAAACTGAAGCAAGAAC-ATTTTCTAAAGCTCAAGGCTGGGAGgtaatcatta ... tattgaacagACTGATAATGTTGAAGAAATAGCTTTAAAGATT
EST: gi|16348521|gb|BI974116.1|BI974116
EST:     TTGGAAATGAAACTGAAGCAAGAACATTTTCTAAAGCTCAAGGCTGGGAG                         ACTGATAATGTTGAAGAAATAGCTTTAAAGATTTCTCAATTGCCAAAAGCA
genomic: TTGGAAATGAAACTGAAGCAAGAACATTTTCTAAAGCTCAAGGCTGGGAGgtaatcatta ... tattgaacagACTGATAATGTTGAAGAAATAGCTTTAAAGATTTCTCAATTGCCAAAAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtttaagttttaatttgtgtattttgactcttttcttattgtcctattgaacagACTGATAATGTTGAAGAAATAGCTTTAAAGATTTCTCAATTGCCAAAAGCATCAGAAAAACATAAAAGGATTACTGTTATCACCCAAGGTGCAGATCCTG
                      ttttgac  putative branch site (score: 3)
                            ctcttttcttattgtc  CT-rich tract
     aagttttaatttgtgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcattaattaacagatctgaaggcttgcagttttggtttaagttttaatttgtgtattttgactcttttcttattgtcctattgaacagACTGATAATGTTGAAGAAATAGCTTTAAAGATTTCTCAATTGCCAAAAGCATCAGAAAAACATAAAAGGATTACTGTTATCACCCAAGGTGCAGATCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT