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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgctttagtccgaagctcttagctgaaaagaattttcagcagttagaaagtatagatggtcccgacttaacagctttgctttgttcctcttcttcatcatcatcaatttgcagTCCATATCACACCTGGATCACTGCCAAAGGGCCTTCACATCCTCAATTTGTCCAGAAACAAGATCAGCACCATTGAAGGACTCAGAGAATTAACCCGATT

Basic information

species Vitis vinifera
transcript Vv18s0001g05780.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g05780.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA06G10780.1 (Glycine max), 3'ss of exon 4
gtatgtgctttagtccgaagctcttagctgaaaagaattttcagcagttagaaagtatagatggtcccgacttaacagctttgctttgttcctcttct-tcatcatcatcaatttgcagTCCATATCACACCTGGATCACTGCCAAAGGGCCTTCACATCCTCAATTTGTCCAGAAACAAGATCAGCACCATTGAAGGACTCAGAGAATTAACCCGATT
                  | |   |    || |||||| ||   |  ||| |||    || |  |    |     |    | | |    |  |   || || |  ||||  ||||| ||| || |||||||||||||  || |||||||| ||||| |  || ||| |||| |||||||| |||||||||||||| || |||||||||||||||||  |
--------------gtataacatgtcagagagaagaatgtt--acccttaaaaacatcagctaataataataatgctaactagatcaactgattggctctccttttcattgatttgtagTTCACATCACACCTGGATTTCTCCCAAAGGGTCTTCATACTCTGAATCTGTCAAGAAACAAAATCAGCACCATTGAGGGCCTCAGAGAATTAACCCGGCT

upper sequence: Vv18s0001g05780.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA04G10940.1 (Glycine max), 3'ss of exon 2
gtatg--tgctttagtccgaagctcttagctgaaaagaattttcagcagttagaaagtatagatggtcccgacttaacagctttgctttgttcctcttcttcatcatcatcaatttgcagTCCATATCACACCTGGATCACTGCCAAAGGGCCTTCACATCCTCAATTTGTCCAGAAACAAGATCAGCACCATTGAAGGACTCAGAGAATTAACCCGATT
||| |  ||  | ||    ||    ||  |   ||   |  |  | || | ||  | |    ||  |       ||||     || || | ||  |||||       |||  ||||| ||| |||||||| || ||||  || ||||||||  |||| |  || ||| |||| |||||||| |||||||| |||||||| || ||||||||||| ||  |
gtaagcttgtctgagagaaaaaaagttgtccttaatataactataaca-tcagctaatcctaataataata--ctaactaaactgattggctctccttct-------cattgatttgtagTTCATATCACGCCCGGATTTCTCCCAAAGGGTATTCATACACTGAATCTGTCAAGAAACAAAATCAGCACTATTGAAGGCCTTAGAGAATTAACACGGCT
















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|161714193|gb|FC062938.1|FC062938
EST:     ATCACACTTCTCCAGTCTACGATCAGTCAACTTATCAAGCAACTACATAG                         TCCATATCACACCTGGATCACTGCCAAAGGGCCTTCACATCCTCAATTTGT
genomic: ATCACACTTCTCCAGTCTACGATCAGTCAACTTATCAAGCAACTACATAGgtatgtgctt ... caatttgcagTCCATATCACACCTGGATCACTGCCAAAGGGCCTTCACATCCTCAATTTGT
EST: gi|37189709|gb|CF609058.1|CF609058
EST:     ATCACACTTCTCCAGTCTACGATCAGTCAACTTATCAAGCAACTACATAG                         TCCATATCACACCTGGATCACTGCCAAAGGGCCTTCACATCCTCAATTTGT
genomic: ATCACACTTCTCCAGTCTACGATCAGTCAACTTATCAAGCAACTACATAGgtatgtgctt ... caatttgcagTCCATATCACACCTGGATCACTGCCAAAGGGCCTTCACATCCTCAATTTGT
EST: gi|33403648|gb|CF209275.1|CF209275
EST:     ATCACACTTCTCCAGTCTACGATCAGTCAACTTATCAAGCAACTACATAG                         TCCATATCACACCTGGATCACTGCCAAAGGGCCTTCACATCCTCAATTTGT
genomic: ATCACACTTCTCCAGTCTACGATCAGTCAACTTATCAAGCAACTACATAGgtatgtgctt ... caatttgcagTCCATATCACACCTGGATCACTGCCAAAGGGCCTTCACATCCTCAATTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcccgacttaacagctttgctttgttcctcttcttcatcatcatcaatttgcagTCCATATCACACCTGGATCACTGCCAAAGGGCCTTCACATCCTCAATTTGTCCAGAAACAAGATCAGCACCATTGAAGGACTCAGAGAATTAACCCGATT
      acttaac  putative branch site (score: 3)
                         ttcctcttcttcatca  putative PPT
                                           atcaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgctttagtccgaagctcttagctgaaaagaattttcagcagttagaaagtatagatggtcccgacttaacagctttgctttgttcctcttcttcatcatcatcaatttgcagTCCATATCACACCTGGATCACTGCCAAAGGGCCTTCACATCCTCAATTTGTCCAGAAACAAGATCAGCACCATTGAAGGACTCAGAGAATTAACCCGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG