Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgtttcggtgtctcggtgtctcggtcattctttttgtccaagccctaatctctttgactacataatttgtcaaaatttatgtcaatttttttaccatagGGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGGAAGCACTGAATCGGCTTCCTCGGGAGATCGTGGATGCTAGGCATCAGAG

Basic information

species Vitis vinifera
transcript Vv04s0008g05000.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g05000.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os03g59220.1 (Oryza sativa), 3'ss of exon 1
-------gtactgtttcg---gtgtctcggtgtctcggtc-----------attctttttgtccaagccctaatctctttgactacataatttgtcaaaatttatgt-caatttttttaccat-agGGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGGAAGCACTGAATCGGCTTCCTCGGGAGATCGTGGATGCTAGGCATCAGAG
        | |||| |||   |  ||| ||||||||| |                  ||| |  |      ||| |  | |  |       |||| |   | |||||   |||  |      | |||  |||| |||||||||||||| || |||||| ||||||| ||||||||||| || ||  |  |||||||  ||||| | || || ||  | || ||| |
gtagggtttgctgtctcgcctggatctgggtgtctcgattcggggggggtggggggctttcttgatctggaaatttgatgggattttgttcttgttattctgtatgtgtgattgatccgttgttagGCCTGAGGTACGACGATCTGTACGACCCGAAGCATGATCTGGACATCAAGGAGGCGCTCGAGAGGCTTCCCAGGGAGGTGGTCGACGCCCGCCACCAGCG
















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|37187810|gb|CF607163.1|CF607163
EST:     GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACG                         GGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
genomic: GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACGgtactgtttc ... tttaccatagGGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
EST: gi|110422668|gb|EC988995.1|EC988995
EST:     GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACG                         GGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
genomic: GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACGgtactgtttc ... tttaccatagGGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
EST: gi|34320043|gb|CF372797.1|CF372797
EST:     GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACG                         GGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
genomic: GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACGgtactgtttc ... tttaccatagGGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
EST: gi|110691335|gb|EE069317.1|EE069317
EST:     GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACG                         GGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
genomic: GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACGgtactgtttc ... tttaccatagGGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
EST: gi|71862342|gb|DT011397.1|DT011397
EST:     GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACG                         GGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGATATCAAGG
genomic: GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACGgtactgtttc ... tttaccatagGGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
EST: gi|110410838|gb|EC976532.1|EC976532
EST:     GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACG                         GGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
genomic: GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACGgtactgtttc ... tttaccatagGGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
EST: gi|71856242|gb|DT005297.1|DT005297
EST:     GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACG                         GGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
genomic: GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACGgtactgtttc ... tttaccatagGGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
EST: gi|30136290|gb|CB921628.1|CB921628
EST:     GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACG                         GGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
genomic: GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACGgtactgtttc ... tttaccatagGGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
EST: gi|27586796|gb|CB009491.1|CB009491
EST:     GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACG                         GGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
genomic: GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACGgtactgtttc ... tttaccatagGGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
EST: gi|110709607|gb|EE085214.1|EE085214
EST:     GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACG                         GGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
genomic: GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACGgtactgtttc ... tttaccatagGGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
EST: gi|71876470|gb|DT025525.1|DT025525
EST:     GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACG                         GGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
genomic: GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACGgtactgtttc ... tttaccatagGGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
EST: gi|110373387|gb|EC937618.1|EC937618
EST:     GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACG                         GGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
genomic: GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACGgtactgtttc ... tttaccatagGGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
EST: gi|110708770|gb|EE086691.1|EE086691
EST:     CCTTCGCAAATACG                         GGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
genomic: CCTTCGCAAATACGgtactgtttc ... tttaccatagGGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
EST: gi|110373678|gb|EC937942.1|EC937942
EST:     GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACG                         GGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
genomic: GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACGgtactgtttc ... tttaccatagGGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
EST: gi|71866308|gb|DT015363.1|DT015363
EST:     GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACG                         GGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
genomic: GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACGgtactgtttc ... tttaccatagGGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
EST: gi|18459173|gb|BM437451.1|BM437451
EST:     GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACG                         GGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
genomic: GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACGgtactgtttc ... tttaccatagGGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
EST: gi|110715170|gb|EE092915.1|EE092915
EST:     GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACG                         GGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
genomic: GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACGgtactgtttc ... tttaccatagGGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
EST: gi|110377516|gb|EC942585.1|EC942585
EST:     GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACG                         GGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
genomic: GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACGgtactgtttc ... tttaccatagGGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
EST: gi|110425892|gb|EC992287.1|EC992287
EST:     GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACG                         GGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
genomic: GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACGgtactgtttc ... tttaccatagGGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
EST: gi|32245255|gb|CD711074.1|CD711074
EST:     GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACG                         GGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
genomic: GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACGgtactgtttc ... tttaccatagGGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
EST: gi|110402060|gb|EC968693.1|EC968693
EST:     GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACG                         GGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
genomic: GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACGgtactgtttc ... tttaccatagGGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
EST: gi|110362089|gb|EC925597.1|EC925597
EST:     GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACG                         GGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG
genomic: GTTTGCACGTCAACACATGAAAACCATCTCCACGCGCCTTCGCAAATACGgtactgtttc ... tttaccatagGGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaatctctttgactacataatttgtcaaaatttatgtcaatttttttaccatagGGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGGAAGCACTGAATCGGCTTCCTCGGGAGATCGTGGATGCTAGGCATCAGAG
                                         tttttttacc  CT-rich tract
              tacataatttgtcaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgtttcggtgtctcggtgtctcggtcattctttttgtccaagccctaatctctttgactacataatttgtcaaaatttatgtcaatttttttaccatagGGTTGAGATACGACGATCTGTATGATCCGAAGTATGATCTTGACATCAAGGAAGCACTGAATCGGCTTCCTCGGGAGATCGTGGATGCTAGGCATCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC