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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atggtttttgcagttacccataattaatcttcatggttacattccatcgcttgactgtaagactcctctgatgaagttccatattgcttttatgtggcagTTCTCCTCTGCTGGGTTACCCCGGAGTTTGAACTTTATGCAGCATTTGATCCACTTGCAGATAAG

Basic information

species Vitis vinifera
transcript Vv06s0004g02820.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g02820.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA12G29450.1 (Glycine max), 3'ss of exon 12
atggtttttgcagttacccataattaatcttcatggttacattccatcgcttgactg--taagactcctctgatgaagttccatattgcttttatgtggcagTTCTCCTCTGCTGGGTTACCCCGGAGTTTGAACTTTATGCAGCATTTGATCCACTTGCAGATAAG
 |  |          | | |||  |       ||  || |  |    |  |||  ||  |       | || || |   |   || |  |||||| |||||||||| ||||| ||||| || ||||| ||||| |||||||| ||||||||||| |||||||| |||
-taatagacaagccaatctatacatgtgggatataattgctctattacatttggatgcttcgatgaacactaatcagactt-gtaataattttatttggcagTTCTGCTCTGTTGGGTAACACCGGATTTTGAGCTTTATGCTGCATTTGATCCCCTTGCAGACAAG

upper sequence: Vv06s0004g02820.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA12G29450.3 (Glycine max), 3'ss of exon 12
atggtttttgcagttacccataattaatcttcatggttacattccatcgcttgactg--taagactcctctgatgaagttccatattgcttttatgtggcagTTCTCCTCTGCTGGGTTACCCCGGAGTTTGAACTTTATGCAGCATTTGATCCACTTGCAGATAAG-----------------------------------
 |  |          | | |||  |       ||  || |  |    |  |||  ||  |       | || || |   |   || |  |||||| |||||||||| ||||| ||||| || ||||| ||||| |||||||| ||||||||||| |||||||| |||                                   
-taatagacaagccaatctatacatgtgggatataattgctctattacatttggatgcttcgatgaacactaatcagactt-gtaataattttatttggcagTTCTGCTCTGTTGGGTAACACCGGATTTTGAGCTTTATGCTGCATTTGATCCCCTTGCAGACAAGGTATTGTTTTTGCTTGCCTTCATCATTTCTCAAAT

upper sequence: Vv06s0004g02820.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA13G40080.1 (Glycine max), 3'ss of exon 13
atggtttttgcagttacccataattaatcttcatggttacatt-ccatcgcttgactg--taagactcctctgatgaagttccatattgcttttatgtggcagTTCTCCTCTGCTGGGTTACCCCGGAGTTTGAACTTTATGCAGCATTTGATCCACTTGCAGATAAG
    |          | | |||  |       || ||| || |   ||   |||  ||  |       ||||||| |   |   || |  |||||| |||||||||| ||||| ||||| || | ||| ||||| |||||||| ||||||||||| |||||||| |||
--aatagacaagccaatctatacatgtgggatatagttgcactattatattttggatgctttgatgaactctgatcagactt-gtaataattttatttggcagTTCTGCTCTGTTGGGTAACACAGGATTTTGAGCTTTATGCTGCATTTGATCCCCTTGCAGACAAG

upper sequence: Vv06s0004g02820.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT2G28390.1 (Arabidopsis thaliana), 3'ss of exon 12
-atggtttttgcagttacccataattaatcttcatggttacattccatcgcttgactgtaagactcctctgatgaagttccatattgcttttatgtggcagTTCTCCTCTGCTGGGTTACCCCGGAGTTTGAACTTTATGCAGCATTTGATCCACTTGCAGATAAG
    |||         || |||  || |     | | | | |    |||   |  |||    |||   || |  |||||    ||||   | |  || ||| ||| || || ||||| || || || |||||||| |||||||||||||||||||||||||| |||
gtaagttcgaatttgcacacatgtttgacacgaaagatgaga----atcttctcgctgcggaactga-ctaa--aagttg---attgtgataacttg-cagCTCTTCTATGTTGGGTCACACCAGATTTTGAACTCTATGCAGCATTTGATCCACTTGCAGACAAG

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|22014769|gb|BQ799803.1|BQ799803
EST:     AGGAGTGGGNNNNNNNNATAAAACACAGTTTAGAAGGGATGAAAACTATG                         TTCTCCTCTGCTGGGTTACCCCGGAGTTTGAACTTTATGCAGCATTTGATC
genomic: AGGAGTGGGCCCCCCCCATAAAACACAGTTTAGAAGGGATGAAAACTATGgtaaaatgtt ... tatgtggcagTTCTCCTCTGCTGGGTTACCCCGGAGTTTGAACTTTATGCAGCATTTGATC
EST: gi|22014874|gb|BQ799908.1|BQ799908
EST:     AGGAGTGGGNNNNNNNNATAAAACACAGTTTAGAAGGGATGAAAACTATG                         TTCTCCTCTGCTGGGTTACCCCGGAGTTTGAACTTTATGCAGCATTTGATC
genomic: AGGAGTGGGCCCCCCCCATAAAACACAGTTTAGAAGGGATGAAAACTATGgtaaaatgtt ... tatgtggcagTTCTCCTCTGCTGGGTTACCCCGGAGTTTGAACTTTATGCAGCATTTGATC
EST: gi|110360647|gb|EC923921.1|EC923921
EST:     AGGAGTGGGNNNNNNNNATAAAACACAGTTTAGAAGGGATGAAAACTATG                         TTCTCCTCTGCTGGGTTACCCCGGAGTTTGAACTTTATGCAGCATTTGATC
genomic: AGGAGTGGGCCCCCCCCATAAAACACAGTTTAGAAGGGATGAAAACTATGgtaaaatgtt ... tatgtggcagTTCTCCTCTGCTGGGTTACCCCGGAGTTTGAACTTTATGCAGCATTTGATC
EST: gi|22014663|gb|BQ799697.1|BQ799697
EST:     AGGAGTGGGNNNNNNNNATAAAACACAGTTTAGAAGGGATGAAAACTATG                         TTCTCCTCTGCTGGGTTACCCCGGAGTTTGAACTTTATGCAGCATTTGATC
genomic: AGGAGTGGGCCCCCCCCATAAAACACAGTTTAGAAGGGATGAAAACTATGgtaaaatgtt ... tatgtggcagTTCTCCTCTGCTGGGTTACCCCGGAGTTTGAACTTTATGCAGCATTTGATC
EST: gi|33403777|gb|CF209404.1|CF209404
EST:     AGGAGTGGGNNNNNNNNATAAAACACAGTTTAGAAGGGATGAAAACTATG                         TTCTCCTCTGCTGGGTTACCCCGGAGTTTGAACTTTATGCAGCATTTGATC
genomic: AGGAGTGGGCCCCCCCCATAAAACACAGTTTAGAAGGGATGAAAACTATGgtaaaatgtt ... tatgtggcagTTCTCCTCTGCTGGGTTACCCCGGAGTTTGAACTTTATGCAGCATTTGATC
EST: gi|22014543|gb|BQ799577.1|BQ799577
EST:     AGGAGTGGGNNNNNNNNATAAAACACAGTTTAGAAGGGATGAAAACTATG                         TTCTCCTCTGCTGGGTTACCCCGGAGTTTGAACTTTATGCAGCATTTGATC
genomic: AGGAGTGGGCCCCCCCCATAAAACACAGTTTAGAAGGGATGAAAACTATGgtaaaatgtt ... tatgtggcagTTCTCCTCTGCTGGGTTACCCCGGAGTTTGAACTTTATGCAGCATTTGATC
EST: gi|110412539|gb|EC978290.1|EC978290
EST:     AGGAGTGGGNNNNNNNNATAAAACACAGTTTAGAAGGGATGAAAACTATG                         TTCTCCTCTGCTGGGTTACCCCGGAGTTTGAACTTTATGCAGCATTTGATC
genomic: AGGAGTGGGCCCCCCCCATAAAACACAGTTTAGAAGGGATGAAAACTATGgtaaaatgtt ... tatgtggcagTTCTCCTCTGCTGGGTTACCCCGGAGTTTGAACTTTATGCAGCATTTGATC
EST: gi|110375913|gb|EC940942.1|EC940942
EST:     AGGAGTGGGNNNNNNNNATAAAACACAGTTTAGAAGGGATGAAAACTATG                         TTCTCCTCTGCTGGGTTACCCCGGAGTTTGAACTTTATGCAGCATTTGATC
genomic: AGGAGTGGGCCCCCCCCATAAAACACAGTTTAGAAGGGATGAAAACTATGgtaaaatgtt ... tatgtggcagTTCTCCTCTGCTGGGTTACCCCGGAGTTTGAACTTTATGCAGCATTTGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcgcttgactgtaagactcctctgatgaagttccatattgcttttatgtggcagTTCTCCTCTGCTGGGTTACCCCGGAGTTTGAACTTTATGCAGCATTTGATCCACTTGCAGATAAG
                    ctctgat  putative branch site (score: 4)
                                      ttgctttt  putative PPT
                                          ttttatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atggtttttgcagttacccataattaatcttcatggttacattccatcgcttgactgtaagactcctctgatgaagttccatattgcttttatgtggcagTTCTCCTCTGCTGGGTTACCCCGGAGTTTGAACTTTATGCAGCATTTGATCCACTTGCAGATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - tgcagtt
- - - - - - - - cccataa
- - - - - - - - - - - - - - -ttcatgg
- - - - - - - - - - - - - - - - - - - acattcc
- - - - - - - - - - - - - - - - - - - - - - - - gcttgac