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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttcatattcttttccttcatctttggtcttatctataatgttttttgaattgagtttgttttctagtttatttgaggtctccctgcaggtgtattgtatcactgttttctctattatattgtcctcgccttttctgctggaaatattgtaggtttggttttccaagtaaacattgtcaatttatttccccagGCATAGATGGACTGGTAGATATGAAGCCCATCTTTGGGATAATAGTTGCAAGAAGGAGGGGCAGACTAGGAAAGGAAGACAAG

Basic information

species Vitis vinifera
transcript Vv18s0001g08610.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g08610.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os03g12950.1 (Oryza sativa), 3'ss of exon 2
gttagttcatattcttttccttcatctttggtcttatctataatgttttttgaattgagtttgttttctagtttatttgaggtctccctgcaggtgtattgtatcactgttttctctattatattgtcctcgccttttctgctggaaatattgtaggtttggttttccaagt--aaacattgtcaatttatttccccagGCATAGATGGACTGGTAGATATGAAGCCCATCTTTGGGATAATAGTTGCAAGAAGGAGGGGCAGACTAGGAAAGGAAGACAAG
                                                                                                   |||||   ||      ||| | | ||||  | |          | ||    || ||  ||   |     | ||       |  |  ||| | |    |||||| || |||||||| |||||||||||||| || |||||||| |||||||| ||||| || ||||| ||||| ||||| ||||
---------------------------------------------------------------------------------------------------tgtattgatgaggcacctactcttttgtttttgagcaaatcatttgaccctttttatattgaatgacgaaggtttgtgtgtgtttgattcactggagcagGCACAGGTGGACTGGAAGATATGAAGCCCACCTCTGGGATAACAGTTGCAAAAAGGATGGACAGACAAGGAAGGGAAGGCAAG

upper sequence: Vv18s0001g08610.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os03g56050.1 (Oryza sativa), 3'ss of exon 2
gttagttcatattcttttccttcatctttggtcttatctataatgttttttgaattgagtttgttttctagtttatttgaggtctccctgcaggtgtattgtatcactgttttctctattatattgtcctcgccttttctgctggaaatattgtaggtttggttttccaagtaaacattgtcaatttatttccccagGCATAGATGGACTGGTAGATATGAAGCCCATCTTTGGGATAATAGTTGCAAGAAGGAGGGGCAGACTAGGAAAGGAAGACAAG
                                                                             |     ||  | || |   || ||    ||   | || | |  ||   | | | || |   |      |  |    |     |    |   ||  |||| |||| ||          ||||||||| |||||||| |||||||| || || || ||||| || || ||||||||||| || ||||| || |||||| | ||||
----------------------------------------------------------------------------gtagtagctagcagc-gccatagtgacagacacctctcgccaccatgccgccatggcttccaccttcacagcttcacttaacctcaagt---aaaaaaaccttgtaaaaag-------cagGCATAGGTGGACTGGGAGATATGAGGCACACCTCTGGGACAACAGCTGCAAGAAGGAAGGCCAGACCAGAAAAGGACGCCAAG

upper sequence: Vv18s0001g08610.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G021573_T02 (Zea mays), 3'ss of exon 1
gttagttcatattcttttccttcatctttggtcttatctataatgttttttgaattgagtttgttttctagtttatttgaggtctccctgcaggtgtattgtatcactgttttctctattatattgtcctcgccttttctgctggaaatattgtaggtttggttttccaagtaaacattgtcaatttatttccccagGCATAGATGGACTGGTAGATATGAAGCCCATCTTTGGGATAATAGTTGCAAGAAGGAGGGGCAGACTAGGAAAGGAAGACAAG
                                                                                             || | ||    |       |    | | | |   || || || || |      |||  || ||| ||  || |    ||    ||||   ||| | |    |||||| || |||||||| ||||| |||||||| || ||||| || || |||| |||||| ||||||||||| ||||| |||||||
--------------------------------------------------------------------------------------------tgtctgttagggccaaacagttcagactgtttgaaccgcgactgttttatactgaatgatggagggtt--ttgtttgtgttgg-attg--gattcactggagcagGCACAGGTGGACTGGGAGATACGAAGCCCACCTCTGGGACAACAGCTGCAGGAAGGATGGGCAGACTAGAAAAGGCAGACAAG

upper sequence: Vv18s0001g08610.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G021573_T01 (Zea mays), 3'ss of exon 2
gttagttcatattcttttccttcatctttggtcttatctataatgttttttgaattgagtttgttttctagtttatttgaggtctccctgcaggtgtattgtatcactgttttctctattatattgtcctcgccttttctgctggaaatattgtaggtttggttttccaagtaaacattgtcaatttatttccccagGCATAGATGGACTGGTAGATATGAAGCCCATCTTTGGGATAATAGTTGCAAGAAGGAGGGGCAGACTAGGAAAGGAAGACAAG
                                                                                     | |||   || ||  |    || |||    || ||   |   || || || || |      |||  || ||| ||  || |    ||    ||||   ||| | |    |||||| || |||||||| ||||| |||||||| || ||||| || || |||| |||||| ||||||||||| ||||| |||||||
-------------------------------------------------------------------------------------ctctgtctgt-tagggccaaacagttcagactgtt---tgaaccgcgactgttttatactgaatgatggagggtt--ttgtttgtgttgg-attg--gattcactggagCAGGCACAGGTGGACTGGGAGATACGAAGCCCACCTCTGGGACAACAGCTGCAGGAAGGATGGGCAGACTAGAAAAGGCAGACAAG

upper sequence: Vv18s0001g08610.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G05170.1 (Glycine max), 3'ss of exon 4
gttagttcatattcttttccttcatctttggtcttatctataatgttttttgaattgagtttgttttctagtttatttgaggtctccctgcaggtgtattgtatcactgttttctctattatattgtcctcgccttttctg-ctggaaatattgtaggtttggttttccaagtaaacattgtcaatttatttcccc--agGCATAGATGGACTGGTAGATATGAAGCCCATCTTTGGGATAATAGTTGCAAGAAGGAGGGGCAGACTAGGAAAGGAAGACAAG
                                                                                               || ||| | |  | |||  |    ||  || | |||   ||| |   |||  ||||    |  | | |||     | |     |  |   ||| ||| ||   |||||||||||||||||||| |||||||| ||| | ||||||||||||||||||||||| |||||||||||||||||||||||||
-----------------------------------------------------------------------------------------------gttttgaagctttctttgtttgtgtaccttttactctaatttccaatctgataata----aattcttgttaattgaattctggtgattgttttcttttcctttagGCATAGATGGACTGGTAGGTATGAAGCGCATTTGTGGGATAATAGTTGCAAGAAGGAAGGGCAGACTAGGAAAGGAAGACAAG

upper sequence: Vv18s0001g08610.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA04G05080.1 (Glycine max), 3'ss of exon 3
gttagttcatattcttttccttcatctttggtcttatctataatgttttttgaattgagtttgttt-tctagtttat-ttgaggtctccctgcaggtgtattgtatcactgttttctctattatattgtcctcgccttttctgctggaaatattgtaggtttggttttccaagtaaacattgtcaatttatttccccagGCATAGATGGACTGGTAGATATGAAGCCCATCTTTGGGATAATAGTTGCAAGAAGGAGGGGCAGACTAGGAAAGGAAGACAAG
                                 |||  ||  ||  ||||  || |   ||||||| | ||  || |   ||  | |||   | ||   | |  ||    ||||||| | |    |    |  |  |||| |  | ||  | | || | ||  |||      ||  |   |  |  | | || |   |||||||||||||||||||| |||||||| ||| | ||||||||||||||||||||||| ||||| |||||||||||| ||||||
--------------------------------gttagtta--atagttttgaaactttctttgtttgtgtaacttttaccgaaatttccaatctgga--aataaattg--gttttctttgtctagtcaatcctgttttttttaataga--tgtcgttgattgagtt------gtggattattgctttcttttccattagGCATAGATGGACTGGTAGGTATGAAGCGCATTTGTGGGATAATAGTTGCAAGAAGGAAGGGCAAACTAGGAAAGGACGACAAG

upper sequence: Vv18s0001g08610.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA14G10130.1 (Glycine max), 3'ss of exon 5
gttagttcatattcttttccttcatctttggtcttatctataatgttttttgaattgagtttgttttctagtttatttgaggtctccctgcaggtgtattgtatcactgttttctctattatattgtcctcgccttttctgctggaaatattgtaggtttggttttccaagtaaacattgtcaatttatttccccagGCATAGATGGACTGGTAGATATGAAGCCCATCTTTGGGATAATAGTTGCAAGAAGGAGGGGCAGACTAGGAAAGGAAGACAAG
                                                                                    | | ||  |||   |  | |    ||||    || | | ||||   |    ||| |   | |||| |||| |   ||   |||   ||             || | |   |||||||||||||||||||||||||||||| ||| | |||||||| |||||||||||||| ||||| || ||||||||| ||||||
-----------------------------------------------------------------------------------attcatggtggttgttactttttgagtttaacttaatgtgttgtttgctttgttttttgagtaaattttgtgg---tgacattcttggttg-----------ttgtgtatgcagGCATAGATGGACTGGTAGATATGAAGCGCATTTGTGGGATAACAGTTGCAAGAAGGAAGGGCAAACCAGGAAAGGACGACAAG

upper sequence: Vv18s0001g08610.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA0041S00200.1 (Glycine max), 3'ss of exon 5
gttagttcatattcttttccttcatctttggtcttatctataatgttttttgaattgagtttgttttctagtttatttgaggtctccctgcaggtgtattgtatcactgttttctctattatattgtcctcgccttttctgctggaaatattgtaggtttggttttccaagtaaacattgtcaatttatttccccagGCATAGATGGACTGGTAGATATGAAGCCCATCTTTGGGATAATAGTTGCAAGAAGGAGGGGCAGACTAGGAAAGGAAGACAAG
                                                                                                ||||   |||   |  |    ||| |    |  |    ||  ||  |||   | || || ||    |||     |  |   |||    ||  | |   |||||||||||||||||||||||||||||| ||| | |||||||| |||||||||||||| ||||| || ||||||||| ||||||
------------------------------------------------------------------------------------------------tatttagtcaaattcatggggatttttactttttgagtttaacttatggtgtttttttaagtaaattttgtggtgacattcttggtggtt-gtgtatgcagGCATAGATGGACTGGTAGATATGAAGCACATTTGTGGGATAACAGTTGCAAGAAGGAAGGGCAAACAAGGAAAGGACGACAAG

upper sequence: Vv18s0001g08610.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 2
gttagttcatattcttttccttcatctttggtcttatctataatgttttttgaattgagtttgttttctagtttatttgaggtctccctgcaggtgtattgtatcactgttttctc-tattatattgtcctcgccttttctgctggaaatattgtaggtttggttttccaagtaaacattgtcaatttatttccccagGCATAGATGGACTGGTAGATATGAAGCCCATCTTTGGGATAATAGTTGCAAGAAGGAGGGGCAGACTAGGAAAGGAAGACAAG
                                                                                                  |||| |   | |||| |  ||||| | | |  | | ||||   | | | ||| ||  |  |     || |  |  |     ||| ||          ||| |||||||||||||||||||||||||| ||||| ||||| ||||||| ||||||||| || || | ||| |||||||||||||
-------------------------------------------------------------------------------------------------gttgtttttttattttataatattaaactttgtttgactttc--gttagtaatgttacatat---acttacttaaaaggttatgtgaaa---------cagACATAGATGGACTGGTAGATATGAAGCTCATCTATGGGACAATAGTTTCAAGAAGGAAGGTCACAGTAGAAAAGGAAGACAAG

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|34542668|gb|CF510900.1|CF510900
EST:     TCCATTGACACATTTGGGCAGAGGACTTCACAATATAGAGGAGTTACAAG                         GCATAGATGGACTGGTAGATATGAAGCCCATCTTTGGGATAATAGTTGCAA
genomic: TCCATTGACACATTTGGGCAGAGGACTTCACAATATAGAGGAGTTACAAGgttagttcat ... atttccccagGCATAGATGGACTGGTAGATATGAAGCCCATCTTTGGGATAATAGTTGCAA
EST: gi|110700948|gb|EE078047.1|EE078047
EST:     TCCATTGACACATTTGGGCAGAGGACTTCACAATATAGAGGAGTTACAAG                         GCATAGATGGACTGGTAGATATGAAGCCCATCTTTGGGATAATAGTTGCAA
genomic: TCCATTGACACATTTGGGCAGAGGACTTCACAATATAGAGGAGTTACAAGgttagttcat ... atttccccagGCATAGATGGACTGGTAGATATGAAGCCCATCTTTGGGATAATAGTTGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggaaatattgtaggtttggttttccaagtaaacattgtcaatttatttccccagGCATAGATGGACTGGTAGATATGAAGCCCATCTTTGGGATAATAGTTGCAAGAAGGAGGGGCAGACTAGGAAAGGAAGACAAG
                                          tttatttcccc  CT-rich tract
                                  attgtcaatttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagttcatattcttttccttcatctttggtcttatctataatgttttttgaattgagtttgttttctagtttatttgaggtctccctgcaggtgtattgtatcactgttttctctattatattgtcctcgccttttctgctggaaatattgtaggtttggttttccaagtaaacattgtcaatttatttccccagGCATAGATGGACTGGTAGATATGAAGCCCATCTTTGGGATAATAGTTGCAAGAAGGAGGGGCAGACTAGGAAAGGAAGACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA