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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgtattgatcttataatgcattactcgtcattttgagttaatgaataatgttatctagggaaatttttaatgatccctttttttttttttgtaatgcagCCTGTGAAAAGCCCTGTGACAATCTGTGGTGATATCCATGGCCAGTTTCATGATCTAGCGGAGCTTTTCCGAATTGGAGGAAAG

Basic information

species Vitis vinifera
transcript Vv06s0004g00830.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g00830.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os03g59060.1 (Oryza sativa), 3'ss of exon 2
---ctgtattgatcttataatgcattactcgtcattttgagttaatgaataatg--ttatctagggaaatttttaatgatccctttttttttttttgtaatgcagCCTGTGAAAAGCCCTGTGACAATCTGTGGTGATATCCATGGCCAGTTTCATGATCTAGCGGAGCTTTTCCGAATTGGAGGAAAG
    |  | ||||    | |     |  | ||   |   |  |||| ||| |||  || | | |   |   |||||   |  ||||    |  ||     |||||||||| || || ||||| ||||| ||||||||||| ||||| ||||||||||| || || || || |||||||| || ||||||
aacttacagtgattccttgagatggttat-gtgcctcccatataataaattatgaattcttttgttgataatttaacattttctttgccatgcttc----tgcagCCTGTAAAGAGTCCTGTTACAATATGTGGTGATATTCATGGGCAGTTTCATGACCTTGCAGAACTGTTCCGAATCGGTGGAAAG

upper sequence: Vv06s0004g00830.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G062394_T01 (Zea mays), 3'ss of exon 2
-------ctgtattgatcttataatgcattactcgtcattttgagttaatgaataatgttatctagggaaatttttaatgatccctttttttttttttgtaatgcagCCTGTGAAAAGCCCTGTGACAATCTGTGGTGATATCCATGGCCAGTTTCATGATCTAGCGGAGCTTTTCCGAATTGGAGGAAAG
        | |   | |   ||  || |||    |          |   |   | ||||||| |      | ||   | |||   |||| |  |  ||||  |||||||||| || || ||||| || || || |||||||| ||||| || ||||||||||| || || || ||||||||||| ||||||
ggacaatttatgccgtttagatgctggattcacagatgcagctcttattttggtcatgttatttg-----acttaagacgatttgttttgtcatcattgt--tgcagCCTGTAAAGAGTCCTGTTACTATATGCGGTGATATTCATGGACAATTTCATGATCTTGCTGAACTCTTCCGAATTGGTGGAAAG

upper sequence: Vv06s0004g00830.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G108355_T01 (Zea mays), 3'ss of exon 2
-ctgtattgatcttataatgcattactcgtcatttt---gagttaatgaataatgttatctagggaaatttttaatgatccctttttttttttttgtaatgcagCCTGTGAAAAGCCCTGTGACAATCTGTGGTGATATCCATGGCCAGTTTCATGATCTAGCGGAGCTTTTCCGAATTGGAGGAAAG
 || |    |   |    ||  |   | |    ||    ||     |   |  |||||| |   ||   ||||   |||   |||| || |  ||||  |||||||||| || || ||||| || || || |||||||| ||||| || ||||||||||| || || || |||||||| || ||||||
tctttggataatctgcgctgtttatatggcggattcacagatgcggttggtcgtgttatttgttga--cttttgccgatttgttttgttatcattgt--tgcagCCTGTAAAGAGTCCTGTTACTATATGCGGTGATATTCATGGACAATTTCATGATCTTGCTGAACTCTTCCGAATCGGTGGAAAG

upper sequence: Vv06s0004g00830.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA05G28790.2 (Glycine max), 3'ss of exon 2
ctgtattgatcttataatgcattactcgtcat-tttgagttaatgaataatgttatctagggaaatttttaatgatccctttttttttttttgtaat-gcagCCTGTGAAAAGCCCTGTGACAATCTGTGGTGATATCCATGGCCAGTTTCATGATCTAGCGGAGCTTTTCCGAATTGGAGGAAAG
 | || |    |||  |||   || | ||     || |  | ||||  | | | |   |  ||||    ||| ||     |||  |||     |||| ||||||||||||||| ||||| ||||| ||||||||||| ||||| || || |||||||| || |||||||| || |||||||| |||
-tatactttgtttaatatgt-ctatttgtagggctttaactcatgatgattttgaatgactgaaaaaactaaagagattatttcatttgccaataattgcagCCTGTGAAAAGTCCTGTTACAATTTGTGGTGATATTCATGGGCAATTCCATGATCTTGCAGAGCTTTTTCGCATTGGAGGGAAG

upper sequence: Vv06s0004g00830.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G11940.1 (Glycine max), 3'ss of exon 2
ctgtattgatcttataatgcattactcgtcat-tttgagttaatgaataatgttatctagggaaatttttaatgatccctttttttttttttgtaat-gcagCCTGTGAAAAGCCCTGTGACAATCTGTGGTGATATCCATGGCCAGTTTCATGATCTAGCGGAGCTTTTCCGAATTGGAGGAAAG
 | || |    |||  |||  ||| | ||     || |  | ||||  | | | |   |  || |    ||| ||     |||  |||     |||| ||||||||||||||| ||||| ||||| ||||||||||| ||||| || || |||||||| || |||||||| || |||||||| |||
-tttactttgtttaatatgt-ttatttgtagggctttaactcatgatgattttgaatgactgagaaaactaaagacattatttcatttgccaataattgcagCCTGTGAAAAGTCCTGTTACAATTTGTGGTGATATTCATGGGCAATTCCATGATCTTGCAGAGCTTTTTCGCATTGGAGGGAAG

upper sequence: Vv06s0004g00830.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S81_198V6.3 (Physcomitrella patens), 3'ss of exon 3
ctgtattgatcttataatgcattactcgtcattttgagttaatgaataatgttatctagggaaatttttaatgatccctttttttttttttgtaa-----tgcagCCTGTGAAAAGCCCTGTGACAATCTGTGGTGATATCCATGGCCAGTTTCATGATCTAGCGGAGCTTTTCCGAATTGGAGGAAAG
    ||||  |   | |||| ||  ||  |   || ||   |||  |    ||    |     |  ||||    |   |||| || || | ||       | ||||| |||||  | || || ||||| ||||||||||| |||||||||||||||||||| || || || |||||||||||||||| |
----attgggcaggtcatgc-ttggtcagcgcatttaggacatgcttctgtttcaaaactctgagatttacctgttgtttttgttgttgtggtggatgattacagCCAGTGAAGTGTCCAGTCACAATTTGTGGTGATATTCATGGCCAGTTTCATGATCTTGCTGAACTCTTCCGAATTGGAGGAATG

upper sequence: Vv06s0004g00830.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S88_180V6.1 (Physcomitrella patens), 3'ss of exon 2
ctgtattgatcttataatgcattactcgtcatt-ttgagttaatgaataatgt-tatctaggg-aaatttttaatgatccctttttttttttttgtaatg---cagCCTGTGAAAAGCCCTGTGACAATCTGTGGTGATATCCATGGCCAGTTTCATGATCTAGCGGAGCTTTTCCGAATTGGAGGAAAG
     |  ||  |||| |  ||| | ||  ||  || ||       |  |||  |||||     |||  | |    ||    | |  |  |  ||  |     ||||| || ||  ||||||| ||||| ||||||||||| |||||||| || |||||||| || || || |||||||| || |||| |
-----taaattatatattatatt-cacgctatggttcagcacgctcaggatgcgtatctgacccaaaactctggaaattttctgtggtggtgatgggagataacagCCAGTAAAGTGCCCTGTCACAATTTGTGGTGATATTCATGGCCAATTCCATGATCTTGCTGAACTCTTCCGAATCGGGGGAATG

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|33404623|gb|CF210250.1|CF210250
EST:     TGCTTTGTGAGAAGGCTAAGGAGATATTAATGGAAGAAAGCAATGTCCAG                         CCTGTGAAAAGCCCTGTGACAATCTGTGGTGATATCCATGGCCAGTTTCAT
genomic: TGCTTTGTGAGAAGGCTAAGGAGATATTAATGGAAGAAAGCAATGTCCAGgtatgcccct ... tgtaatgcagCCTGTGAAAAGCCCTGTGACAATCTGTGGTGATATCCATGGCCAGTTTCAT
EST: gi|110684715|gb|EE062310.1|EE062310
EST:     TGCTTTGTGAGAAGGCTAAGGAGATATTAATGGAAGAAAGCAATGTCCAG                         CCTGTGAAAAGCCCTGTGACAATCTGTGGTGATATCCATGGCCAGTTTCAT
genomic: TGCTTTGTGAGAAGGCTAAGGAGATATTAATGGAAGAAAGCAATGTCCAGgtatgcccct ... tgtaatgcagCCTGTGAAAAGCCCTGTGACAATCTGTGGTGATATCCATGGCCAGTTTCAT
EST: gi|161716085|gb|FC065837.1|FC065837
EST:     TGCTTTGTGAGAAGGCTAAGGAGATATTAATGGAAGAAAGCAATGTCCAG                         CCTGTGAAAAGCCCTGTGACAATCTGTGGTGATATCCATGGCCAGTTTCAT
genomic: TGCTTTGTGAGAAGGCTAAGGAGATATTAATGGAAGAAAGCAATGTCCAGgtatgcccct ... tgtaatgcagCCTGTGAAAAGCCCTGTGACAATCTGTGGTGATATCCATGGCCAGTTTCAT
EST: gi|110377055|gb|EC942116.1|EC942116
EST:     TGCTTTGTGAGAAGGCTAAGGAGATATTAATGGAAGAAAGCAATGTCCAG                         CCTGTGAAAAGCCCTGTGACAATCTGTGGTGATATCCATGGCCAGTTTCAT
genomic: TGCTTTGTGAGAAGGCTAAGGAGATATTAATGGAAGAAAGCAATGTCCAGgtatgcccct ... tgtaatgcagCCTGTGAAAAGCCCTGTGACAATCTGTGGTGATATCCATGGCCAGTTTCAT
EST: gi|71860995|gb|DT010050.1|DT010050
EST:     TGCTTTGTGAGAAGGCTAAGGAGATATTGATGGAAGAAAGCAATGTCCAG                         CCTGTGAAAAGCCCTGTGACAATCTGTGGTGATATCCATGGCCAGTTTCAT
genomic: TGCTTTGTGAGAAGGCTAAGGAGATATTAATGGAAGAAAGCAATGTCCAGgtatgcccct ... tgtaatgcagCCTGTGAAAAGCCCTGTGACAATCTGTGGTGATATCCATGGCCAGTTTCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataatgttatctagggaaatttttaatgatccctttttttttttttgtaatgcagCCTGTGAAAAGCCCTGTGACAATCTGTGGTGATATCCATGGCCAGTTTCATGATCTAGCGGAGCTTTTCCGAATTGGAGGAAAG
                    ttttaat  putative branch site (score: 3)
                   tttttaatgatccctt  CT-rich tract
                aaatttttaatgatcc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgtattgatcttataatgcattactcgtcattttgagttaatgaataatgttatctagggaaatttttaatgatccctttttttttttttgtaatgcagCCTGTGAAAAGCCCTGTGACAATCTGTGGTGATATCCATGGCCAGTTTCATGATCTAGCGGAGCTTTTCCGAATTGGAGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - -aatgcat
- - - - - - - - - - - - - - - - - - - - aatgaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -agggaaa