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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttaaaggctcatgtgtttgttgaaaagaaagaatttcccattatattggggatgggctatgattgacctagttctggtttgtttgttgtttacagccagGGCCTCGGGATGGAACCATTCAGTGCTTCATTAAGAGGGACAAGTCCAACTTGACTTACCACCTTTTCCTTTGCCTTAGCCCTG

Basic information

species Vitis vinifera
transcript Vv18s0072g00630.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0072g00630.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G046816_T02 (Zea mays), 3'ss of exon 1
--------cttaaaggctcatgtgtttgttgaaaagaaagaat-ttcccattatattggggatgggctatgattgacctagttctggtttgtttgttgtttacagccagGGCCTCGGGATGGAACCATTCAGTGCTTCATTAAGAGGGACAAGTCCAACTTGACTTACCACCTTTTCCTTTGCCTTAGCCCTG
         |||  |       |  |   || | || |    | | || || ||||| || ||   |||    | | ||  | ||| ||  | |  ||| ||||||| |||||||| |||||||| |||||||| || ||||||||||| |  || | |   |  |||   || | |||| |  ||||| |||
ctgattccgttaccgttgtcaatactccatgtacagtattggtatgccaatcatatttgg-ataatctaa---taagctcatgctg-ttcctcttctgtctacagCCTGGGCCTCGAGATGGAACTATTCAGTGTTTTATTAAGAGGGATACATCTACCCAAATCTACAGTCTGTACCTTAGTTTTAGCTCTG

upper sequence: Vv18s0072g00630.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G046816_T04 (Zea mays), 3'ss of exon 2
------------------------------------------------cttaaaggctcatgtgtttgttgaaaagaaagaatttccca-ttatattggggatgggctatgattgacctagttctggtttgtttgttgtttacagccagGGCCTCGGGATGGAACCATTCAGTGCTTCATTAAGAGGGACAAGTCCAACTTGACTTACCACCTTTTCCTTTGCCTTAGCCCTG
                                                 |||  |       |  |   || | || |    | | ||| | ||||| || ||   |||    | | ||  | ||| ||  | |  ||| ||||||| |||||||| |||||||| |||||||| || ||||||||||| |  || | |   |  |||   || | |||| |  ||||| |||
gtaatcatgcagctatgttataccttattatccatatatactgattccgttaccgttgtcaatactccatgtacagtattggtatgccaatcatatttgg-ataatctaa---taagctcatgctg-ttcctcttctgtctacagCCTGGGCCTCGAGATGGAACTATTCAGTGTTTTATTAAGAGGGATACATCTACCCAAATCTACAGTCTGTACCTTAGTTTTAGCTCTG

upper sequence: Vv18s0072g00630.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA20G30660.1 (Glycine max), 3'ss of exon 2
----------------------cttaaaggctcatgtgtttgttgaaaagaaagaatttcccatt-atattggggatgggctatgattgacctagttctggtttgtttgttgtttacagccagGGCCTCGGGATGGAACCATTCAGTGCTTCATTAAGAGGGACAAGTCCAACTTGACTTACCACCTTTTCCTTTGCCTTAGCCCTG
                            | || |  | | | |  || |   | ||| |   |||  ||    |  ||   | |   |    |  | || | ||| || |||||||||||| |||| | |||||||| |||||||||| ||||| ||||| ||||| || ||  |||| |||||||| |||||||||||||| ||||
gtaagattttcttgttcttctatcctgtgcctaaaatatgtctaaaataattaaaatatgaaatttgtaccatgactgaagtttacat--ttttatgcttggttgattcttgtttacagCCTGGGCATAGGGATGGACCCATTCAGTGTTTCATCAAGAGAGACAAATCTAAGCTGACATACCACCTCTTCCTTTGCCTTAGTCCTG

upper sequence: Vv18s0072g00630.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA07G17890.1 (Glycine max), 3'ss of exon 3
----------------------cttaaaggctcatgtgtttgttgaaaagaaagaatttcccatt-atattggggatgggctatgattgacctagttctggtttgtttgttgtttacagccagGGCCTCGGGATGGAACCATTCAGTGCTTCATTAAGAGGGACAAGTCCAACTTGACTTACCACCTTTTCCTTTGCCTTAGCCCTG
                       |  | | || |  | | | |  || |   | ||| |   |||  ||    |  ||   | |   |    |  | || | ||| || |||||||||||| |||| | |||||||| |||||||||| ||||| ||||| ||||| || ||  |||| |||||||| |||||||||||||| ||||
gtaagattttcttgttcttctattctatgcctaaaatatgtctaaaataattaaaatatgaaatttgtaccatgactgaagtttacat--ttttatgcttggttgattcttgtttacagCCTGGGCATAGGGATGGACCCATTCAGTGTTTCATCAAGAGAGACAAATCTAAGCTGACATACCACCTCTTCCTTTGCCTTAGTCCTG

upper sequence: Vv18s0072g00630.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA12G13060.1 (Glycine max), 3'ss of exon 1
----------------------cttaaaggctcatgtgtttgttgaaaagaaagaatttcccatt-atattggggatgggctatgattgacctagttctggtttgtttgttgtttacagccagGGCCTCGGGATGGAACCATTCAGTGCTTCATTAAGAGGGACAAGTCCAACTTGACTTACCACCTTTTCCTTTGCCTTAGCCCTG
                       |  | | || |  | | | |  || |   | ||| |   |||  ||    |  ||   | | | |    |  | || | ||| || |||||||||||| |||| | |||||||| |||||||||| ||||| ||||| ||||| || | || ||| |||||||| |||||||||||||| ||||
gtaagattttcttgttcttctattctatgcctaaaatatgtctaaaataagtaaaatatgaaatttgtaccatgactgaagtttaaat--ttttatgcttggttgattcttgtttacagcctgggcatagGGATGGACCCATTCAGTGTTTCATCAAGAGAGACAAATCAAGCT-GACATACCACCTCTTCCTTTGCCTTAGTCCTG

upper sequence: Vv18s0072g00630.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G36940.2 (Glycine max), 3'ss of exon 2
----------------cttaaa----ggctcatgtgtttgttgaaaagaaagaatttcccattatattggggatgg-gctatgattgacctagttctggtttgtttgttgtttacagccagGGCCTCGGGATGGAACCATTCAGTGCTTCATTAAGAGGGACAAGTCCAACTTGACTTACCACCTTTTCCTTTGCCTTAGCCCTG
                | ||||    |  | |  |  ||| |  ||| |||||  |     || ||    |   |  |||   ||| |  |  ||   | ||| || ||||| |||||| |||| | |||||||| |||| ||||| ||||| ||||| ||||| || ||  |||| |||||||| |||||| ||||||||||||
gtaagacttttttgtgcctaaaatatgtttaaaataattgcttcaaaaaaagatatgaaatttgtaccatgaccgaagcttacatttatatgctt---ggttgattcttgttcacagCCTGGGCATAGGGATGGACCCATCCAGTGTTTCATCAAGAGAGACAAATCTAAGCTGACATACCACCTCTTCCTTGGCCTTAGCCCTG

upper sequence: Vv18s0072g00630.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA02G09030.3 (Glycine max), 3'ss of exon 2
--------cttaaaggctcatgtgtt-tgttgaaaaga-------aagaatttcccattatattggggat---------gggctatgat---tgacctagttctggtttgtttgttg--------tttacagccagGGCCTCGGGATGGAACCATTCAGTGCTTCATTAAGAGGGACAAGTCCAACTTGACTTACCACCTTTTCCTTTGCCTTAGCCCTG
         | |    ||  | |  | |||| || | |        |||| |   |  |  ||  | |||         |  |||  ||   ||| |  ||| || ||| ||| |||        ||||||||| ||  |  ||||||||||||| ||||| ||||| ||||| ||||| || ||  |||| |||||||| |||||||| ||||| ||||
gtgagactttcattatcttctatcctgtgttcaagatatattttagagaactggtccatgcatgagagatataaattttgtactagaatgcatgatcatgttttgatttttttattgactcttgttttacagCCTGGTTCAAGGGATGGAACCATCCAGTGTTTCATCAAGAGAGACAAATCTAATCTGACATACCACCTATTCCTTTGTCTTAGTCCTG

upper sequence: Vv18s0072g00630.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA16G28200.2 (Glycine max), 3'ss of exon 2
-----------------------------------------cttaaaggctcatgtgtttgtt---gaaaagaaagaatttcccattatattg--gggatgggctatgatt---gacctagttctggtttgt---ttgttgtttacagccagGGCCTCGGGATGGAACCATTCAGTGCTTCATTAAGAGGGACAAGTCCAACTTGACTTACCACCTTTTCCTTTGCCTTAGCCCTG
                                          | ||| |  |  ||   || |   || |   |  ||||    | || | ||   |       | ||| |   ||  |  |  ||  |  |   ||    ||||||||| ||  |  ||||||||||||| ||||| ||||| ||||| ||||| || ||  |||| |||||||| |||||||| ||||| ||||
gtgagatttttgttatctcctatcttgtgtaaattatatatttcaaaagaactggttcatgcttgtgagagatataaattgtgtactagaatgcatgatcatattttgacttatgattttttattgactcttgttttacaatttacagCCTGGTTCAAGGGATGGAACCATCCAGTGTTTCATCAAGAGAGACAAATCTAATCTGACGTACCACCTATTCCTTTGTCTTAGTCCTG

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|110732567|gb|EE107967.1|EE107967
EST:     TCCAGAGTTCTCTGGGAAGCTAACTTTCCCCATCTCTCTGAAACAGCCAG                         GGCCTCGGGATGGAATCATTCAGTGCTTCATTAAGAGGGACAAGTCCAACT
genomic: TCCAGAGTTCTCTGGGAAGCTTACTTTCCCCATCTCTCTGAAACAGGCATgtttttttat ... ttacagccagGGCCTCGGGATGGAACCATTCAGTGCTTCATTAAGAGGGACAAGTCCAACT
EST: gi|110731881|gb|EE106679.1|EE106679
EST:     TCCAGAGTTCTCTGGGAAGCTTACTTTCCCCATCTCTCTGAAACAGCCAG                         GGCCTCGGGATGGAATCATTCAGTGCTTCATTAAGAGGGACAAGTCCAACT
genomic: TCCAGAGTTCTCTGGGAAGCTTACTTTCCCCATCTCTCTGAAACAGGCATgtttttttat ... ttacagccagGGCCTCGGGATGGAACCATTCAGTGCTTCATTAAGAGGGACAAGTCCAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attggggatgggctatgattgacctagttctggtttgtttgttgtttacagccagGGCCTCGGGATGGAACCATTCAGTGCTTCATTAAGAGGGACAAGTCCAACTTGACTTACCACCTTTTCCTTTGCCTTAGCCCTG
                gattgac  putative branch site (score: 3)
             tatgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttaaaggctcatgtgtttgttgaaaagaaagaatttcccattatattggggatgggctatgattgacctagttctggtttgtttgttgtttacagccagGGCCTCGGGATGGAACCATTCAGTGCTTCATTAAGAGGGACAAGTCCAACTTGACTTACCACCTTTTCCTTTGCCTTAGCCCTG

- - - - - catgtgt
- - - - - - - - - - - - aaagaaa
- - - - - - - - - - - - - - - - - -ttcccat
- - - - - - - - - - - - - - - - - - - - - - - - - ggatggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttctgg