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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattaactgctttagtcataaacattggttcaagcagagatctttaaatcaaattgttgctttaatattttattaatattcagatggtttctgtgtttagGTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACATGAAGCTTACG

Basic information

species Vitis vinifera
transcript Vv14s0171g00490.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G130230_T02 (Zea mays), 3'ss of exon 12
tattaactgctttagtcataaacattggttcaagcagagatctttaaatcaaatt--gttgctttaatattttattaatattcagatggtttctgtgtttagGTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACATGAAGCTTACG
 |   | |  ||||         |||   |    | |  || | | ||| | | |  | |    |  ||||| |   | ||  | ||     |||  |  |||  | | ||| || |||||||| ||||| |||||||||||||| | ||| ||||| |||||||| || || 
-aacgaatattttatattggtttattatgttgctctgttatgtctgaataagaattagatatcctggtatttgaactaaatataaatataacctg-atgaagGCAAGAAGCAAGGAAGAAATGAGTTTGTTATACGCCTCCAACCATCAGAAGCCATGTACATGAAACTAACT

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA19G22690.1 (Glycine max), 3'ss of exon 12
tattaactgctttagtcataaacattggttca-agcagagatctttaaatcaaattgttgctttaatattttattaatattcagatggtttctgtgtttagGTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACATGAAGCTTACG
||||| ||    |     |   | |   || |  |||     || | |||| || | |    ||| | ||| |    || |   |   | |   ||||||||||||| ||||||||||||||| ||||| |||||||| ||||||| ||| || || |||||||||||||| 
tattagctagagtgtatgtttccttatcttgatggcaagtgcctattaatctaaatatcaactta-tgtttaaaccttactgtaaacttattcctgtttagGTCAAAAGCAGGGGAGAAATGAGTTTGTTATACGCCTGCAACCTTCAGAAGCTATGTACATGAAGCTTACA

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA19G24250.1 (Glycine max), 3'ss of exon 12
tattaactgctttagtcataaacattggttcaagcagagatctttaa-----atcaaattgttgctttaatattttattaatattcagatggtttctgtgtttagGTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACATGAAGCTTACG
   || |  |  |   ||| || ||| | |  |||     |  ||       |||||| | |   ||||  ||   | |||   | |  |  ||    | ||||||| ||| ||||||||||||||| ||||| || ||||| ||||||||||| || || |||||||||||||||
---taccaacaattaacatcaatattagctatagccttttttctttgttgtcatcaaaatatcagtttagcataaaagtaactcttaatt--ttaacatttttagGTAAAAAGCAGGGGAGAAATGAGTTTGTTATCCGCCTACAACCTTTAGAAGCTATGTACATGAAGCTTACG

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA16G06850.3 (Glycine max), 3'ss of exon 12
tattaactgctttagtcataaacattggttcaagcagagatctttaa-----atcaaattgttgctttaatattttattaatattcagatggtttctgtgtttagGTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACATGAAGCTTACG
|| ||||   |     ||| || ||| | |  |||  |  |  ||       |||||| | |   ||||  ||     |||   | |  |   |      ||||||| ||| ||||||||||||||| | ||| || ||||| || |||| ||| || ||||||||||||||||||
tactaacaatt---aacatcaatattagctatagcctattttcttcgttgtcatcaaaatatcagtttagcataaagataactcttaatt--ctaacaattttagGTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAGCTATTTACATGAAGCTTACG

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|110716825|gb|EE092144.1|EE092144
EST:     GATATCTACAGAT                         GTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTTAGAGG
genomic: GATATCTACAGATgtatggcatc ... ctgtgtttagGTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTTAGAGG
EST: gi|351015046|gb|FQ444335.1|FQ444335
EST:     GGCAGAAATCCGCATTCAATTCAAGGATGTTCCTGGTGATATCTACAGAT                         GTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTCAGAGG
genomic: GGCAGAAATTCGCATTCAATTCAAGGATGTTCCTGGTGATATCTACAGATgtatggcatc ... ctgtgtttagGTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTTAGAGG
EST: gi|110365367|gb|EC928242.1|EC928242
EST:     GGCAGAAATCCGCATTCAATTTAAGGATGTTCCTGGTGATATCTACAGAT                         GTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTCAGAGG
genomic: GGCAGAAATTCGCATTCAATTCAAGGATGTTCCTGGTGATATCTACAGATgtatggcatc ... ctgtgtttagGTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTTAGAGG
EST: gi|110715492|gb|EE093605.1|EE093605
EST:     GGCAGAAATTCGCATTCAATTCAAGGATGTTCCTGGTGATATCTACAGAT                         GTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTTAGAGG
genomic: GGCAGAAATTCGCATTCAATTCAAGGATGTTCCTGGTGATATCTACAGATgtatggcatc ... ctgtgtttagGTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTTAGAGG
EST: gi|33405782|gb|CF211409.1|CF211409
EST:     GGCAGAAATTCGCATTCAATTCAAGGATGTTCCTGGTGATATCTACAGAT                         GTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTTAGAGG
genomic: GGCAGAAATTCGCATTCAATTCAAGGATGTTCCTGGTGATATCTACAGATgtatggcatc ... ctgtgtttagGTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTTAGAGG
EST: gi|110361886|gb|EC925389.1|EC925389
EST:     GGCAGAAATCCGCATTCAATTTAAGGATGTTCCTGGTGATATCTACAGAT                         GTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTCAGAGG
genomic: GGCAGAAATTCGCATTCAATTCAAGGATGTTCCTGGTGATATCTACAGATgtatggcatc ... ctgtgtttagGTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTTAGAGG
EST: gi|294967142|gb|GW840017.1|GW840017
EST:     GGCAGAAATTCGCATTCAATTCAAGGATGTTCCTGGTGATATCTACAGAT                         GTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTT
genomic: GGCAGAAATTCGCATTCAATTCAAGGATGTTCCTGGTGATATCTACAGATgtatggcatc ... ctgtgtttagGTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTT
EST: gi|110696408|gb|EE072500.1|EE072500
EST:     GGCAGAAATCCGCATTCAATTCAAGGATGTTCCTGGTGATATCTACAGAT                         GTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTCAGAGG
genomic: GGCAGAAATTCGCATTCAATTCAAGGATGTTCCTGGTGATATCTACAGATgtatggcatc ... ctgtgtttagGTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTTAGAGG
EST: gi|110390234|gb|EC955134.1|EC955134
EST:     GCAGAAATCCGCATTCAATTTAAGGATGTTCCTGGTGATATCTACAGAT                         GTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTCAGAGG
genomic: GCAGAAATTCGCATTCAATTCAAGGATGTTCCTGGTGATATCTACAGATgtatggcatc ... ctgtgtttagGTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTTAGAGG
EST: gi|352763934|gb|FQ465384.1|FQ465384
EST:     TTCCTGGTGATATCTACAGAT                         GTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTTAGAGG
genomic: TTCCTGGTGATATCTACAGATgtatggcatc ... ctgtgtttagGTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTTAGAGG
EST: gi|56409520|gb|CX017772.1|CX017772
EST:     GGCAGAAATTCGCATTCAATTCAAGGATGTTCCTGGTGATATCTACAGAT                         GTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTTAGAGG
genomic: GGCAGAAATTCGCATTCAATTCAAGGATGTTCCTGGTGATATCTACAGATgtatggcatc ... ctgtgtttagGTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTTAGAGG
EST: gi|352781474|gb|FQ468318.1|FQ468318
EST:     GGCAGAAATTCGCATTCAATTCAAGGATGTTCCTGGTGATATCTACAGAT                         GTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTTAGAGG
genomic: GGCAGAAATTCGCATTCAATTCAAGGATGTTCCTGGTGATATCTACAGATgtatggcatc ... ctgtgtttagGTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTTAGAGG
EST: gi|110416304|gb|EC982275.1|EC982275
EST:     GGCAGAAATTCGCATTCAATTCAAGGATGTTCCTGGTGATATCTACAGAT                         GTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTTAGAGG
genomic: GGCAGAAATTCGCATTCAATTCAAGGATGTTCCTGGTGATATCTACAGATgtatggcatc ... ctgtgtttagGTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTTAGAGG
EST: gi|110373098|gb|EC937308.1|EC937308
EST:     GGCAGAAATTCGCATTCAATTCAAGGATGTTCCTGGTGATATCTACAGAT                         GTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTTAGAGG
genomic: GGCAGAAATTCGCATTCAATTCAAGGATGTTCCTGGTGATATCTACAGATgtatggcatc ... ctgtgtttagGTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTTAGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatcaaattgttgctttaatattttattaatattcagatggtttctgtgtttagGTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACATGAAGCTTACG
                         tattaat  putative branch site (score: 2)
                                          tttctgt  putative PPT
     aaattgttgctttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattaactgctttagtcataaacattggttcaagcagagatctttaaatcaaattgttgctttaatattttattaatattcagatggtttctgtgtttagGTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACATGAAGCTTACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - ctgcttt
- - - - - - - - cataaac
- - - - - - - - - - - - - - -tcaagca
- - - - - - - - - - - - - - - - - - - - - - -aaatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cagatgg