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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttctaattttgttcttgagtatttttaatcaagtaccccattgaattcttcaaactcatcactgatgcttgtgatgcaaactacttattgcaactgcagGTATCTGCTGCCCGAGAAGAAGTTCCCGGGAGGCGTGGGTATCCTGGGTATATGTATACTGATCTGGCGACGATTTATGAACGTGCTGGACGTATTGAAG

Basic information

species Vitis vinifera
transcript Vv03s0038g02760.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 9
-cttctaattttgttcttgagtatttttaatcaagtaccccattgaattcttcaaactcatcactgatgcttgtgatgcaaactacttat-tgcaactgcagGTATCTGCTGCCCGAGAAGAAGTTCCCGGGAGGCGTGGGTATCCTGGGTATATGTATACTGATCTGGCGACGATTTATGAACGTGCTGGACGTATTGAAG
 | |||  |||| |  | || |    | ||| |  ||      |||| | ||     |  | | ||   ||  |    ||   || || |    |  || ||||||| || |||||||||||||| || || ||||||||||||||||| |||||||||||||||||||| || || ||||| || ||||| ||||||||||
acatctccttttatgttcgactgcaataaatga--taaattgctgaaattttatttattgtgattggcactaatacaacacggtaattgtgcttatatgtagGTATCAGCAGCCCGAGAAGAAGTGCCAGGTAGGCGTGGGTATCCTGGATATATGTATACTGATCTGGCAACCATATATGAGCGAGCTGGGCGTATTGAAG

upper sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 9
---cttctaattttgttcttgagtatttttaatcaagtaccccattgaattcttcaaactcatcactgatgcttgtgatgcaaactacttattgcaactgcagGTATCTGCTGCCCGAGAAGAAGTTCCCGGGAGGCGTGGGTATCCTGGGTATATGTATACTGATCTGGCGACGATTTATGAACGTGCTGGACGTATTGAAG
    ||  |  |      |||  | |   ||||||| |     |||||    ||||   |      |  |  |  || | ||      || |      || |||| ||||| ||||||||||| || || || |||||||| |||||||| |||||||||||||||||||| || || ||||| |||||||| ||||||||||
agtatttaagatcaacctttgtatttaggtaatcaaatggtaaattga---tttcatgtttgatgtttctaataatgctacatgggcattgtgctttttgtagGTTTCTGCAGCCCGAGAAGAGGTGCCAGGTAGGCGTGGTTATCCTGGATATATGTATACTGATCTGGCAACAATATATGAGCGTGCTGGGCGTATTGAAG

upper sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G094497_T01 (Zea mays), 3'ss of exon 9
cttctaattttgttcttgagtatttttaatcaagtaccccattgaattcttcaaactcatcactgatgcttgtgatgcaaactacttattgca----actgcagGTATCTGCTGCCCGAGAAGAAGTTCCCGGGAGGCGTGGGTATCCTGGGTATATGTATACTGATCTGGCGACGATTTATGAACGTGCTGGACGTATTGAAG
 || ||  | | ||   || ||   ||  || | || |  ||| |||     |      ||  || | ||  | |||| |  |    ||||        || |||| ||||| ||||||||||| || || || |||||||| |||||||| ||||||||||||||| |||| || || ||||| |||||||| ||||||||||
-tttta--tatatttaagattaaccttt-tctattagctaattaaatgacaaattgatgtcgttgtttctaataatgctacatgggcattgtgcttttttgtagGTTTCTGCAGCCCGAGAAGAGGTGCCAGGTAGGCGTGGTTATCCTGGATATATGTATACTGATTTGGCAACAATATATGAGCGTGCTGGGCGTATTGAAG

upper sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 10
cttctaattttgttcttgagtattttt-aatcaagtaccccattgaattcttcaaactcatcactgatgcttgtgatgcaaactactta----ttgcaactgcagGTATCTGCTGCCCGAGAAGAAGTTCCCGGGAGGCGTGGGTATCCTGGGTATATGTATACTGATCTGGCGACGATTTATGAACGTGCTGGACGTATTGAAG
     ||| | |  |||| || ||||  |||           ||| | | |   || | |      ||  || | |  |||  | | |     |||   |   ||||||||||||||||||||||||| || || || ||||| |||||||| ||||||||||| ||||| || || ||||||||||| |||||  | ||||| |
-----aatgtgggacttgggttttttccaatatgacttatttttggagtatgagaaataactgaacatatttctcaaacaatttgcatgacacttgatcccatagGTATCTGCTGCCCGAGAAGAAGTGCCGGGTAGACGTGGTTATCCTGGATATATGTATACAGATCTTGCAACAATTTATGAACGAGCTGGGAGAATTGAGG

upper sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA10G42940.2 (Glycine max), 3'ss of exon 9
-----------------------------------------------------------------------------cttctaattttgttcttgagtatttttaa---tcaagtaccccattgaattcttcaaactcatcactgatgcttgtgatgcaaactactta----ttgcaactgcagGTATCTGCTGCCCGAGAAGAAGTTCCCGGGAGGCGTGGGTATCCTGGGTATATGTATACTGATCTGGCGACGATTTATGAACGTGCTGGACGTATTGAAG
                                                                              |  | ||||     |    |  |||||    |   ||      ||| | | |   || | |      ||  || |    |||  | | |     |||   | | ||||||||||||||||||||||||| || || || ||||| |||||||| ||||||||||| ||||| || || ||||||||||| |||||  | ||||| |
gtaatttaccttcaactgttattagtttggaagaagcaacaaaaagataggggacttgaaaccttttataggctttaatgatgatttaaaattgacattcttttatgcctttggtttattcttggagtatgagaaataactgaaaatatttctataacaatttgcatgacacttgatcccgtagGTATCTGCTGCCCGAGAAGAAGTGCCAGGAAGACGTGGTTATCCTGGATATATGTATACAGATCTTGCAACAATTTATGAACGAGCTGGGAGAATTGAGG

upper sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA18G48280.1 (Glycine max), 3'ss of exon 9
cttctaattttgttcttgagtatttttaatcaagtaccccattgaattcttcaaactcatc-actgatgcttgtgatgcaaactacttattgcaactgcagGTATCTGCTGCCCGAGAAGAAGTTCCCGGGAGGCGTGGGTATCCTGGGTATATGTATACTGATCTGGCGACGATTTATGAACGTGCTGGACGTATTGAAG
| | || || | |  ||   |     || | |       ||  | ||| | |||||   |  | |||   | |   |   |||  ||| | |    || ||||||||||||||||||||||||| || || || ||||||||||| || || |||||||| ||||| || || || || |||||||||||| | ||||| |
catgtatttatatctttttctcagagta-ttagaagtaacaaagtattttgcaaacaattagattgacaatggaactattaaccccttctggatcttgtagGTATCTGCTGCCCGAGAAGAAGTACCTGGTAGACGTGGGTATCCCGGCTACATGTATACAGATCTTGCAACAATATACGAACGTGCTGGAAGAATTGAGG

upper sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 9
cttctaattttgttcttgagtattttta-atcaagtaccccattgaattcttcaaactcatc-actgatgcttgtgatgcaaactacttattgcaactgcagGTATCTGCTGCCCGAGAAGAAGTTCCCGGGAGGCGTGGGTATCCTGGGTATATGTATACTGATCTGGCGACGATTTATGAACGTGCTGGACGTATTGAAG
| | || || | |  ||   |     || |  ||||| |  | |  ||| | |||||   |  | |||   | |   |    ||  ||| | |   ||| ||||||||||||||||||||||||| || || || |||||||| || || || |||||||| ||||| || || || || |||||||||||| | ||||| |
catttatttatctctttttctccgactataaaaagtaactaagt--attttgcaaacaattagattgacaatggaactattgaccccttctggatcctgtagGTATCTGCTGCCCGAGAAGAAGTACCTGGTAGACGTGGGTACCCCGGTTACATGTATACAGATCTTGCAACAATATACGAACGTGCTGGAAGAATTGAGG

upper sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 9
cttctaattttgttcttgagtattt--ttaatcaagtaccccattgaattcttcaaactcatcactgatgc--ttgtgatgcaaactacttattg-caactgc------agGTATCTGCTGCCCGAGAAGAAGTTCCCGGGAGGCGTGGGTATCCTGGGTATATGTATACTGATCTGGCGACGATTTATGAACGTGCTGGACGTATTGAAG
          ||  || |  || ||  |||||||||||     |||||  ||  | |   |      |||   |   |||  |   |  |  ||  ||| | |      |||| |||||||| || |||||||| |||||  | |||||||| ||||| |||||||| || ||||| || || |||||||||||||||||||||||||| |
--------gctgcactcggttacttagttaatcaagtatt---ttgaaacctcgatatcgagggtctatgtaatgacgatatatttttgtcgttttcaattacttaaacagGTGTCTGCTGCTCGTGAAGAAGTACCCGGTCGTCGTGGGTACCCTGGTTATATGTACACCGATCTTGCCACCATTTATGAACGTGCTGGACGTATTGAGG

upper sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 8
----------------------------------------------cttctaattttgttcttgagtatt------------tttaatcaagtaccccattgaattcttcaaactcatcactgatgcttgtgatgc--aaactacttattgc----------aactg------cagGTATCTGCTGCCCGAGAAGAAGTTCCCGGGAGGCGTGGGTATCCTGGGTATATGTATACTGATCTGGCGACGATTTATGAACGTGCTGGACGTATTGAAG
                                              ||||| | | |||| |||  | ||            ||  |  || | ||||  |   || ||    || |      |   ||   ||||   ||  || ||||            ||||       ||||| ||||| || || |||||||| || ||| | ||||| |||||||| || ||||| || ||||| || || ||||| ||||||||||| || ||||| |
gtaccagtctttaccttaaagatctgcttgcccttgtggtatggtacttctgactctgtttttggtttttgaaatgttagtgttctaaaaaatgcccctctattttgttggttctaagtctgcacctttagtatgccagaatgacatattcttatgatccttaactatgcgaacagGTTTCTGCAGCTCGTGAAGAAGTACCTGGGCGTCGTGGATATCCTGGTTACATGTACACGGATCTTGCCACTATTTACGAACGTGCTGGGCGAATTGAGG

upper sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 8
-----------------------------------------------------------------------------------------cttctaattttgttcttgagtatttttaatcaagtaccccattgaattct--tcaaactcatcactgatgcttgtgatgcaaactactt---attgcaactgcagGTATCTGCTGCCCGAGAAGAAGTTCCCGGGAGGCGTGGGTATCCTGGGTATATGTATACTGATCTGGCGACGATTTATGAACGTGCTGGACGTATTGAAG
                                                                                           ||| |  | ||| || || |  |||  | |  ||  |  |||  || |  | ||   | ||| || ||||    ||     | |||    |||        |||| |||||||| || |||||||| || ||| | ||||| |||||||| || ||||||||||||||||| || |||||||||||||||||||| || ||||
gtacaagtgtttctcttaaagacttttcgcttggactcctttttcagaagttagctcctgtgaaattctacatgctactccgcagttggtatctgaaatagtttttaagcaaatttg-taatctattcagttggtttttaattaagaccttcagtg-tgctacaaattttttccactctcaattcttcaaatagGTTTCTGCTGCTCGTGAAGAAGTGCCTGGGCGTCGTGGATATCCTGGTTACATGTATACTGATCTGGCCACCATTTATGAACGTGCTGGACGAATCGAAG

upper sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 8
cttctaattttgttcttgagtatttttaatcaagtaccccattgaattcttcaaactcatcactgatgcttgtgatgcaaactacttattgcaactgcagGTATCTGCTGCCCGAGAAGAAGTTCCCGGGAGGCGTGGGTATCCTGGGTATATGTATACTGATCTGGCGACGATTTATGAACGTGCTGGACGTATTGAAG
                                        || | ||  |||||  |  ||| |||    | ||||    |   |||  ||    || |||| ||||| || || || || || || ||  | ||||| |||||||| ||||||||||| ||| |||| || ||||| || ||||||||||| |||||||
--------------------------------------gtatggtatgtttcaagtttgtca-tgagagctatgataaccagggctt--tg----tgtagGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTATATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAG

upper sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: EFJ13375 (Selaginella moellendorffii), 3'ss of exon 8
cttctaattttgttcttgagtatttttaatcaagtaccccattgaattcttcaaactcatcactgatgcttgtgatgcaaactacttattgcaactgcagGTATCTGCTGCCCGAGAAGAAGTTCCCGGGAGGCGTGGGTATCCTGGGTATATGTATACTGATCTGGCGACGATTTATGAACGTGCTGGACGTATTGAAG
                                        || | ||  |||||  |  ||| |||   || ||||    |   |||  ||    || |||| ||||| || || || || || || ||  | ||||| |||||||| ||||||||||| ||| |||| || ||||| || ||||||||||| |||||||
-----------------------------------gtatgatcgtatgtttcaagtttttca-tgagagttatgataaccatggctt--tg----tgtagGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTATATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAG

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|110720101|gb|EE095728.1|EE095728
EST:     TTCTTGTCATACTAACAGATATGAGTTCTTATGCAGATGCTCTTCGTGAG                         GTATCTGCTGCCCGAGAAGAAGTTCCCGGGAGGCGTGGGTATCCTGGGTAT
genomic: TTCTTGTCATACTAACAGATATGAGTTCTTATGCAGATGCTCTTCGTGAGgtaacgattt ... gcaactgcagGTATCTGCTGCCCGAGAAGAAGTTCCCGGGAGGCGTGGGTATCCTGGGTAT
EST: gi|110719306|gb|EE097131.1|EE097131
EST:     TTCTCGTCATACTAACAGATATGAGTTCTTATGCAGATGCTCTTCGTGAG                         GTATCTGCTGCCCGAGAAGAAGTTCCCGGGAGGCGTGGGTATCCTGGGTAT
genomic: TTCTTGTCATACTAACAGATATGAGTTCTTATGCAGATGCTCTTCGTGAGgtaacgattt ... gcaactgcagGTATCTGCTGCCCGAGAAGAAGTTCCCGGGAGGCGTGGGTATCCTGGGTAT
EST: gi|110712807|gb|EE088186.1|EE088186
EST:     TTCTTGTCATACTAACAGATATGAGTTCTTATGCAGATGCTCTTCGTGAG                         GTATCTGCTGCCCGAGAAGAAGTTCCCGGGAGGCGTGGGTATCCTGGGTAT
genomic: TTCTTGTCATACTAACAGATATGAGTTCTTATGCAGATGCTCTTCGTGAGgtaacgattt ... gcaactgcagGTATCTGCTGCCCGAGAAGAAGTTCCCGGGAGGCGTGGGTATCCTGGGTAT
EST: gi|33402634|gb|CF208261.1|CF208261
EST:     TTCTTGTCATACTAACAGATATGAGTTCTTATGCAGATGCTCTTCGTGAG                         GTATCTGCTGCCCGAGAAGAAGTTCCTGGAAGGCGTGGGTATCCTGGGTAT
genomic: TTCTTGTCATACTAACAGATATGAGTTCTTATGCAGATGCTCTTCGTGAGgtaacgattt ... gcaactgcagGTATCTGCTGCCCGAGAAGAAGTTCCCGGGAGGCGTGGGTATCCTGGGTAT
EST: gi|110723346|gb|EE100552.1|EE100552
EST:     TTCTTGTCATACTAACAGATATGAGTTCTTATGCAGATGCTCTTCGTGAG                         GTATCTGCTGCCCGAGAAGAAGTTCCCGGGAGGCGTGGGTATCCTGGGTAT
genomic: TTCTTGTCATACTAACAGATATGAGTTCTTATGCAGATGCTCTTCGTGAGgtaacgattt ... gcaactgcagGTATCTGCTGCCCGAGAAGAAGTTCCCGGGAGGCGTGGGTATCCTGGGTAT
EST: gi|156737783|gb|EV241904.1|EV241904
EST:     TTCTTGTCATACTAACAGATATGAGTTCTTATGCAGATGCTCTTCGTGAG                         GTATCTGCTGCCCGAGAAGAAGTTCCCGGGAGGCGTGGGTATCCTGGGTAT
genomic: TTCTTGTCATACTAACAGATATGAGTTCTTATGCAGATGCTCTTCGTGAGgtaacgattt ... gcaactgcagGTATCTGCTGCCCGAGAAGAAGTTCCCGGGAGGCGTGGGTATCCTGGGTAT
EST: gi|71862037|gb|DT011092.1|DT011092
EST:     TTCTTGTCATACTAACAGATATGAGTTCTTATGCAGATGCTCTTCGTGAG                         GTATCTGCTGCCCGAGAAGAAGTTCCTGGAAGGCGTGGGTATCCTGGGTAT
genomic: TTCTTGTCATACTAACAGATATGAGTTCTTATGCAGATGCTCTTCGTGAGgtaacgattt ... gcaactgcagGTATCTGCTGCCCGAGAAGAAGTTCCCGGGAGGCGTGGGTATCCTGGGTAT
EST: gi|34542425|gb|CF510657.1|CF510657
EST:     TTCTTGTCATACTAACAGATATGAGTTCTTATGCAGATGCTCTTCGTGAG                         GTATCTGCTGCCCGAGAAGAAGTTCCTGGAAGGCGTGGGTATCCTGGGTAT
genomic: TTCTTGTCATACTAACAGATATGAGTTCTTATGCAGATGCTCTTCGTGAGgtaacgattt ... gcaactgcagGTATCTGCTGCCCGAGAAGAAGTTCCCGGGAGGCGTGGGTATCCTGGGTAT
EST: gi|27755418|gb|CB036173.1|CB036173
EST:     TTCTTGTCATACTAACAGATATGAGTTCTTATGCAGATGCTCTTCGTGAG                         GTATCTGCTGCCCGAGAAGAAGTTCCCGGAAGGCGTGGGTATCCTGGGTAT
genomic: TTCTTGTCATACTAACAGATATGAGTTCTTATGCAGATGCTCTTCGTGAGgtaacgattt ... gcaactgcagGTATCTGCTGCCCGAGAAGAAGTTCCCGGGAGGCGTGGGTATCCTGGGTAT
EST: gi|110424996|gb|EC991371.1|EC991371
EST:     TTCTTGTCATACTAACAGATATGAGTTCTTATGCAGATGCTCTTCGTGAG                         GTATCTGCTGCCCGAGAAGAAGTTCCCGGGAGGCGTGGGTATCCTGGGTAT
genomic: TTCTTGTCATACTAACAGATATGAGTTCTTATGCAGATGCTCTTCGTGAGgtaacgattt ... gcaactgcagGTATCTGCTGCCCGAGAAGAAGTTCCCGGGAGGCGTGGGTATCCTGGGTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcttcaaactcatcactgatgcttgtgatgcaaactacttattgcaactgcagGTATCTGCTGCCCGAGAAGAAGTTCCCGGGAGGCGTGGGTATCCTGGGTATATGTATACTGATCTGGCGACGATTTATGAACGTGCTGGACGTATTGAAG
               cactgat  putative branch site (score: 3)
                                     tacttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttctaattttgttcttgagtatttttaatcaagtaccccattgaattcttcaaactcatcactgatgcttgtgatgcaaactacttattgcaactgcagGTATCTGCTGCCCGAGAAGAAGTTCCCGGGAGGCGTGGGTATCCTGGGTATATGTATACTGATCTGGCGACGATTTATGAACGTGCTGGACGTATTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - -tcaagta
- - - - - - - - - - - - - - - - - - ccccatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -catcact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaacta