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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctcagatgaaaacaagcagagcctcgatgtaaaattttctttaagagttagcatctcacttcgtgacctgtaacttatactgcttgtatgttgtgatagTTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGTGATACTTGGATGAACATTCATCTTCGGGAAGTTATCTGTACCTCAAAA

Basic information

species Vitis vinifera
transcript Vv07s0005g00230.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g00230.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g15310.1 (Oryza sativa), 3'ss of exon 2
cctcagatgaaaacaagcagagcctcgatgta-aaattttctttaagagttagcatctcact--tcgtgacctgtaacttatactgcttgtatgttgtgatagTTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGTGATACTTGGATGAACATTCATCTTCGGGAAGTTATCTGTACCTCAAAA
    |   ||| |   || |   | || |||      |   | |  |  || |  ||| |        |   || |||||    ||  ||  | || |  ||| | ||||||||||| || || || || ||||| ||||| ||||| ||||| || || ||||||||||| || || ||||| ||||| || |||||||| 
--gtaagagaagatccgccgcttcgcgctgtgcgtggtggttgtttggtttggtttctgatcggctagggtttgaaactt---ttgtgtg-gtttttttttagCTCGTGGAGCTTAAGAACGGCGAGACGTACAACGGGCACTTGGTGAACTGCGACACGTGGATGAACATCCACCTCCGGGAGGTTATTTGCACCTCAAAG

upper sequence: Vv07s0005g00230.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G038606_T03 (Zea mays), 3'ss of exon 2
cctcagatgaaaacaagcagagcctcgatgtaaaattttctttaagagt------tagcatctca--cttcgt--gacctgtaacttatactgcttgta----------tgttgtgat---agTTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGTGATACTTGGATGAACATTCATCTTCGGGAAGTTATCTGTACCTCAAAA-
        | ||  | | |  | | || ||     | ||||||    ||      | || ||| |  || |||   | || |   |  | |||   ||           | |||||||   || | |||||||| || ||||| || || ||||| |||||| |||| || || || || ||||||||||| |||||| |||| ||||| || ||||||||  
--------gtaaggacgtaaggtcccgttg-gccttcttctttcgtcgtcgtttttggcgtctgattctccgttcaatctattgttagtcctgaccgttgaattgaaactattgtgatctcagCTCGTGGAGCTGAAGAATGGTGAGACATACAACGGGCATCTGGTCAATTGCGACACGTGGATGAACATCCATCTTAGGGAGGTTATTTGCACCTCAAAGG

upper sequence: Vv07s0005g00230.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G038606_T02 (Zea mays), 3'ss of exon 2
cctcagatgaaaacaagcagagcctcgatgtaaaattttctttaagagt------tagcatctca--cttcgt--gacctgtaacttatactgcttgta----------tgttgtgat---agTTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGTGATACTTGGATGAACATTCATCTTCGGGAAGTTATCTGTACCTCAAAA
        | ||  | | |  | | || ||     | ||||||    ||      | || ||| |  || |||   | || |   |  | |||   ||           | |||||||   || | |||||||| || ||||| || || ||||| |||||| |||| || || || || ||||||||||| |||||| |||| ||||| || |||||||| 
--------gtaaggacgtaaggtcccgttg-gccttcttctttcgtcgtcgtttttggcgtctgattctccgttcaatctattgttagtcctgaccgttgaattgaaactattgtgatctcagCTCGTGGAGCTGAAGAATGGTGAGACATACAACGGGCATCTGGTCAATTGCGACACGTGGATGAACATCCATCTTAGGGAGGTTATTTGCACCTCAAAG

upper sequence: Vv07s0005g00230.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G02380.1 (Glycine max), 3'ss of exon 2
-------------------------cctcagatgaaaacaagcagagcctcgatgtaaaattttctttaagagttagcatctcacttcgtgacctgtaacttatactgcttgtatgttgtgatagTTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGTGATACTTGGATGAACATTCATCTTCGGGAAGTTATCTGTACCTCAAAA
                           |               || |   || | |     | | | ||  | |||   |   ||| | |||  |||||||| |         || |||| | || | ||||| || |||||||| || ||||| || ||||| |||||||| |||||||| ||||||||||||||||| || ||||| || |||||||| |||
gtgagttaaaccctcttttgctttatttttaccctctttttttagggttacgttattgttatatgtatagaaattatgttaatactgcttgatttgtaacttgtg------acatattgtaacagCTAGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGTGATACATGGATGAACATTCATCTCCGAGAAGTCATTTGTACCTCTAAA

upper sequence: Vv07s0005g00230.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G17430.1 (Glycine max), 3'ss of exon 2
cctcagatgaaaacaagcagagcctcgatgtaaa---attttctttaagagttagcatctcacttcgtgacctgt--aacttatactgct--tgtatg--ttgtgatagTTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGTGATACTTGGATGAACATTCATCTTCGGGAAGTTATCTGTACCTCAAAA
     ||   ||||   | | || |   | | |     |||| ||| || |||| | | |   |     |  |||  ||||| |  |  |  ||| ||  |||| | || ||||||| || |||||||| || ||||| || ||||| |||||||| |||||||| ||||||||||| ||||| || ||||| || |||||||| |||
---gtgagtcaaaccccctgtgctttatttttaccctctttttttttagggttaccttattgttattatatgtgtagaacttgtgttaatactgtttgatttgtaacagCTGGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGTGATACATGGATGAACATCCATCTCCGAGAAGTCATTTGTACCTCTAAA

upper sequence: Vv07s0005g00230.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA19G39780.1 (Glycine max), 3'ss of exon 2
cctcagatgaaaacaagcagagcctcgatgtaaaattttctttaagagttagcatctcacttcgtgacctgtaactt----atactgcttgt-atgttgtgatagTTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGTGATACTTGGATGAACATTCATCTTCGGGAAGTTATCTGTACCTCAAAA
              ||        |  ||     ||||||||| |    || | | | | |       || | |  |    ||  || | || ||| ||| | |||||||||| || |||||||| || || || || |||||||||||||| || ||||| ||||||||||| ||||| || ||||| || ||||| || |||
------------gtaactcattttttcattctctattttctttgatttctaacttattattattattactatgatatgatgatggtgatggtgatgatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGCGATACATGGATGAACATCCATCTCCGAGAAGTCATTTGTACATCTAAA

upper sequence: Vv07s0005g00230.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA03G37170.2 (Glycine max), 3'ss of exon 2
cctcagatgaaaacaagcagagcctcgatgtaaaattttctttaagagttagcatctcact-tcgtgacctgtaacttatactgcttgt-atgttgtgatagTTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGTGATACTTGGATGAACATTCATCTTCGGGAAGTTATCTGTACCTCAAAA
             |||        ||  | |    || ||||| |    || | | | | | |  |||  ||    |  |  || |  | ||| ||| | |||||||||| || |||||||| || || || || |||||||||||||| || || || ||||||||||| ||||| || ||||| || ||||| || |||
------------gcaactcacttttcattctc---ttctcttttatttctaacttattattattatga--tggtgatggtgatgttgatgatgatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGCGACACATGGATGAACATCCATCTGCGAGAAGTCATTTGTACATCTAAA

upper sequence: Vv07s0005g00230.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G27720.1 (Arabidopsis thaliana), 3'ss of exon 3
----------------------------------cctcagatgaaaacaagcagagcctcgatgtaaaattttctttaagagttagcatctcacttcgtgacctgtaacttatactgcttgtatgttgtgatagTTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGTGATACTTGGATGAACATTCATCTTCGGGAAGTTATCTGTACCTCAAAA
                                      | |||||   |||| |||  |  | || |   || | ||| |  |    |      | | |   |||||| ||  | |  |  | |||| || ||| | ||||||||||| |||||||| || ||||||||||||||||| || |||||||||||||||||||| ||||| || ||||| || ||||| ||||| 
gtgagtaaaatttcgacccttgattacaattttgttatatatgaagtgaagctgagttt--aagtgagcattgcattagggatctaaaggaacttccttttactgtaattttgaatcttgttttgttttggtagCTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGTGATACTTGGATGAACATCCATCTGCGTGAAGTCATATGTACATCAAAG

upper sequence: Vv07s0005g00230.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S36_327V6.2 (Physcomitrella patens), 3'ss of exon 1
-------------------------------------------------------------------cctcagatgaaaacaagcagagcctcgatgtaaaatt----ttctttaagagttagcatctcacttcgtgacctgtaacttatactgcttgtatgtt-------gtgat----agTTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGTGATACTTGGATGAACATTCATCTTCGGGAAGTTATCTGTACCTCAAAA
                                                                     ||| ||   ||   |  |||      || |  | |    |  ||| | |    |||| |    |||| || || | ||| ||   ||   |||         || ||    || | || ||||| ||||||||||| ||||| || || ||||| || ||||||||||| |||||||||||||| || || |||||||| || |||||||| 
gtacgggtcacctttgccataacacttcttgaatatattctttggaacatcatgagaaaagatagaatttcacat---aatgcgaggagttgttgtgcacgactgtaatcattttatatcctgcatgttggatcgttacatggatcttttaggtctaacatgacctcgtcggtaatctgcagCTTGTCGAGCTCAAAAATGGAGAGACTTATAACGGCCATTTAGTAAACTGTGATACATGGATGAACATTCACCTACGTGAAGTTATTTGCACCTCAAAG

upper sequence: Vv07s0005g00230.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ10085 (Selaginella moellendorffii), 3'ss of exon 1
cctcagatgaaaacaagcagagcctcgatgtaaaattttctttaagagttagcatctcacttcgtgacctgtaacttatactgcttgtatgttgtgatagTTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGTGATACTTGGATGAACATTCATCTTCGGGAAGTTATCTGTACCTCAAAA-
                                               || ||       ||||||  |||    |||   |||    |  | |  | ||| | |||||||| || |||||||| |||||||||||||||||||| | ||| ||||  ||||||||||| ||||| || |||||||| || || || ||  
-----------------------------------------------gtgagtgatgttcttcgtttcctt---ctttgtctgaaaattcgcttgggtagCTAGTGGAGCTCAAGAATGGAGAGACTTACAATGGGCATTTGGTGAGCTGCGATAGCTGGATGAACATCCATCTACGAGAAGTTATTTGCACTTCCAAGG

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|349828814|gb|FQ419147.1|FQ419147
EST:     CTTCCTCTCTCCCTATTGAAAACTGCGCAAGGGCATCCTATG                         TTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGT
genomic: CTTCCTCTCTCCCTATTGAAAACTGCGCAAGGGCATCCTATGgtaagtgttt ... gttgtgatagTTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGT
EST: gi|349819985|gb|FQ404707.1|FQ404707
EST:     CTTCCTCTCTCCCTATTGAAAACTGCGCAAGGGCATCCTATG                         TTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGT
genomic: CTTCCTCTCTCCCTATTGAAAACTGCGCAAGGGCATCCTATGgtaagtgttt ... gttgtgatagTTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGT
EST: gi|349819983|gb|FQ404705.1|FQ404705
EST:     CTTCCTCTCTCCCTATTGAAAACTGCGCAAGGGCATCCTATG                         TTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGT
genomic: CTTCCTCTCTCCCTATTGAAAACTGCGCAAGGGCATCCTATGgtaagtgttt ... gttgtgatagTTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGT
EST: gi|110372194|gb|EC936345.1|EC936345
EST:     CTTCCTCTCTCCCTATTGAAAACTGCGCAAGGGCATCCTATG                         TTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGT
genomic: CTTCCTCTCTCCCTATTGAAAACTGCGCAAGGGCATCCTATGgtaagtgttt ... gttgtgatagTTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGT
EST: gi|110383606|gb|EC947989.1|EC947989
EST:     CTTCCTCTCTCCCTATTGAAAACTGCGCAAGGGCATCCTATG                         TTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGT
genomic: CTTCCTCTCTCCCTATTGAAAACTGCGCAAGGGCATCCTATGgtaagtgttt ... gttgtgatagTTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGT
EST: gi|349827595|gb|FQ422463.1|FQ422463
EST:     CTTCCTCTCTCCCTATTGAAAACTGCGCAAGGGCATCCTATG                         TTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGT
genomic: CTTCCTCTCTCCCTATTGAAAACTGCGCAAGGGCATCCTATGgtaagtgttt ... gttgtgatagTTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGT
EST: gi|351029470|gb|FQ436864.1|FQ436864
EST:     CTTCCTCTCTCCCTATTGAAAACTGCGCAAGGGCATCCTATG                         TTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGT
genomic: CTTCCTCTCTCCCTATTGAAAACTGCGCAAGGGCATCCTATGgtaagtgttt ... gttgtgatagTTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGT
EST: gi|110692708|gb|EE068197.1|EE068197
EST:     CTTCCTCTCTCCCTATTGAAAACTGCGCAAGGGCATCCTATG                         TTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGT
genomic: CTTCCTCTCTCCCTATTGAAAACTGCGCAAGGGCATCCTATGgtaagtgttt ... gttgtgatagTTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGT
EST: gi|351012236|gb|FQ426958.1|FQ426958
EST:     CTTCCTCTCTCCCTATTGAAAACTGCGCAAGGGCATCCTATG                         TTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGT
genomic: CTTCCTCTCTCCCTATTGAAAACTGCGCAAGGGCATCCTATGgtaagtgttt ... gttgtgatagTTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGT
EST: gi|351044635|gb|FQ443166.1|FQ443166
EST:     CTTCCTCTCTCCCTATTGAAAACTGCGCAAGGGCATCCTATG                         TTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGT
genomic: CTTCCTCTCTCCCTATTGAAAACTGCGCAAGGGCATCCTATGgtaagtgttt ... gttgtgatagTTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGT
EST: gi|351025082|gb|FQ433499.1|FQ433499
EST:     CTTCCTCTCTCCCTATTGAAAACTGCGCAAGGGCATCCTATG                         TTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGT
genomic: CTTCCTCTCTCCCTATTGAAAACTGCGCAAGGGCATCCTATGgtaagtgttt ... gttgtgatagTTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGT
EST: gi|349828184|gb|FQ415512.1|FQ415512
EST:     CTTCCTCTCTCCCTATTGAAAACTGCGCAAGGGCATCCTATG                         TTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGT
genomic: CTTCCTCTCTCCCTATTGAAAACTGCGCAAGGGCATCCTATGgtaagtgttt ... gttgtgatagTTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGT
EST: gi|351056955|gb|FQ443582.1|FQ443582
EST:     CTTCCTCTCTCCCTATTGAAAACTGCGCAAGGGCATCCTATG                         TTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGT
genomic: CTTCCTCTCTCCCTATTGAAAACTGCGCAAGGGCATCCTATGgtaagtgttt ... gttgtgatagTTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGT
EST: gi|110374587|gb|EC939452.1|EC939452
EST:     CTTCCTCTCTCCCTATTGAAAACTGCGCAAGGGCATCCTATG                         TTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGT
genomic: CTTCCTCTCTCCCTATTGAAAACTGCGCAAGGGCATCCTATGgtaagtgttt ... gttgtgatagTTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGT
EST: gi|351038850|gb|FQ448493.1|FQ448493
EST:     CTTCCTCTCTCCCTATTGAAAACTGCGCAAGGGCATCCTATG                         TTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGT
genomic: CTTCCTCTCTCCCTATTGAAAACTGCGCAAGGGCATCCTATGgtaagtgttt ... gttgtgatagTTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGT
EST: gi|110372487|gb|EC936658.1|EC936658
EST:     CTTCCTCTCTCCCTATTGAAAACTGCGCAAGGGCATCCTATG                         TTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGT
genomic: CTTCCTCTCTCCCTATTGAAAACTGCGCAAGGGCATCCTATGgtaagtgttt ... gttgtgatagTTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGT
EST: gi|352790730|gb|FQ478278.1|FQ478278
EST:     CTTCCTCTCTCCCTATTGAAAACTGCGCAAGGGCATCCTATG                         TTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGT
genomic: CTTCCTCTCTCCCTATTGAAAACTGCGCAAGGGCATCCTATGgtaagtgttt ... gttgtgatagTTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGT
EST: gi|349828185|gb|FQ415513.1|FQ415513
EST:     CTTCCTCTCTCCCTATTGAAAACTGCGCAAGGGCATCCTATG                         TTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGT
genomic: CTTCCTCTCTCCCTATTGAAAACTGCGCAAGGGCATCCTATGgtaagtgttt ... gttgtgatagTTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagttagcatctcacttcgtgacctgtaacttatactgcttgtatgttgtgatagTTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGTGATACTTGGATGAACATTCATCTTCGGGAAGTTATCTGTACCTCAAAA
                       ctgtaac  putative branch site (score: 3)
                          taacttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctcagatgaaaacaagcagagcctcgatgtaaaattttctttaagagttagcatctcacttcgtgacctgtaacttatactgcttgtatgttgtgatagTTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGTGATACTTGGATGAACATTCATCTTCGGGAAGTTATCTGTACCTCAAAA

cctcaga
- - - - -aaaacaa
- - - - - - - - - - - - - -atgtaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttgt