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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtttccctctcttttctttgtgtgtatattcccctcttgctccccatgccccatctgcttaatccttttgtcctccttttgtcctccctttgaacttctgttgtaatctcggttattacttgctatcagATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGATACATATGTCATTTTTGGCGAGGCAAAGATTGAAGACTTGAGCTCACAGC

Basic information

species Vitis vinifera
transcript Vv13s0067g00710.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0067g00710.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os05g31000.1 (Oryza sativa), 3'ss of exon 3
gttagtttccctctcttttctttgtgtgtatattcccctcttgctccccatgccccatctgcttaatccttttgtcctccttttgtcctccctttgaacttctgttgtaatctcggttattacttgctatcagATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGATACATATGTCATTTTTGGCGAGGCAAAGATTGAAGACTTGAGCTCACAGC
                           ||    |  |  ||         |  || ||||   || | || ||         |||   |||  ||||  ||    ||  || ||   | || |    | ||||||| | |||||||| || ||||| ||||||||||||||||| ||||| || || |||||||||||||||||||| ||||| || ||| ||||||| ||||
---------------------------gtgagcttacgactgctcttatctagccaatctaaatagttctattag-------ttggattcctgttgatgtt----tgctatttc---ttttgccccatttcagATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGACACCTATGTCATTTTTGGCGAGGCCAAGATCGAGGACCTGAGCTCGCAGC

upper sequence: Vv13s0067g00710.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g71230.2 (Oryza sativa), 3'ss of exon 3
gttagtttccctctcttttctttgtgtgtatattcccctcttgctccccatgccccatctgcttaatccttttgtcctccttttgtcctccctttgaacttctgttgtaatctcggttattacttgc--tatcagATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGATACATATGTCATTTTTGGCGAGGCAAAGATTGAAGACTTGAGCTCACAGC
                                          ||| |  |  | |  |      | |  || |      ||       |   | |  ||   ||   |   ||    | || | |||  || |||||  |||| ||||| || |||||||||||||||||||||||||  ||||| || || ||||| || || ||||| ||||| || ||  ||||||| ||||
--------------------------------------gtgagctgcttaatcactgttatgccattgtttcttgtaggctcacagaattgttatataccattgcattttgcttaacttttccctgcactaccagATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGACACCTACGTCATCTTCGGTGAGGCGAAGATCGAGGATCTGAGCTCGCAGC

upper sequence: Vv13s0067g00710.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G465333_T01 (Zea mays), 3'ss of exon 3
gttagtttccctctcttttctttgtgtgtatattcccctcttgctccccatgccccatctgcttaatccttttgtcctccttttgtcctccctttgaacttctgttgtaatctcggttattacttgctatcagATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGATACATATGTCATTTTTGGCGAGGCAAAGATTGAAGACTTGAGCTCACAGC
                |   |      | | | |  ||| |   |     || |       | |  |   | |   ||  | ||||  ||    | |       |  |||   |   ||||  |      |||||  |||||||||| || || |||||||| ||||||||||| |  ||||| ||||| ||||| || |||||||| ||||| || ||| | ||||| ||||
---------------gtaattcaccacgcaaactggcctatctttattgttgtctggctaacatggtatatattatctt-tattgttgtctggctaa-----catgataaatgcacatatttttc----ccagATACTGTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCGAACTCAGACACATACGTCATATTCGGCGAGGCCAAGATCGAGGACCTCAGCTCCCAGC

upper sequence: Vv13s0067g00710.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G000923_T01 (Zea mays), 3'ss of exon 3
gttagtttccctctcttttctttgtgtgtatattcccctcttgctccccatgccccatctgcttaatccttttgtcctccttttgtcctccctttgaacttctgttgtaatctcggttattacttgctatcagATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGATACATATGTCATTTTTGGCGAGGCAAAGATTGAAGACTTGAGCTCACAGC
                                                 || | |||| | || |   |       ||   ||     |    |||     ||    | || |  | |||| |       |||||  | |||||||| || ||||||||||| ||||||||||| |  || || || |||||||| || |||||||| ||||| || ||| | ||||| ||||
----------------------------------------------gtaattcaccatttactcagatcacacaaactggcttatctttattgttgcctggctaacatgatat--gctatttc-------cagATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGACACGTATGTCATATTCGGCGAGGCTAAGATCGAGGACCTCAGCTCCCAGC

upper sequence: Vv13s0067g00710.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA03G27580.2 (Glycine max), 3'ss of exon 3
gttagtttccctctcttttctttgtgtgtatattcccctcttgctccccatgccccatctgcttaatccttttgtcctccttttgtcctccctttgaacttctgttgtaatctcggttattacttgcta--tcagATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGATACATATGTCATTTTTGGCGAGGCAAAGATTGAAGACTTGAGCTCACAGC
                                        | ||     |   |   |    || |     || || |  |||  ||       |     ||  |  | |  |   || |   ||| |   | ||||| ||||||| ||||||||||||||||| ||||||||||| || || || |||||  | || || ||||| || |||||||||||||||||||||||||
--------------------------------------gttagcatttgacatctatttattttgaagaacttttcattgtttcatctatttcgtacttgtcaatattgaatttatttctcctttgtttgtttagATCCTGTTTGTTATATCAAAACCAGATGTTTTCAAGAGCCCGACTTCTGACACATACATTATATTCGGCGAAGCCAAGATTGAAGACTTGAGCTCACAGC

upper sequence: Vv13s0067g00710.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA19G30540.1 (Glycine max), 3'ss of exon 3
gttagtttccctctcttttctttgtgtgtatattcccctcttgctccccatgccccatctgcttaatccttttgtcctccttttgtcctccctttgaacttctgttgtaatctcggttattacttgctatcagATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGATACATATGTCATTTTTGGCGAGGCAAAGATTGAAGACTTGAGCTCACAGC
                         ||    |||   ||| |  |   ||     || |    |  | | ||||||     | | |        | ||      ||| ||  | ||   ||  ||| |   ||||| |||| || || |||||||||||||| |||||||| |||||||| || || ||  | || ||||| || || |||||||||||||||||||||||| 
-------------------------gttagcatttgactcatctttttcacttttcaccactctttttcatttgtcagatctattttgctttggtaaaa----attgaaactttggactttgtttgtt--tagATCCTGTTCGTTATCTCAAAACCAGATGTTTTCAAGAGTCCAACATCTGAAACTTACATTATATTTGGGGAAGCCAAGATTGAAGACTTGAGCTCACAGT

upper sequence: Vv13s0067g00710.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA19G30550.1 (Glycine max), 3'ss of exon 3
gttagtttccctctcttttctttgtgtgtatattcccctcttgctccccatgccccatctgcttaatccttttgtcctccttttgtcctccctttgaacttctgttgtaatctcggttattacttgctatcagATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGATACATATGTCATTTTTGGCGAGGCAAAGATTGAAGACTTGAGCTCACAGC
                         ||    |||   ||| |  |   |      || |  | |  | | ||||||     | | |        | ||      ||| ||  | ||   ||  ||| |   ||||| |||| || || ||||||||||| || |||||||| |||||||| || || ||  | || ||||| || || |||||||||||||||||||||||||
-------------------------gttagcatttgactcatctttttcgcttttcaccaccctttttcatttgtcagatctattttgctttggtaaaa----attgaaactttggactttgtttgtt--tagATCCTGTTCGTAATCTCAAAACCAGACGTTTTCAAGAGTCCAACATCTGACACGTACATTATATTTGGGGAAGCCAAGATTGAAGACTTGAGCTCACAGC

upper sequence: Vv13s0067g00710.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA03G27570.1 (Glycine max), 3'ss of exon 3
gttagtttccctctcttttctttgtgtgt-atattcccctcttgctccccatgccccatctgcttaatccttttgtcctccttttgtcctccctttgaacttctgttgtaatctcgg-ttattacttgctatcagATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGATACATATGTCATTTTTGGCGAGGCAAAGATTGAAGACTTGAGCTCACAGC
                 ||  | |  | | | |   |  | | |||   ||   ||  |||  ||  | | ||||||    || | |        | ||      ||| ||  | ||  | ||  ||| |   ||||| |||| ||||| ||||||||||| || |||||||| ||||| || || || ||  | || ||||| || || |||||||||||||||||||||||||
----------------gttagtagcatttgacacgtctttttagcttttca---ccactcttttt--tgcatttgtcagatttattttgctttggtaaaa----attgaaactttggacttttgtttgtt--tagATCCTGTTCGTCATCTCAAAACCAGACGTTTTCAAGAGTCCAACGTCTGACACGTACATTATATTTGGGGAAGCCAAGATTGAAGACTTGAGCTCACAGC

upper sequence: Vv13s0067g00710.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G13850.1 (Arabidopsis thaliana), 3'ss of exon 3
gttagtttccctctcttttctttgtgtgtatattcccctcttgctccccatgccccatctgcttaatccttttgtcctccttttgtcctccctttgaactt-ctgttgtaatctcggttattacttgctatcagATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGATACATATGTCATTTTTGGCGAGGCAAAGATTGAAGACTTGAGCTCACAGC
                                      |  |||||  ||      |  |   |    ||| |||      |||    |   |   || |   || |  ||| | | ||   | ||||    ||||||||||||| ||||||||||| ||||| |||||||| ||| | |||||||||||||| || ||||| ||||| ||||| || || |||||||| ||||
------------------------------------gtttgtgctcttcagaa---aattaaatctctcttgtgttaattgtttcctatgtttccaaattcattgatagaatgtggattgaaaattgc----agATCTTGTTTGTGATATCAAAACCTGATGTGTTCAAGAGTCCAGCTTCAGATACATATGTGATCTTTGGTGAGGCCAAGATAGAGGATTTGAGCTCGCAGC

upper sequence: Vv13s0067g00710.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT3G12390.1 (Arabidopsis thaliana), 3'ss of exon 3
gttagtttccctctcttttctttgtgtgtatattcccctcttgctccccatgccccatctgcttaatccttttgtcctc-cttttgtcctccctttgaacttctgttgtaatctcggttattacttgctatcagATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGATACATATGTCATTTTTGGCGAGGCAAAGATTGAAGACTTGAGCTCACAGC
                         || | | ||  |   ||  |   ||    | ||||  | | | ||||| | | | | |  | | |   | |  |  |||||| |     |  ||  |       | ||||||||||||||||||||||| || ||||| |||||||| ||| ||||||| |||||||| || ||||| ||||| ||||| || || |||||||| ||| 
-------------------------gtttgtgttttctctttaatattcag--tcaatct--taatttcttttattcacacatcaggctttaatattga--tctgttttggggacatttgctttggaaca-cagATCTTGTTTGTCATATCAAAGCCTGATGTGTTCAAGAGTCCAGCATCAGACACATATGTGATCTTTGGAGAGGCGAAGATCGAGGATTTGAGCTCTCAGA

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|71871526|gb|DT020581.1|DT020581
EST:     TGAAACCCATTCCAGGTGTTAGCCGTGTTACGGTGAAGAAAAGCAAAAAT                         ATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGAT
genomic: TGAAACCCATTCCAGGTGTTAGCCGTGTTACGGTGAAGAAAAGCAAAAATgttagtttcc ... ttgctatcagATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGAT
EST: gi|28961091|gb|CB340554.1|CB340554
EST:     GAAAAGCAAAAAT                         ATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGAT
genomic: GAAAAGCAAAAATgttagtttcc ... ttgctatcagATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGAT
EST: gi|110376812|gb|EC941890.1|EC941890
EST:     TGAAACCCATTCCAGGTGTTAGCCGTGTTACGGTGAAGAAAAGCAAAAAT                         ATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGAT
genomic: TGAAACCCATTCCAGGTGTTAGCCGTGTTACGGTGAAGAAAAGCAAAAATgttagtttcc ... ttgctatcagATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGAT
EST: gi|34546063|gb|CF514295.1|CF514295
EST:     TGAAACCCATTCCAGGTGTTAGCCGTGTTACGGTGAAGAAAAGCAAAAAT                         ATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGAT
genomic: TGAAACCCATTCCAGGTGTTAGCCGTGTTACGGTGAAGAAAAGCAAAAATgttagtttcc ... ttgctatcagATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGAT
EST: gi|110376452|gb|EC941519.1|EC941519
EST:     TGAAACCCATTCCAGGTGTTAGCCGTGTTACGGTGAAGAAAAGCAAAAAT                         ATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGAT
genomic: TGAAACCCATTCCAGGTGTTAGCCGTGTTACGGTGAAGAAAAGCAAAAATgttagtttcc ... ttgctatcagATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGAT
EST: gi|71866471|gb|DT015526.1|DT015526
EST:     TGAAACCCATTCCAGGTGTTAGCCGTGTTACGGTGAAGAAAAGCAAAAAT                         ATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGAT
genomic: TGAAACCCATTCCAGGTGTTAGCCGTGTTACGGTGAAGAAAAGCAAAAATgttagtttcc ... ttgctatcagATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGAT
EST: gi|30306354|gb|CB983148.1|CB983148
EST:     TGAANTCCATTCCAGGTGTTAGCCGTGTTACGGTGAAGAAAAGCAAAAAT                         ATCTTGTTTGTCATATCAAAACCAGGTGTCTTCAAGAGCCCAACATCAGAT
genomic: TGAAACCCATTCCAGGTGTTAGCCGTGTTACGGTGAAGAAAAGCAAAAATgttagtttcc ... ttgctatcagATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGAT
EST: gi|71867142|gb|DT016197.1|DT016197
EST:     TTCCAGGTGTTAGCCGTGTTACGGTGAAGAAAAGCAAAAAT                         ATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGAT
genomic: TTCCAGGTGTTAGCCGTGTTACGGTGAAGAAAAGCAAAAATgttagtttcc ... ttgctatcagATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGAT
EST: gi|30253437|gb|CB970988.1|CB970988
EST:     TGAAACCCATTCCAGGTGTTAGCCGTGTTACGGTGAAGAAAAGCAAAAAT                         ATTTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGAT
genomic: TGAAACCCATTCCAGGTGTTAGCCGTGTTACGGTGAAGAAAAGCAAAAATgttagtttcc ... ttgctatcagATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGAT
EST: gi|110377341|gb|EC942403.1|EC942403
EST:     TGAAACCCATTCCAGGTGTTAGCCGTGTTACGGTGAAGAAAAGCAAAAAT                         ATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGAT
genomic: TGAAACCCATTCCAGGTGTTAGCCGTGTTACGGTGAAGAAAAGCAAAAATgttagtttcc ... ttgctatcagATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGAT
EST: gi|30302985|gb|CB979779.1|CB979779
EST:     TGAAACCCATTCCAGGTGTTAGCCGTGTTACGGTGAAGAAAAGCAAAAAT                         ATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGAT
genomic: TGAAACCCATTCCAGGTGTTAGCCGTGTTACGGTGAAGAAAAGCAAAAATgttagtttcc ... ttgctatcagATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGAT
EST: gi|34416518|gb|CF415272.1|CF415272
EST:     TGAAACCCATTCCAGGTGTTAGCCGTGTTACGGTGAAGAAAAGCAAAAAT                         ATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGAT
genomic: TGAAACCCATTCCAGGTGTTAGCCGTGTTACGGTGAAGAAAAGCAAAAATgttagtttcc ... ttgctatcagATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGAT
EST: gi|34545069|gb|CF513301.1|CF513301
EST:     TGAAACCCATTCCAGGTGTTAGCCGTGTTACGGTGAAGAAAAGCAAAAAT                         ATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGAT
genomic: TGAAACCCATTCCAGGTGTTAGCCGTGTTACGGTGAAGAAAAGCAAAAATgttagtttcc ... ttgctatcagATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGAT
EST: gi|37185033|gb|CF604386.1|CF604386
EST:     TGAAACCCATTCCAGGTGTTAGCCGTGTTACGGTGAAGAAAAGCAAAAAT                         ATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGAT
genomic: TGAAACCCATTCCAGGTGTTAGCCGTGTTACGGTGAAGAAAAGCAAAAATgttagtttcc ... ttgctatcagATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttttgtcctccctttgaacttctgttgtaatctcggttattacttgctatcagATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGATACATATGTCATTTTTGGCGAGGCAAAGATTGAAGACTTGAGCTCACAGC
                                      ttattactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtttccctctcttttctttgtgtgtatattcccctcttgctccccatgccccatctgcttaatccttttgtcctccttttgtcctccctttgaacttctgttgtaatctcggttattacttgctatcagATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGATACATATGTCATTTTTGGCGAGGCAAAGATTGAAGACTTGAGCTCACAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA