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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatttagtaaccatttctctctttgcatttcataatatgactatgctattgcttttccccccataattaacatctctgatttctactttttttttctcagGATAAATACATGCAGAACCGGCTTGTGAGACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAACATTATTAATG

Basic information

species Glycine max
transcript GLYMA10G00610.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G00610.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os12g09610.1 (Oryza sativa), 3'ss of exon 9
aatttagtaaccatttctctctttgcatttcataata---tgactatgctattgcttttccccccataattaacatctctgatttctactttttttttctcagGATAAATACATGCAGAACCGGCTTGTGAGACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAACATTATTAATG
   | | |      |      |||||||||  |       | |||     | ||| || |   |   || |  | ||  | ||   || ||| || |   ||||||||||||||||||||| || | |||||||| || |||||||| || ||    ||||| || ||||| || || || |
--ctcattgggtgatgggtaatttgcattttgtggctgcctcacttgttaaatgcgttactttcttgaagttccttcagt-atgattattttattatgtgcagGATAAATACATGCAGAACAGGTTGGTGAGACTAGTTTGTGTTTTCCTTCAGTCTCTCATCCGAAACAAGATCATAAACG

upper sequence: GLYMA10G00610.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G098815_T04 (Zea mays), 3'ss of exon 10
aatttagtaaccatttctctctttgcatttcataatatgactatgctattgcttt-tccccccataattaacatctctgatttctactttttttttct-cagGATAAATACATGCAGAACCGGCTTGTGAGACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAACATTATTAATG
 |     |     ||  |        ||||    | |   |  || || ||     |   |  |||| |      |   ||    | | ||||||| | ||||||||||||||||| ||| | ||||||||||| || |||||||||||||| || || || || ||||| ||||| || |
-acgccttgtgttttgtttatcggttattttgagacaccgc-gtgttaatgtgcagtatactgataaatgtttatttgaatgataattatttttttgtgcagGATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACG

upper sequence: GLYMA10G00610.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G011575_T01 (Zea mays), 3'ss of exon 10
---aatttagtaaccatttctctctttgcatttcataatatgactatgctattgcttttccccccataattaacatctctgatttctactttt-tttttctcagGATAAATACATGCAGAACCGGCTTGTGAGACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAACATTATTAATG
   | || | | |  | |      |    |     | | ||| |||  | || ||  ||      |   || |||   ||  | |  |||    || ||  ||||| || || ||||| ||  | || |||||||| || ||||||||||| || ||||||||||||||||  || ||  |||
actatttgaatgaaaactgaatattactaagcgtgttaaatg-ctactc-atggcactttgtttaagtgttgacaaacct--tcttaactaacattgtttgcagGACAAGTATATGCAAAATAGACTAGTGAGACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATG

upper sequence: GLYMA10G00610.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv07s0130g00310.t01 (Vitis vinifera), 3'ss of exon 10
aatttagtaaccatttctctctttgcatttcataatatgactatgctattgcttttccccccataattaacatctctgatttctactttttttttct---cagGATAAATACATGCAGAACCGGCTTGTGAGACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAACATTATTAATG
   ||  |       |   |  ||   |||| |  | ||   ||   |                 |  ||||||||    |||| |||  ||| |||   |||||||  |||||||||||| | |||||||||||||| ||||| ||  |||| ||||| ||||| || || |||||||| |
--cttcctgttgtagtgggtggttatgtttc-tggtttgttcatatcagcaaacccagttagggtagaaacatctcaatcttcttcttcctttatctttccagGATAGGTACATGCAGAACAGACTTGTGAGACTTGTATGTGTATTCTTGCAGAGCCTAATTCGAAATAAAATTATTAACG

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|208282132|gb|GE076814.1|GE076814
EST:     TCATTCACATGTACATAACTAATTGTATAGCATCCTGTGTGGGCATCAAG                         GATAAATACATGCAGAACCGGCTTGTGAGACTTGTCTGTGTTTTTCTGCAA
genomic: TCATTCACATGTACATAACTAATTGTATAGCATCCTGTGTGGGCATCAAGgtaagccttt ... tttttctcagGATAAATACATGCAGAACCGGCTTGTGAGACTTGTCTGTGTTTTTCTGCAA
EST: gi|31474652|gb|CD416680.1|CD416680
EST:     TCATTCACATGTACATAACTAATTGTATAGCATCCTGTGTGGGCATCAAG                         GATAAATACATGCAGAACCGGCTTGTGAGACTTGTCTGTGTTTTTCTGCAA
genomic: TCATTCACATGTACATAACTAATTGTATAGCATCCTGTGTGGGCATCAAGgtaagccttt ... tttttctcagGATAAATACATGCAGAACCGGCTTGTGAGACTTGTCTGTGTTTTTCTGCAA
EST: gi|10232329|gb|BE801217.1|BE801217
EST:     TCATTCACATGTACATAACTAATTGTATAGCATCCTGTGTGGGCATCAAG                         GATAAATACATGCANAACCGGCTTGTGAGACTTGTCTGTGTTTTTCTGCAA
genomic: TCATTCACATGTACATAACTAATTGTATAGCATCCTGTGTGGGCATCAAGgtaagccttt ... tttttctcagGATAAATACATGCAGAACCGGCTTGTGAGACTTGTCTGTGTTTTTCTGCAA
EST: gi|16344608|gb|BI970203.1|BI970203
EST:     TCATTCACATGTACATAACTAATTGTATAGCATCCTGTGTGGGCATCAAG                         GATAAATACATGCAGAACAGGCTTGTGAGACTTGTCTGTGTTTTTCTGCAA
genomic: TCATTCACATGTACATAACTAATTGTATAGCATCCTGTGTGGGCATCAAGgtaagccttt ... tttttctcagGATAAATACATGCAGAACCGGCTTGTGAGACTTGTCTGTGTTTTTCTGCAA
EST: gi|26057582|gb|CA800496.1|CA800496
EST:     TCATTCACATGTACATAACTAATTGTATAGCATCCTGTGTGGGCATCAAG                         GATAAATACATGCAGAACCGGCTTGTGAGACTTGTCTGTGTTTTTCTGCAA
genomic: TCATTCACATGTACATAACTAATTGTATAGCATCCTGTGTGGGCATCAAGgtaagccttt ... tttttctcagGATAAATACATGCAGAACCGGCTTGTGAGACTTGTCTGTGTTTTTCTGCAA
EST: gi|214009017|gb|DB987096.1|DB987096
EST:     TCATTCACATGTACATAACTAATTGTATAGCATCCTGTGTGGGCATCAAG                         GATAAATACATGCAGAACCGGCTTGTGAGACTTGTCTGTGTTTTTCTGCAA
genomic: TCATTCACATGTACATAACTAATTGTATAGCATCCTGTGTGGGCATCAAGgtaagccttt ... tttttctcagGATAAATACATGCAGAACCGGCTTGTGAGACTTGTCTGTGTTTTTCTGCAA
EST: gi|31458111|gb|CD400139.1|CD400139
EST:     ACTAATTGTATAGCATCCTGTGTGGGCATCAAG                         GATAAATACATGCAGAACCGGCTTGTGAGACTTGTCTGTGTTTTTCTGCAA
genomic: ACTAATTGTATAGCATCCTGTGTGGGCATCAAGgtaagccttt ... tttttctcagGATAAATACATGCAGAACCGGCTTGTGAGACTTGTCTGTGTTTTTCTGCAA
EST: gi|14008705|gb|BG725309.1|BG725309
EST:     TCATTCACATGTACATAACTAATTGTATAGCATCCTGTGTGGGCATCAAG                         GATAAATACATGCAGAACCGGCTTGTGAGACTTGTCTGTGTTTTTCTGCAA
genomic: TCATTCACATGTACATAACTAATTGTATAGCATCCTGTGTGGGCATCAAGgtaagccttt ... tttttctcagGATAAATACATGCAGAACCGGCTTGTGAGACTTGTCTGTGTTTTTCTGCAA
EST: gi|10710646|gb|BF010364.1|BF010364
EST:     TCATTCACATGTACATAACTAATTGTATAGCATCCTGTGTGGGCATCAAG                         GATAAATACATGCAGAACCGGCTTGTGAGACTTGTCTGTGTTTTTCTGCAA
genomic: TCATTCACATGTACATAACTAATTGTATAGCATCCTGTGTGGGCATCAAGgtaagccttt ... tttttctcagGATAAATACATGCAGAACCGGCTTGTGAGACTTGTCTGTGTTTTTCTGCAA
EST: gi|23053081|gb|BU577572.1|BU577572
EST:     TCATTCACATGTACATAACTAATTGTATAGCATCCTGTGTGGGCATCAAG                         GATAAATACATGCAGAACCGGCTTGTGAGACTTGTCTGTGTTTTTCTGCAA
genomic: TCATTCACATGTACATAACTAATTGTATAGCATCCTGTGTGGGCATCAAGgtaagccttt ... tttttctcagGATAAATACATGCAGAACCGGCTTGTGAGACTTGTCTGTGTTTTTCTGCAA
EST: gi|151393880|gb|EV263751.1|EV263751
EST:     TCATTCACATGTACATAACTAATTGTATAGCATCCTGTGTGGGCATCAAG                         GATAAATACATGCAGAACCGGCTTGTGAGACTTGTTTGTGTTTTTCTGCAA
genomic: TCATTCACATGTACATAACTAATTGTATAGCATCCTGTGTGGGCATCAAGgtaagccttt ... tttttctcagGATAAATACATGCAGAACCGGCTTGTGAGACTTGTCTGTGTTTTTCTGCAA
EST: gi|9900317|gb|BE609285.1|BE609285
EST:     TCATTCACATGTACATAACTAATTGTATAGCATCCTGTGTGGGCATCAAG                         GATAAATACATGCAGAACCGGCTTGTGAGACTTGTCTGTGTTTTTCTGCAA
genomic: TCATTCACATGTACATAACTAATTGTATAGCATCCTGTGTGGGCATCAAGgtaagccttt ... tttttctcagGATAAATACATGCAGAACCGGCTTGTGAGACTTGTCTGTGTTTTTCTGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctattgcttttccccccataattaacatctctgatttctactttttttttctcagGATAAATACATGCAGAACCGGCTTGTGAGACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAACATTATTAATG
                         catctctgatttctac  CT-rich tract
                                 atttctactttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatttagtaaccatttctctctttgcatttcataatatgactatgctattgcttttccccccataattaacatctctgatttctactttttttttctcagGATAAATACATGCAGAACCGGCTTGTGAGACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAACATTATTAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - ccatttc
- - - - - - - - - - - - gcatttc