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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattgaataagcatggtaacaaaagttaaatctagtttcagcatcactaatgaaatgttcacacggatcatgacttatgcgatgctttgattttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTAGAAGAGAGGGGGATGAGGTATGTGACAGCTGTGGTGGAGGAAGGAGGAATCCAGGTGGACCAGGTGT

Basic information

species Glycine max
transcript GLYMA11G07940.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G07940.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0023g03040.t01 (Vitis vinifera), 3'ss of exon 2
tattgaataagcatg--gtaacaaaagttaaatctagtttcagcatcactaatgaaatgttcacacggatcatgacttatgcgatgctttgattttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTAGAAGAGAGGGGGATGAGGTATGTGACAGCTGTGGTGGAGGAAGGAGG---AATCCAGGTGGACCAGGTGT
       |||| ||   |||| || |   ||          |  ||| ||  ||||||  |     |      ||  |   | |||   |   | ||  |||||||||||||| | | |||| ||||||||| |  |||| | |||||||||||| |||||||| ||||||||||| |  |     | | ||||||| ||||   
------gtaagtattacgtaataagaacgaag---------ataatctctcttgaaattctttt-tgagcagagaactgaac-atgggattgctgtgaacagTGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGGTACGTGACAGCAGTGGTGGAGGACGACGATGCGAACAAGGTGGATCAGG---
















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|298165055|gb|HO011104.1|HO011104
EST:     TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGACGTTGAACTTGTTAAGAAGAGGTTAGAAGAGAGGGGGATGAGG
genomic: TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTAGAAGAGAGGGGGATGAGG
EST: gi|15288048|gb|BI471939.1|BI471939
EST:     TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTAGAAGAGAGGGGGATGAGG
genomic: TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTAGAAGAGAGGGGGATGAGG
EST: gi|193463680|gb|FK426960.1|FK426960
EST:     TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTT
genomic: TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTT
EST: gi|298196497|gb|HO041240.1|HO041240
EST:     TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTAGAAGAGAGGGGGATGAGG
genomic: TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTAGAAGAGAGGGGGATGAGG
EST: gi|298187665|gb|HO034814.1|HO034814
EST:     TGGTTGAAGAAAGGCCAATTAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTAGAAGAGAGGGGGATGAGG
genomic: TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTAGAAGAGAGGGGGATGAGG
EST: gi|14258681|gb|BG881589.1|BG881589
EST:     TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTAGAAGAGAGGGGGATGAGG
genomic: TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTAGAAGAGAGGGGGATGAGG
EST: gi|208156119|gb|GD952355.1|GD952355
EST:     TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTAAGAAAGAGAGGGGGATGA
genomic: TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTA-GAA-GAGAGGGGGATGA
EST: gi|298181480|gb|HO022919.1|HO022919
EST:     TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTAGAAGAGAGGGGGATGAGG
genomic: TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTAGAAGAGAGGGGGATGAGG
EST: gi|192332138|gb|FK026376.1|FK026376
EST:     TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTAGAAGAGAGGGGGATGAGG
genomic: TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTAGAAGAGAGGGGGATGAGG
EST: gi|193476151|gb|FK439978.1|FK439978
EST:     TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGA
genomic: TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGA
EST: gi|193563937|gb|FK517458.1|FK517458
EST:     CCTATTAATCCCAAGGACAACCATATCTCATTCCAG                         CGTACTGATGTTGAACTTGTTAAGAAGAGGTTAGAAGAGAGGGGGATGAGG
genomic: CCTATTAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTAGAAGAGAGGGGGATGAGG
EST: gi|208071392|gb|GD872993.1|GD872993
EST:     TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTAGAAGAGAGGGGGATGA
genomic: TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTAGAAGAGAGGGGGATGA
EST: gi|192332137|gb|FK026375.1|FK026375
EST:     TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTAGAAGAGAGGGGGATGAGG
genomic: TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTAGAAGAGAGGGGGATGAGG
EST: gi|10235840|gb|BE804728.1|BE804728
EST:     TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAA
genomic: TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAA
EST: gi|151395334|gb|EV265205.1|EV265205
EST:     TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTAGAAGAGAGGGGGATGAGG
genomic: TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTAGAAGAGAGGGGGATGAGG
EST: gi|208155295|gb|GD953184.1|GD953184
EST:     TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAAGAAAGAGGTTAGAAGAGAGGGG
genomic: TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAA-GAA-GAGGTTAGAAGAGAGGGG
EST: gi|193644716|gb|FK589132.1|FK589132
EST:     TGGTTGAAGAA-GGCCTATTAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTT
genomic: TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTT
EST: gi|193663255|gb|FK602713.1|FK602713
EST:     TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTT
genomic: TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTT
EST: gi|298192816|gb|HO033250.1|HO033250
EST:     TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTAGAAGAGAGGGGGATGAGG
genomic: TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTAGAAGAGAGGGGGATGAGG
EST: gi|6964084|gb|AW432777.1|AW432777
EST:     TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTAGAAGAGAGGGGGATGAGG
genomic: TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTAGAAGAGAGGGGGATGAGG
EST: gi|298197105|gb|HO041848.1|HO041848
EST:     TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTAGAAGAGAGGGGGATGAGG
genomic: TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTAGAAGAGAGGGGGATGAGG
EST: gi|208279180|gb|GE076677.1|GE076677
EST:     TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTAGAAGAGAGGGGGATGAGG
genomic: TGGTTGAAGAAAGGCCTATTAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTAGAAGAGAGGGGGATGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actaatgaaatgttcacacggatcatgacttatgcgatgctttgattttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTAGAAGAGAGGGGGATGAGGTATGTGACAGCTGTGGTGGAGGAAGGAGGAATCCAGGTGGACCAGGTGT
                                        tttgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattgaataagcatggtaacaaaagttaaatctagtttcagcatcactaatgaaatgttcacacggatcatgacttatgcgatgctttgattttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTAGAAGAGAGGGGGATGAGGTATGTGACAGCTGTGGTGGAGGAAGGAGGAATCCAGGTGGACCAGGTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - gcatggt
- - - - - - - - -aacaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatgctt