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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttgttgtttctctaatcccatatgttggtttcttttatgctcaaccattatatttctaatttcacatgaaatttaggggaatatagtgttctgaaaattttgatttctttgatggatttgtagCTGGTTGGGAAAATTTTAAGGATAAAAATGTCTTCTCCAAGCAAGAGGAGAGAAATGGATGTCATGAAGTT

Basic information

species Vitis vinifera
transcript Vv17s0000g07960.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g07960.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA17G09940.1 (Glycine max), 3'ss of exon 1
gtatgttgttgtttctctaatcccatatgttggtttcttttatgctcaaccattatatttctaatttcacatgaaatttaggggaatatagtgttctgaaaattttgatttctttgatggatttgtagCTGGTTGGGAAAA-----TTTTAAGGATAAAAATGTCTTCTCCAAGCAAGAGGAGAGAAATGGATGTCATGAAGTT
                         ||| | ||   |    |   | ||  ||| | ||| |  ||| | |     | | | ||   | |  ||    || |||    || |||   |    ||||||| |||||  | ||     || |    || |||||||| |||||||||||||| |||||||||||||| |||||  |
------------------------ttatataggcagc----acattgaa--attgt-tttttgtttttaaaccttttgttgtggtgaagatggtgacaaatattaactttccttaattttccttgtagcagGTTGAAATAAGTGATTTGTTGTAATCAAAATGTCATCTCCAAGCAAGAGAAGAGAAATGGATGTAATGAAACT

upper sequence: Vv17s0000g07960.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA05G01980.1 (Glycine max), 3'ss of exon 1
gtatgttgttgtttctctaatcccatatgttggtttcttttatgctcaaccattatatttctaatttcacatgaaatttaggggaatatagtgttctgaaaattttgatttctttgatggatttgtagCTGGTTGGGAAAATTTTAAGGATAAAAATGTCTTCTCCAAGCAAGAGGAGAGAAATGGATGTCATGAAGTT
                       || ||     ||  ||||    | |  | || |  || |  |     | ||   | |     || | |  ||  |||||| || |||    |  | |             |  |  | || | |  || || ||||| |||||||||||||| |||||||||||||| |||||  |
------------------ggcggcacattgaaattgttttttgttttagacctttttgttgtggtg----aagatggtaacaaatatgt-gcatttggaaaatattaattatccttgtag---cagGTTGAAATAAGTGATTTGTTATAATCAACATGTCATCTCCAAGCAAGAGAAGAGAAATGGATGTAATGAAACT
















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|32271062|gb|CD720221.1|CD720221
EST:     ACTTCACCATCTCGG---AT--CATAATCTTGTGGATCTCTTTGAGGACA                         CTGGTTGGGAAAATTTTAAGGATAAAAATGTCTTCTCCAAGCAAGAGGAGA
genomic: ACTTCACCATCTCGGATCATCACATAATCTTGTGGATCTCTTTGAGGACAgtatgttgtt ... ggatttgtagCTGGTTGGGAAAATTTTAAGGATAAAAATGTCTTCTCCAAGCAAGAGGAGA
EST: gi|32271807|gb|CD720966.1|CD720966
EST:     ACTTCACCATCTCGG---AT--CATAATCTTGTGGATCTCTTTGAGGACA                         CTGGTTGGGAAAATTTTAAGGATAAAAATGTCTTCTCCAAGCAAGAGGAGA
genomic: ACTTCACCATCTCGGATCATCACATAATCTTGTGGATCTCTTTGAGGACAgtatgttgtt ... ggatttgtagCTGGTTGGGAAAATTTTAAGGATAAAAATGTCTTCTCCAAGCAAGAGGAGA
EST: gi|32272372|gb|CD721531.1|CD721531
EST:     ACTTCACCATCTCGG---AT--CATAATCTTGTGGATCTCTTTGAGGACA                         CTGGTTGGGAAAATTTTAAGGATAAAAATGTCTTCTCCAAGCAAGAGGAGA
genomic: ACTTCACCATCTCGGATCATCACATAATCTTGTGGATCTCTTTGAGGACAgtatgttgtt ... ggatttgtagCTGGTTGGGAAAATTTTAAGGATAAAAATGTCTTCTCCAAGCAAGAGGAGA
EST: gi|30327528|gb|CD010790.1|CD010790
EST:     ACTTCACCATCTCGG---AT--CATAATCTTGTGGATCTCTTTGAGGACA                         CTGGTTGGGAAAATTTTAAGGATAAAAATGTCTTCTCCAAGCAAGAGGAGA
genomic: ACTTCACCATCTCGGATCATCACATAATCTTGTGGATCTCTTTGAGGACAgtatgttgtt ... ggatttgtagCTGGTTGGGAAAATTTTAAGGATAAAAATGTCTTCTCCAAGCAAGAGGAGA
EST: gi|32272391|gb|CD721550.1|CD721550
EST:     ACTTCACCATCTCGG---AT--CATAATCTTGTGGATCTCTTTGAGGACA                         CTGGTTGGGAAAATTTTAAGGATAAAAATGTCTTCTCCAAGCAAGAGGAGA
genomic: ACTTCACCATCTCGGATCATCACATAATCTTGTGGATCTCTTTGAGGACAgtatgttgtt ... ggatttgtagCTGGTTGGGAAAATTTTAAGGATAAAAATGTCTTCTCCAAGCAAGAGGAGA
EST: gi|32271578|gb|CD720737.1|CD720737
EST:     ACTTCACCATCTCGG---AT--CATAATCTTGTGGATCTCTTTGAGGACA                         CTGGTTGGGAAAATTTTAAGGATAAAAATGTCTTCTCCAAGCAAGAGGAGA
genomic: ACTTCACCATCTCGGATCATCACATAATCTTGTGGATCTCTTTGAGGACAgtatgttgtt ... ggatttgtagCTGGTTGGGAAAATTTTAAGGATAAAAATGTCTTCTCCAAGCAAGAGGAGA
EST: gi|32272363|gb|CD721522.1|CD721522
EST:     ACTTCACCATCTCGG---AT--CATAATCTTGTGGATCTCTTTGAGGACA                         CTGGTTGGGAAAATTTTAAGGATAAAAATGTCTTCTCCAAGCAAGAGGAGA
genomic: ACTTCACCATCTCGGATCATCACATAATCTTGTGGATCTCTTTGAGGACAgtatgttgtt ... ggatttgtagCTGGTTGGGAAAATTTTAAGGATAAAAATGTCTTCTCCAAGCAAGAGGAGA
EST: gi|30324813|gb|CD008075.1|CD008075
EST:     ACTTCACCATCTCGG---AT--CATAATCTTGTGGATCTCTTTGAGGACA                         CTGGTTGGGAAAATTTTAAGGATAAAAATGTCTTCTCCAAGCAAGAGGAGA
genomic: ACTTCACCATCTCGGATCATCACATAATCTTGTGGATCTCTTTGAGGACAgtatgttgtt ... ggatttgtagCTGGTTGGGAAAATTTTAAGGATAAAAATGTCTTCTCCAAGCAAGAGGAGA
EST: gi|32270967|gb|CD720126.1|CD720126
EST:     ACTTCACCATCTCGG---AT--CATAATCTTGTGGATCTCTTTGAGGACA                         CTGGTTGGGAAAATTTTAAGGATAAAAATGTCTTCTCCAAGCAAGAGGAGA
genomic: ACTTCACCATCTCGGATCATCACATAATCTTGTGGATCTCTTTGAGGACAgtatgttgtt ... ggatttgtagCTGGTTGGGAAAATTTTAAGGATAAAAATGTCTTCTCCAAGCAAGAGGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatttaggggaatatagtgttctgaaaattttgatttctttgatggatttgtagCTGGTTGGGAAAATTTTAAGGATAAAAATGTCTTCTCCAAGCAAGAGGAGAGAAATGGATGTCATGAAGTT
                         aaaattttgatttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttgttgtttctctaatcccatatgttggtttcttttatgctcaaccattatatttctaatttcacatgaaatttaggggaatatagtgttctgaaaattttgatttctttgatggatttgtagCTGGTTGGGAAAATTTTAAGGATAAAAATGTCTTCTCCAAGCAAGAGGAGAGAAATGGATGTCATGAAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA