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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatcatttctttataactttcagggctgtgcctttttaacttcctggaaaactattgtattaagttgtttatatcttaccatggacatggcccttgcagATGTTCCTTTGAGTGCTAGAAATATTTTGGAAGACCCTGAGCTGAAGATTGCTGTAAAAAAATTCAG

Basic information

species Vitis vinifera
transcript Vv09s0002g06040.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g06040.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G44000.2 (Glycine max), 3'ss of exon 2
----------taatcatttctttataactttcagggctgtgcctttttaacttcctggaaaactattgtattaagttgtttatatcttaccatggacatggcccttgcagATGTTCCTTTGAGTGCTAGAAATATTTTGGAAGACCCTGAGCTGAAGATTGCTGTAAAAAAATTCAG
           ||  | ||  |  ||| ||| |      |     ||| | || ||     || ||| |||  |||||    ||||  |  |||    | ||  |||||||||||||||| ||||||||||| |||||||| || ||||| ||||| | ||||||||||   |||||
cctatggtctaaagaaatttatcttaaattttaaaa---tataaatttgaattactatgtgacaattttat-gagttgcaattatc--attatg----ttgctattgcagATGTTCCTTTAAGTGCTAGAAACATTTTGGAGGATCCTGAACTGAAAAATGCTGTAAAAGCTTTCAG

upper sequence: Vv09s0002g06040.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G22430.1 (Glycine max), 3'ss of exon 3
----------------------------------------------taatcatttctttataac----tttcaggg-----ctgtgcctttttaacttcctggaaaactattgta-ttaagttgtttatatcttaccatggacatggcccttgcagATGTTCCTTTGAGTGCTAGAAATATTTTGGAAGACCCTGAGCTGAAGATTGCTGTAAAAAAATTCAG
                                              |  |  ||||| ||| |     |   ||        |||  |  | | | |||     |    ||   | ||  ||   ||| |     |  |  | |  || ||||||||||||||| | ||||||||||| |||||||| || ||||| || || | ||||||||||   |||||
gtaagtactaagttcaagacaagcttttctgttgatatttttgttctttttgtttctctatgatgaagtcgtagaagaaatttgttacagtatgaattcacatcacttgataacaattctgtaagttacaatcatcattatataatgctcttgcagATGTTCCTATTAGTGCTAGAAACATTTTGGATGATCCTGACCTTAAAAATGCTGTAAAAGCCTTCAG

upper sequence: Vv09s0002g06040.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA07G03660.1 (Glycine max), 3'ss of exon 3
----------------------------------------------taatcatttctttat-----aactttcagggctgtgcctt----------tttaacttcctggaaaactattgtattaagttgtttatatcttaccatggacatggcccttgcagATGTTCCTTTGAGTGCTAGAAATATTTTGGAAGACCCTGAGCTGAAGATTGCTGTAAAAAAATTCAG
                                              |  |  |||||||||     |  | |    |   |   ||          || |  || || || ||| ||| | | ||||||     ||| |    |  | |  |  ||||||||||||||| | ||||||||||| |||||||| || ||||| || || | ||||||||||   |||||
gtaagtactaagttcaagacaagcttttctgttgatatttttgttctttttgtttctttatggtgaagttgtagaagaaatatgttagaatatgaattcacattacttgataacaattctgt-aagttgcaatcatcat----tatataatgttcttgcagATGTTCCTATTAGTGCTAGAAACATTTTGGAGGATCCTGAACTTAAAAATGCTGTAAAAGCCTTCAG

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|110362287|gb|EC925809.1|EC925809
EST:     GCCTCGATGTGGATTCAGCTCACTAGCAGTAAGAGTGTTGAAAGAATACA                         ATGTTCCTTTGAGTGCTAGAAATATTTTGGAAGACCCTGAGCTGAAGATTG
genomic: GCCTCGATGTGGATTCAGCTCACTAGCAGTAAGAGTGTTGAAAGAATACAgtaagtattc ... gcccttgcagATGTTCCTTTGAGTGCTAGAAATATTTTGGAAGACCCTGAGCTGAAGATTG
EST: gi|26265925|gb|CA816988.1|CA816988
EST:     GCCTCGATGTGGATTCAGCTCACTAGCAGTAAGAGTGTTGAAAGAATACA                         ATGTTCCTTTGAGTGCTAGAAATATTTTGGAAGACCCTGAGCTGAAGATTG
genomic: GCCTCGATGTGGATTCAGCTCACTAGCAGTAAGAGTGTTGAAAGAATACAgtaagtattc ... gcccttgcagATGTTCCTTTGAGTGCTAGAAATATTTTGGAAGACCCTGAGCTGAAGATTG
EST: gi|110382727|gb|EC947047.1|EC947047
EST:     GCCTCGATGTGGATTCAGCTCACTAGCAGTAAGAGTGTTGAAAGAATACA                         ATGTTCCTTTGAGTGCTAGAAATATTTTGGAAGACCCTGAGCTGAAGATTG
genomic: GCCTCGATGTGGATTCAGCTCACTAGCAGTAAGAGTGTTGAAAGAATACAgtaagtattc ... gcccttgcagATGTTCCTTTGAGTGCTAGAAATATTTTGGAAGACCCTGAGCTGAAGATTG
EST: gi|110382466|gb|EC946757.1|EC946757
EST:     GCCTCGATGTGGATTCAGCTCACTAGCAGTAAGAGTGTTGAAAGAATACA                         ATGTTCCTTTGAGTGCTAGAAATATTTTGGAAGACCCTGAGCTGAAGATTG
genomic: GCCTCGATGTGGATTCAGCTCACTAGCAGTAAGAGTGTTGAAAGAATACAgtaagtattc ... gcccttgcagATGTTCCTTTGAGTGCTAGAAATATTTTGGAAGACCCTGAGCTGAAGATTG
EST: gi|28959221|gb|CB339611.1|CB339611
EST:     GCCTCGATGTGGATTCAGCTCACTAGCAGTAAGAGTGTTGAAAGAATACA                         ATGTTCCTTTGAGTGCTAGAAATATTTTGGAAGACCCTGAGCTGAAGATTG
genomic: GCCTCGATGTGGATTCAGCTCACTAGCAGTAAGAGTGTTGAAAGAATACAgtaagtattc ... gcccttgcagATGTTCCTTTGAGTGCTAGAAATATTTTGGAAGACCCTGAGCTGAAGATTG
EST: gi|33409086|gb|CF214713.1|CF214713
EST:     GCCTCGATGTGGATTCAGCTCACTAGCAGTAAGAGTGTCGAATGAATACA                         ATGTTCCTTTGAGTGCTAGAAATATTTTGGAAGACCCTGAGCTGAAGATTG
genomic: GCCTCGATGTGGATTCAGCTCACTAGCAGTAAGAGTGTTGAAAGAATACAgtaagtattc ... gcccttgcagATGTTCCTTTGAGTGCTAGAAATATTTTGGAAGACCCTGAGCTGAAGATTG
EST: gi|26263944|gb|CA815007.1|CA815007
EST:     GCCTCGATGTGGATTCAGCTCACTAGCAGTAAGAGTGTTGAAAGAATACA                         ATGTTCCTTTGAGTGCTAGAAATATTTTGGAAGACCCTGAGCTGAAGATTG
genomic: GCCTCGATGTGGATTCAGCTCACTAGCAGTAAGAGTGTTGAAAGAATACAgtaagtattc ... gcccttgcagATGTTCCTTTGAGTGCTAGAAATATTTTGGAAGACCCTGAGCTGAAGATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggaaaactattgtattaagttgtttatatcttaccatggacatggcccttgcagATGTTCCTTTGAGTGCTAGAAATATTTTGGAAGACCCTGAGCTGAAGATTGCTGTAAAAAAATTCAG
                            atcttac  putative branch site (score: 3)
                                              cccttgc  putative PPT
        tattgtattaagttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatcatttctttataactttcagggctgtgcctttttaacttcctggaaaactattgtattaagttgtttatatcttaccatggacatggcccttgcagATGTTCCTTTGAGTGCTAGAAATATTTTGGAAGACCCTGAGCTGAAGATTGCTGTAAAAAAATTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - -gggctgt
- - - - - - - - - - - - - - - - - - - - - - - ggaaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatgga