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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagttcctgtatctacgccctttagatttcgtagttagtcatgtttaagttgctcttgtagttgactagattgtacttgaaatgcagGGATGATGGGTTCTGGAAAAACAACTATTGGCAAGATTTTGTCAGAAGTGCTTGGTTATTCATTTTGCGACAG

Basic information

species Vitis vinifera
transcript Vv07s0031g01600.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0031g01600.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G14980.1 (Glycine max), 3'ss of exon 3
gtcagttcctgtatctacgccctttagatttcgtagttagtcatgtttaagttgctcttgtagttgac-tagattgtacttgaaatgcagGGATGATGGGTTCTGGAAAAACAACTATTGGCAAGATTTTGTCAGAAGTGCTTGGTTATTCATTTTGCGACAG
||||||| ||  ||  ||  | | |   |  | | ||  |   ||   || || || | | | |  |  |   ||| | |||| ||||||| |||||||| ||||| ||||||||  | || |||||  ||||| |||||||||||||||||||||| || ||
gtcagtttcttgattgacttcttgtgcttaacatggtatgctttgg--aaattactttggcattaaaaatgctttgaatttgacatgcagGAATGATGGGCTCTGGGAAAACAACGGTGGGGAAGATAATGTCACAAGTGCTTGGTTATTCATTTTGTGATAG

upper sequence: Vv07s0031g01600.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA05G31730.2 (Glycine max), 3'ss of exon 3
gtcagttcctgtatctacgccctttagatttcgtagttagtcatgtttaagttgctcttgtagttgac-tagattgtacttgaaatgcagGGATGATGGGTTCTGGAAAAACAACTATTGGCAAGATTTTGTCAGAAGTGCTTGGTTATTCATTTTGCGACAG
||||||| ||   |  ||  | | | | || | | ||  |   ||   || || || | | | |  |  |   ||| | ||||  |||||| |||||||| ||||| ||||||||  | || |||||  ||||  |||||||||||||||||||||| || ||
gtcagtttcttggttgacttcttgt-gcttacatggtatgctttgg--aaattactttggcattaaaaatgctttgaatttgacgtgcagGAATGATGGGCTCTGGGAAAACAACAGTGGGGAAGATAATGTCGCAAGTGCTTGGTTATTCATTTTGTGATAG
















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|71857264|gb|DT006319.1|DT006319
EST:     GTCACAAGAGATTCTGCCGTATATAGATGGACGCTGTGTATATCTGGTTG                         GGATGATGGGTTCTGGAAAAACAACTATTGGC
genomic: GTCACAAGAGATTCTGCCGTATATAGATGGACGCTGTGTATATCTTGTTGgtcagttcct ... tgaaatgcagGGATGATGGGTTCTGGAAAAACAACTATTGGC
EST: gi|18458639|gb|BM436917.1|BM436917
EST:     GTCACAAGAGATTCTGCCGTATATAGATGGACGCTGTGTATATCTTGTTG                         GGATGATGGGTTCTGGAAAAACAACTATTGGCAAGATTTTGTCAGAAGTGC
genomic: GTCACAAGAGATTCTGCCGTATATAGATGGACGCTGTGTATATCTTGTTGgtcagttcct ... tgaaatgcagGGATGATGGGTTCTGGAAAAACAACTATTGGCAAGATTTTGTCAGAAGTGC
EST: gi|55778155|gb|AJ862939.1|AJ862939
EST:     GTCACAAGAGATTCTGCCGTATATAGATGGACGCTGTGTATATCTTGTTG                         GGATGATGGGTTCTGGAAAAACAACTATTGGCAAGATTTTGTCAGAAGTGC
genomic: GTCACAAGAGATTCTGCCGTATATAGATGGACGCTGTGTATATCTTGTTGgtcagttcct ... tgaaatgcagGGATGATGGGTTCTGGAAAAACAACTATTGGCAAGATTTTGTCAGAAGTGC
EST: gi|71854625|gb|DT003680.1|DT003680
EST:     GTCACAAGAGATTCTGCCGTATATAGATGGACGCTGTGTATATCTTGTTG                         GGATGATGGGTTCTGGAAAAACAACTATTGGCAAGATTTTGTCAGAAGTGC
genomic: GTCACAAGAGATTCTGCCGTATATAGATGGACGCTGTGTATATCTTGTTGgtcagttcct ... tgaaatgcagGGATGATGGGTTCTGGAAAAACAACTATTGGCAAGATTTTGTCAGAAGTGC
EST: gi|30131700|gb|CB917039.1|CB917039
EST:     GTCACAAGAGATTCTGCCGTATATAGATGGACGCTGTGTATATCTTGTTG                         GGATGATGGGTTCTGGAAAAACAACTATTGGCAAGATTTTGTCAGAAGTGC
genomic: GTCACAAGAGATTCTGCCGTATATAGATGGACGCTGTGTATATCTTGTTGgtcagttcct ... tgaaatgcagGGATGATGGGTTCTGGAAAAACAACTATTGGCAAGATTTTGTCAGAAGTGC
EST: gi|110709925|gb|EE085812.1|EE085812
EST:     GTCACAAGAGATTCTGCCGTATATAGATGGACGCTGTATATATCTTGTTG                         GGATGATGGGTTCTGGAAAAACAACTATTGGCAAGATTTTGTCAGAAGTGC
genomic: GTCACAAGAGATTCTGCCGTATATAGATGGACGCTGTGTATATCTTGTTGgtcagttcct ... tgaaatgcagGGATGATGGGTTCTGGAAAAACAACTATTGGCAAGATTTTGTCAGAAGTGC
EST: gi|110713219|gb|EE088948.1|EE088948
EST:     GTCACAAGAGATTCTGCCGTATATAGATGGACGCTGTATATATCTTGTTG                         GGATGATGGGTTCTGGAAAAACAACTATTGGCAAGATTTTGTCAGAAGTGC
genomic: GTCACAAGAGATTCTGCCGTATATAGATGGACGCTGTGTATATCTTGTTGgtcagttcct ... tgaaatgcagGGATGATGGGTTCTGGAAAAACAACTATTGGCAAGATTTTGTCAGAAGTGC
EST: gi|349832444|gb|FQ421005.1|FQ421005
EST:     GTCACAAGAGATTCTGCCTTATATAGATGGACGCTGTGTATATCTTGTTG                         GGATGATGGGTTCTGGAAAAACAACTATTGGCAAGATTTTGTCAGAAGTGC
genomic: GTCACAAGAGATTCTGCCGTATATAGATGGACGCTGTGTATATCTTGTTGgtcagttcct ... tgaaatgcagGGATGATGGGTTCTGGAAAAACAACTATTGGCAAGATTTTGTCAGAAGTGC
EST: gi|161718354|gb|FC065013.1|FC065013
EST:     GTCACAAGAGATTCTGCCGTATATAGATGGACGCTGTGTATATCTTGTTG                         GGATGATGGGTTCTGGAAAAACAACTATTGGCAAGATTTTGTCAGAAGTGC
genomic: GTCACAAGAGATTCTGCCGTATATAGATGGACGCTGTGTATATCTTGTTGgtcagttcct ... tgaaatgcagGGATGATGGGTTCTGGAAAAACAACTATTGGCAAGATTTTGTCAGAAGTGC
EST: gi|110708701|gb|EE086542.1|EE086542
EST:     GTCACAAGAGATTCTGCCGTATATAGATGGACGCTGTATATATCTTGTTG                         GGATGATGGGTTCTGGAAAAACAACTATTGGCAAGATTTTGTCAGAAGTGC
genomic: GTCACAAGAGATTCTGCCGTATATAGATGGACGCTGTGTATATCTTGTTGgtcagttcct ... tgaaatgcagGGATGATGGGTTCTGGAAAAACAACTATTGGCAAGATTTTGTCAGAAGTGC
EST: gi|294966086|gb|GW837453.1|GW837453
EST:     GTCACAATAGATTCTGCCGTATATAGATGGACGCTGTATATATCTTGTAG                         GGATGATGGGTTCTGGAAAAACAACTATTGGAAAGATTTTGTCAGAAGTGC
genomic: GTCACAAGAGATTCTGCCGTATATAGATGGACGCTGTGTATATCTTGTTGgtcagttcct ... tgaaatgcagGGATGATGGGTTCTGGAAAAACAACTATTGGCAAGATTTTGTCAGAAGTGC
EST: gi|71874768|gb|DT023823.1|DT023823
EST:     GTCACAAGAGATTCTGCCGTATATAGATGGACGCTGTGTATATCTTGTTG                         GGATGATGGGTTCTGGAAAAACAACTATTGGCAAGATTTTGTCAGAAGTGC
genomic: GTCACAAGAGATTCTGCCGTATATAGATGGACGCTGTGTATATCTTGTTGgtcagttcct ... tgaaatgcagGGATGATGGGTTCTGGAAAAACAACTATTGGCAAGATTTTGTCAGAAGTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttagtcatgtttaagttgctcttgtagttgactagattgtacttgaaatgcagGGATGATGGGTTCTGGAAAAACAACTATTGGCAAGATTTTGTCAGAAGTGCTTGGTTATTCATTTTGCGACAG
                           agttgac  putative branch site (score: 4)
        atgtttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagttcctgtatctacgccctttagatttcgtagttagtcatgtttaagttgctcttgtagttgactagattgtacttgaaatgcagGGATGATGGGTTCTGGAAAAACAACTATTGGCAAGATTTTGTCAGAAGTGCTTGGTTATTCATTTTGCGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT