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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccctttaaatctactaagatttgaatttttagactactactatttttttggtcagttcatgctcttataggtcagtgtatttccatgtggatgactcagGTTACTGGAGATCCTGGAAAAATGGTTGCTGTGCAGAGAAATTTAAGCAAGTTTGGAATTAAAGAACTTGCCAGAACTGGAAAG

Basic information

species Vitis vinifera
transcript Vv00s0220g00110.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0220g00110.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os11g14950.1 (Oryza sativa), 3'ss of exon 4
-tccctttaaatctactaagatttgaatttttagactactactatttttttggtcagttcatgctcttataggtcagtgtatttccatgtggatgactcagGTTACTGGAGATCCTGGAAAAATGGTTGCTGTGCAGAGAAATTTAAGCAAGTTTGGAATTAAAGAACTTGCCAGAACTGGAAAG
 |     ||  | ||       ||| |  |     | || |  ||| || ||||   || |||     | |      |   |||   | |  |||    |||| |||||||||||||||||||| |||||||| ||||| ||  ||||||| |||||||| |||||| ||||||||||||| |||
gtaatcctatgtttatcttaccttgcagatcacatcgaccataattcttgtggtt--tttatgaaagaaaaaaaatcttctttttttttttcatgttgaagGTAACTGGAGATCCTGGAAAAATTGTTGCTGTACAGAGGAACCTAAGCAAATTTGGAATCAAAGAAATTGCCAGAACTGGCAAG

upper sequence: Vv00s0220g00110.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os02g39570.5 (Oryza sativa), 3'ss of exon 4
tccctttaaatctactaagatttgaatttttagactactactatttttttggtcagttcatgctcttataggtcagtgtatttccatgtggatgactcagGTTACTGGAGATCCTGGAAAAATGGTTGCTGTGCAGAGAAATTTAAGCAAGTTTGGAATTAAAGAACTTGCCAGAACTGGAAAG
                |||| |     ||  |      |   ||   | || |  ||      || | |      ||||||||  ||   | ||    |||| |||||||||||||| ||||| ||||||||||| || ||  | ||||| ||||| || |||||| ||   ||||| ||||| 
-------------gtaaagactcctgattccaacaggtttacatacatatgatt-gtaggaattcctttgat---gtgtatttg-atcaagttg---tagGTAACTGGAGATCCTGGCAAAATTGTTGCTGTGCAAAGGAACCTCAGCAAATTTGGGATAAAAGAAATTTGTAGAACGGGAAAA
















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|349818318|gb|FQ409093.1|FQ409093
EST:     TCTTCAGAGCAAAAATTGTTGACATTTCAGAACATTCATTGACCATTGAG                         GTTACTGGAGATCCTGGAAAAATGGTTGCTGTGCAGAGAAATTTAAGCAAG
genomic: TCTTCAGAGCAAAAATTGTTGACATTTCAGAACATTCATTGACCATTGAGgtgactgcta ... gatgactcagGTTACTGGAGATCCTGGAAAAATGGTTGCTGTGCAGAGAAATTTAAGCAAG
EST: gi|352786516|gb|FQ479125.1|FQ479125
EST:     TCTTCAGAGCAAAAATTGTTGACATTTCAGAACATTCATTGACCATTGAG                         GTTACTGGAGATCCTGGAAAAATGGTTGCTGTGCAGAGAAATTTAAGCAAG
genomic: TCTTCAGAGCAAAAATTGTTGACATTTCAGAACATTCATTGACCATTGAGgtgactgcta ... gatgactcagGTTACTGGAGATCCTGGAAAAATGGTTGCTGTGCAGAGAAATTTAAGCAAG
EST: gi|351035256|gb|FQ458613.1|FQ458613
EST:     TCTTCAGAGCAAAAATTGTTGACATTTCAGAACATTCATTGACCATTGAG                         GTTACTGGAGATCCTGGAAAAATGGTTGCTGTGCAGAGAAATTTAAGCAAG
genomic: TCTTCAGAGCAAAAATTGTTGACATTTCAGAACATTCATTGACCATTGAGgtgactgcta ... gatgactcagGTTACTGGAGATCCTGGAAAAATGGTTGCTGTGCAGAGAAATTTAAGCAAG
EST: gi|351034594|gb|FQ457951.1|FQ457951
EST:     TCTTCAGAGCAAAAATTGTTGACATTTCAGAACATTCATTGACCATTGAG                         GTTACTGGAGATCCTGGAAAAATGGTTGCTGTGCAGAGAAATTTAAGCAAG
genomic: TCTTCAGAGCAAAAATTGTTGACATTTCAGAACATTCATTGACCATTGAGgtgactgcta ... gatgactcagGTTACTGGAGATCCTGGAAAAATGGTTGCTGTGCAGAGAAATTTAAGCAAG
EST: gi|351012893|gb|FQ430456.1|FQ430456
EST:     TCTTCAGAGCAAAAATTGTTGACATTTCAGAACATTCATTGACCATTGAG                         GTTACTGGAGATCCTGGAAAAATGGTTGCTGTGCAGAGAAATTTAAGCAAG
genomic: TCTTCAGAGCAAAAATTGTTGACATTTCAGAACATTCATTGACCATTGAGgtgactgcta ... gatgactcagGTTACTGGAGATCCTGGAAAAATGGTTGCTGTGCAGAGAAATTTAAGCAAG
EST: gi|351031526|gb|FQ459783.1|FQ459783
EST:     TCTTCAGAGCAAAAATTGTTGACATTTCAGAACATTCATTGACCATTGAG                         GTTACTGGAGATCCTGGAAAAATGGTTGCTGTGCAGAGAAATTTAAGCAAG
genomic: TCTTCAGAGCAAAAATTGTTGACATTTCAGAACATTCATTGACCATTGAGgtgactgcta ... gatgactcagGTTACTGGAGATCCTGGAAAAATGGTTGCTGTGCAGAGAAATTTAAGCAAG
EST: gi|351046895|gb|FQ454505.1|FQ454505
EST:     TCTTCAGAGCAAAAATTGTTGACATTTCAGAACATTCATTGACCATTGAG                         GTTACTGGAGATCCTGGAAAAATGGTTGCTGTGCAGAGAAATTTAAGCAAG
genomic: TCTTCAGAGCAAAAATTGTTGACATTTCAGAACATTCATTGACCATTGAGgtgactgcta ... gatgactcagGTTACTGGAGATCCTGGAAAAATGGTTGCTGTGCAGAGAAATTTAAGCAAG
EST: gi|351043332|gb|FQ451384.1|FQ451384
EST:     TCTTCAGAGCAAAAATTGTTGACATTTCAGAACATTCATTGACCATTGAG                         GTTACTGGAGATCCTGGAAAAATGGTTGCTGTGCAGAGAAATTTAAGCAAG
genomic: TCTTCAGAGCAAAAATTGTTGACATTTCAGAACATTCATTGACCATTGAGgtgactgcta ... gatgactcagGTTACTGGAGATCCTGGAAAAATGGTTGCTGTGCAGAGAAATTTAAGCAAG
EST: gi|351040114|gb|FQ425200.1|FQ425200
EST:     TCTTCAGAGCAAAAATTGTTGACATTTCAGAACATTCATTGACCATTGAG                         GTTACTGGAGATCCTGGAAAAATGGTTGCTGTGCAGAGAAATTTAAGCAAG
genomic: TCTTCAGAGCAAAAATTGTTGACATTTCAGAACATTCATTGACCATTGAGgtgactgcta ... gatgactcagGTTACTGGAGATCCTGGAAAAATGGTTGCTGTGCAGAGAAATTTAAGCAAG
EST: gi|351044506|gb|FQ443037.1|FQ443037
EST:     TCTTCAGAGCAAAAATTGTTGACATTTCAGAACATTCATTGACCATTGAG                         GTTACTGGAGATCCTGGAAAAATGGTTGCTGTGCAGAGAAATTTAAGCAAG
genomic: TCTTCAGAGCAAAAATTGTTGACATTTCAGAACATTCATTGACCATTGAGgtgactgcta ... gatgactcagGTTACTGGAGATCCTGGAAAAATGGTTGCTGTGCAGAGAAATTTAAGCAAG
EST: gi|352795642|gb|FQ480230.1|FQ480230
EST:     TCTTCAGAGCAAAAATTGTTGACATTTCAGAACATTCATTGACCATTGAG                         GTTACTGGAGATCCTGGAAAAATGGTTGCTGTGCAGAGAAATTTAAGCAAG
genomic: TCTTCAGAGCAAAAATTGTTGACATTTCAGAACATTCATTGACCATTGAGgtgactgcta ... gatgactcagGTTACTGGAGATCCTGGAAAAATGGTTGCTGTGCAGAGAAATTTAAGCAAG
EST: gi|349822000|gb|FQ408329.1|FQ408329
EST:     TCTTCAGAGCAAAAATTGTTGGCATTTCAGAACATTCATTGACCATTGAG                         GTTACTGGAGATCCTGGAAAAATGGTTGCTGTGCAGAGAAATTTAAGCAAG
genomic: TCTTCAGAGCAAAAATTGTTGACATTTCAGAACATTCATTGACCATTGAGgtgactgcta ... gatgactcagGTTACTGGAGATCCTGGAAAAATGGTTGCTGTGCAGAGAAATTTAAGCAAG
EST: gi|351017801|gb|FQ436154.1|FQ436154
EST:     TCTTCAGAGCAAAAATTGTTGACATTTCAGAACATTCATTGACCATTGAG                         GTTACTGGAGATCCTGGAAAAATGGTTGCTGTGCAGAGAAATTTAAGCAAG
genomic: TCTTCAGAGCAAAAATTGTTGACATTTCAGAACATTCATTGACCATTGAGgtgactgcta ... gatgactcagGTTACTGGAGATCCTGGAAAAATGGTTGCTGTGCAGAGAAATTTAAGCAAG
EST: gi|351032123|gb|FQ460380.1|FQ460380
EST:     TCTTCAGAGCAAAAATTGTTGACATTTCAGAACATTCATTGACCATTGAG                         GTTACTGGAGATCCTGGAAAAATGGTTGCTGTGCAGAGAAATTTAAGCAAG
genomic: TCTTCAGAGCAAAAATTGTTGACATTTCAGAACATTCATTGACCATTGAGgtgactgcta ... gatgactcagGTTACTGGAGATCCTGGAAAAATGGTTGCTGTGCAGAGAAATTTAAGCAAG
EST: gi|351054122|gb|FQ450204.1|FQ450204
EST:     TCTTCAGAGCAAAAATTGTTGACATTTCAGAACATTCATTGACCATTGAG                         GTTACTGGAGATCCTGGAAAAATGGTTGCTGTGCAGAGAAATTTAAGCAAG
genomic: TCTTCAGAGCAAAAATTGTTGACATTTCAGAACATTCATTGACCATTGAGgtgactgcta ... gatgactcagGTTACTGGAGATCCTGGAAAAATGGTTGCTGTGCAGAGAAATTTAAGCAAG
EST: gi|351039410|gb|FQ461277.1|FQ461277
EST:     TCTTCAGAGCAAAAATTGTTGACATTTCAGAACATTCATTGACCATTGAG                         GTTACTGGAGATCCTGGAAAAATGGTTGCTGTGCAGAGAAATTTAAGCAAG
genomic: TCTTCAGAGCAAAAATTGTTGACATTTCAGAACATTCATTGACCATTGAGgtgactgcta ... gatgactcagGTTACTGGAGATCCTGGAAAAATGGTTGCTGTGCAGAGAAATTTAAGCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttggtcagttcatgctcttataggtcagtgtatttccatgtggatgactcagGTTACTGGAGATCCTGGAAAAATGGTTGCTGTGCAGAGAAATTTAAGCAAGTTTGGAATTAAAGAACTTGCCAGAACTGGAAAG
                  tcttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccctttaaatctactaagatttgaatttttagactactactatttttttggtcagttcatgctcttataggtcagtgtatttccatgtggatgactcagGTTACTGGAGATCCTGGAAAAATGGTTGCTGTGCAGAGAAATTTAAGCAAGTTTGGAATTAAAGAACTTGCCAGAACTGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
-cccttta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatgtg