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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaaacttgtgtctcttacatcaagaaagtttttggacgtctcatatgttatgtgtgtctaaatgttgtctttcattatttttctggtgccatatagGTTATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAA

Basic information

species Vitis vinifera
transcript Vv19s0090g00580.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0090g00580.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os08g09240.1 (Oryza sativa), 3'ss of exon 3
gtatgaaacttgtgtctcttacatcaagaaagtttttggacgtctcatatgttatgtgtgtctaaatgttgtctttcattatttt-tctggtgccatatagGTTATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAA
||| |     ||  |   |            |||      ||  |  | ||| |||  | | |   | || | |      | ||  | || |   |||||||| ||||| ||||||||||| || |||||||| |||||||||||||| |||||
gtaagttggatggattcttgttgcttgtggtgtt------cgcttactttgtcatgattattttgttcttatgtgaagcaacttcctgtgattaaatatagGTCATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAA

upper sequence: Vv19s0090g00580.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os04g53240.4 (Oryza sativa), 3'ss of exon 2
gtatgaaacttgtgtctcttacatcaagaaagtttttggacgtctcatatgttatgtgtgtctaaatgttgtctttcattatttttctggtgccatatagGTTATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAA
     || ||||    || ||   |     |||| |  |  || || |   || ||  | | |   || | |  ||  |||  | |||  ||  || ||||| ||||| ||||| |||||||||||||| || |||||||| |||||||| ||
---gtaagcttgctcttcatattgctc---agttat--gttgtttccttcattgtggtttttt---tgctctaatttgttacatatctaatgtaatgtagGTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAAAA

upper sequence: Vv19s0090g00580.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G076826_T02 (Zea mays), 3'ss of exon 4
gtatgaaacttgtgtctcttacatcaagaaagtttttggacgtctcatatgttatgtgtgtctaaatgttgtctttcattatttttctggtgccatatagGTTATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAA
     || |||||  |  |    |  |   | | |||     | || |   ||   | | || ||      | | | | || || | |  |||     |||| ||||| ||||||||||| || |||||||| |||||||| |||||||| ||
---gtaagcttgtacccttcttctgtatgcactgtttc----tttcttcatttgcttttatccaa------tttatgactagttgtataatgc-----agGTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAA

upper sequence: Vv19s0090g00580.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G134613_T04 (Zea mays), 3'ss of exon 3
gtatgaaacttgtgtctcttacatcaagaaagtttttggacgtctcatatgttatgtgtgtctaaatgttgtctttcattatttttctggtgccatatagGTTATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAA-----------------------------------------------
   | |  |||   |   ||  | | |    ||  |  ||    |   ||| ||  | |       |||  || ||||    |  | |  ||  |||||||| ||||| |||||||| || || |||||||| || |||||||||||||| ||                                               
--gtaagccttaattaatttttacccat---gtcctctgattatttccatgatagcttt-------tgtgttcattcaaacctgctttcttgtaatatagGTCATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAAGTCAGCCATTTCACGAGTATCTCTTTAGTGCATTTGTATTTTCTCTA

upper sequence: Vv19s0090g00580.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G134613_T01 (Zea mays), 3'ss of exon 2
gtatgaaacttgtgtctcttacatcaagaaagtttttggacgtctcatatgttatgtgtgtctaaatgttgtctttcattatttttctggtgccatatagGTTATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAA
   | |  |||   |   ||  | | |    ||  |  ||    |   ||| ||  | |       |||  || ||||    |  | |  ||  |||||||| ||||| |||||||| || || |||||||| || |||||||||||||| ||
--gtaagccttaattaatttttacccat---gtcctctgattatttccatgatagcttt-------tgtgttcattcaaacctgctttcttgtaatatagGTCATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAA

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|110407776|gb|EC973391.1|EC973391
EST:     GGCAAGCAGAAGCTGCTCGCATCAGGGAGAAGTATCCTGATAGAATACCA                         GTTATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAG
genomic: GGCAAGCAGAAGCTGCTCGCATCAGGGAGAAGTATCCTGATAGAATACCAgtatgaaact ... tgccatatagGTTATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAG
EST: gi|32459630|gb|CD800804.1|CD800804
EST:     CAAGCAGAAGCTGCTCGCGTCAGGGAGAAGTATATCCTGATAGAATACCA                         GTTATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAG
genomic: CAAGCAGAAGCTGCTCGCATCAGGGAGAAG--TATCCTGATAGAATACCAgtatgaaact ... tgccatatagGTTATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAG
EST: gi|110390932|gb|EC955876.1|EC955876
EST:     GGCAAGCAGAAGCTGCTCGCATCAGGGAGAAGTATCCTGATAGAATACCA                         GTTATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAG
genomic: GGCAAGCAGAAGCTGCTCGCATCAGGGAGAAGTATCCTGATAGAATACCAgtatgaaact ... tgccatatagGTTATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAG
EST: gi|110694887|gb|EE072272.1|EE072272
EST:     GGCAAGCAGAAGCTGCTCGCATCAGGGAGAAGTATCCTGATAGAATACCA                         GTTATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAG
genomic: GGCAAGCAGAAGCTGCTCGCATCAGGGAGAAGTATCCTGATAGAATACCAgtatgaaact ... tgccatatagGTTATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAG
EST: gi|46911389|gb|CN546764.1|CN546764
EST:     GGCAAGCAGAAGCTGCTCGCATCAGGGAGAAGTATCCTGATAGAATACCA                         GTTATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAG
genomic: GGCAAGCAGAAGCTGCTCGCATCAGGGAGAAGTATCCTGATAGAATACCAgtatgaaact ... tgccatatagGTTATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAG
EST: gi|110421257|gb|EC987552.1|EC987552
EST:     GGCAAGCAGAAGCTGCTCGCATCAGGGAGAAGTATCCTGATAGAATACCA                         GTTATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAG
genomic: GGCAAGCAGAAGCTGCTCGCATCAGGGAGAAGTATCCTGATAGAATACCAgtatgaaact ... tgccatatagGTTATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAG
EST: gi|110422502|gb|EC988827.1|EC988827
EST:     GGCAAGCAGAAGCTGCTCGCATCAGGGAGAAGTATCCTGATAGAATACCA                         GTTATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAG
genomic: GGCAAGCAGAAGCTGCTCGCATCAGGGAGAAGTATCCTGATAGAATACCAgtatgaaact ... tgccatatagGTTATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAG
EST: gi|71888297|gb|DT037352.1|DT037352
EST:     GGCAAGCAGAAGCTGCTCGCATCAGGGAGAAGTATCCTGATAGAATACCA                         GTTATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAG
genomic: GGCAAGCAGAAGCTGCTCGCATCAGGGAGAAGTATCCTGATAGAATACCAgtatgaaact ... tgccatatagGTTATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catatgttatgtgtgtctaaatgttgtctttcattatttttctggtgccatatagGTTATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAA
              gtctaaa  putative branch site (score: 3)
                          tctttcattattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaaacttgtgtctcttacatcaagaaagtttttggacgtctcatatgttatgtgtgtctaaatgttgtctttcattatttttctggtgccatatagGTTATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG