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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gggtccttgagatcagttctatgataaatatatagcatggtgtttttcttattagtgaatattgagaggcttaagaatcttgtgctgttgatgattgcagATTCCCTTCTGTGTGGTTGTTGGTTGGATTATGGGACAACCAATGGACTTGAATTTTCAACTCTTTGAGACTGCCACTCTCTTTATCGCGGTGCTAGTAG

Basic information

species Vitis vinifera
transcript Vv09s0018g01840.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0018g01840.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os03g27960.1 (Oryza sativa), 3'ss of exon 8
---------------------------------------gggtccttgagatcagttctatgataaatatatagcatggtgtttttcttattagtg-aatattgaga--ggcttaagaatcttgtgctgttg-atgatt-gcagATTCCCTTCTGTGTGGTTGTTGGTTGGATTATGGGACAACCAATGGACTTGAATTTTCAACTCTTTGAGACTGCCACTCTCTTTATCGCGGTGCTAGTAG
                                       || |     || || || |  | | ||    ||   |  |     |  || ||   | ||| |||| |  |    ||  | |      | ||  |||||| |||||| || |||||||||||  |||| ||||| ||||| |||| ||||||||||||||||||||| || ||||| || ||||| |||||  | || || || |
gtaagaacataaatgaatagcatgcaactaatctgctgtggttttgcaagctctgtaccgttacaagaccatgttaatgacaactagttgttgtagtaatgttgaaactgttccaaccaacacacttttttacatgatttgcagATCCCATTCTGTGTGGTAATTGGCTGGATAATGGGCCAACAAATGGACTTGAATTTTCAACTGTTCGAGACAGCAACTCTTTTTATAACAGTACTGGTGG

upper sequence: Vv09s0018g01840.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G053004_T03 (Zea mays), 3'ss of exon 8
-------------------------------------------------gggtccttgagatcagttctatgataaatata----tagcatggtgtttttcttattagtgaatattgagaggct----taagaatcttg----tgctgttgatgat-tgcagATTCCCTTCTGTGTGGTTGTTGGTTGGATTATGGGACAACCAATGGACTTGAATTTTCAACTCTTTGAGACTGCCACTCTCTTTATCGCGGTGCTAGTAG
                                                    | |   |     ||| ||  ||   | |     ||||    |  | || |    |||  |||         |    |||   |  ||    |  | || ||||| | |||||||| ||||| |||||  |||| ||||| |||||||||  ||||||||||||||||||||| || ||||| || |||||||||||  | || ||||| |
gtaataataataggaattccataataatacatagtgtaacagatacaacaactaccctactctggttttacaatttttttgtcattagccaaatcatgttttagacagtagataccacctttttccaataattgttctggtattctttttcatgatcttcagATTCCATTCTGCGTGGTAATTGGCTGGATGATGGGACAAGAAATGGACTTGAATTTTCAACTGTTCGAGACAGCGACTCTCTTTATAACTGTACTAGTGG

upper sequence: Vv09s0018g01840.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G040017_T02 (Zea mays), 3'ss of exon 9
-----gggtccttgag--atcagttctatgataaatatatagcatggtgtttttcttattagtgaatattgagaggcttaagaatcttgtgctgttgatgattgcagATTCCCTTCTGTGTGGTTGTTGGTTGGATTATGGGACAACCAATGGACTTGAATTTTCAACTCTTTGAGACTGCCACTCTCTTTATCGCGGTGCTAGTAG
       ||| |||||  | |||   |   || | |  ||  |||    |  ||    |     |     | || | ||  | ||  | | ||       | |||||||||| || ||||| ||| |||||||||| |||||||||   ||||||||||||||||| || |||||||| || |||||||| ||  | ||||| || |
aattttagtcattgaggaaccagaagt-caattactgaattacataaaatccttaaattcttctacctccgtgacgtttg-gcatggtatactcc-----aatgcagATTCCATTTTGTGTTGTTATTGGTTGGATGATGGGACAAAGGATGGACTTGAATTTTCAGCTATTTGAGACAGCAACTCTCTTCATAACAGTGCTTGTGG

upper sequence: Vv09s0018g01840.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G143356_T01 (Zea mays), 3'ss of exon 10
gggtccttgagatcagttctatgataaatatatagcatggtgtttttcttattagtgaatattgagaggcttaagaatcttgtgctgttgatgattgcagATTCCCTTCTGTGTGGTTGTTGGTTGGATTATGGGACAACCAATGGACTTGAATTTTCAACTCTTTGAGACTGCCACTCTCTTTATCGCGGTGCTAGTAG-----------------
                             | ||  | |    | ||   | |  ||||   ||||   | |  | | | |             | | |||||||| || ||||| ||| |||||||||  |||||||||   ||||||||||||||||| || |||||||| || |||||||| ||  | || || || |                 
-----------------------------aaatgccttaaattcttctgtctctgtgacatttgacgtggtatatacttt-------------aatacagattccattttgtgttgttattggttggacgatgggacaaaagATGGACTTGAATTTTCAGCTATTTGAGACAGCAACTCTCTTCATAACAGTACTTGTGGTGGCATTTATGTTACAG

upper sequence: Vv09s0018g01840.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G143356_T02 (Zea mays), 3'ss of exon 10
--gggtccttgagatcagttctatg-ataaatatatagcatggtgtttttcttattagtgaatat-tgagaggcttaagaatcttgtgctgttgatgattgcagATTCCCTTCTGTGTGGTTGTTGGTTGGATTATGGGACAACCAATGGACTTGAATTTTCAACTCTTTGAGACTGCCACTCTCTTTATCGCGGTGCTAGTAG
    ||  |  ||  ||  |   |  || | |  ||  |||    |   |   |||  |   | | || ||   || |    | ||   | |   | | | |||||||| || ||||| ||| |||||||||  |||||||||   ||||||||||||||||| || |||||||| || |||||||| ||  | || || || |
tttagttgtcaaggacacataagtacattactgaattacataaaatgccttaaattcttctgtctctgtgacatttga----cgtggtatatactttaatacagATTCCATTTTGTGTTGTTATTGGTTGGACGATGGGACAAAAGATGGACTTGAATTTTCAGCTATTTGAGACAGCAACTCTCTTCATAACAGTACTTGTGG

upper sequence: Vv09s0018g01840.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G046480_T01 (Zea mays), 3'ss of exon 9
--------------------------------------------------gggtccttgagatcagttctatgataaatatatagcatggtgtttttcttattagtgaatattgagaggcttaagaatcttgtgctgttgatgattgcagATTCCCTTCTGTGTGGTTGTTGGTTGGATTATGGGACAACCAATGGACTTGAATTTTCAACTCTTTGAGACTGCCACTCTCTTTATCGCGGTGCTAGTAG
                                                        |||  || ||    || ||   |  ||     |      |  || || |    | || |    ||  |   | ||    | |||||   |||||||||| ||||| |||||  |||| ||||| ||||| |    ||||||||||||||||||| | |||||||| || |||||||||||  | || ||||| |
gtaataatacttagtgcaccagatacaagtacacagctctggttttataaattcttttgtcattagccaaatcatgttttaatcagtagacaacatatttttttgactttttttaataactgcatgttttttccttcttgat--ctgcagATTCCATTCTGCGTGGTAATTGGCTGGATGATGGGGCGGGAAATGGACTTGAATTTTCAATTGTTTGAGACAGCGACTCTCTTTATAACTGTACTAGTGG

upper sequence: Vv09s0018g01840.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA15G00380.2 (Glycine max), 3'ss of exon 8
--------------------------------gggtccttgagat-cagttctatgataaatatat---agcatggtgtttttcttattagtga-atattgagaggcttaagaatcttgtgctgttgatgattgcagATTCCCTTCTGTGTGGTTGTTGGTTGGATTATGGGACAACCAATGGACTTGAATTTTCAACTCTTTGAGACTGCCACTCTCTTTATCGCGGTGCTAGTAG
                                   |  ||| | |  |  | ||  |||  | | |   |  |   | |  |   | |   ||  |||     | | | | || |||| | || ||||  |||| |||| || ||||||||||||||||| |||   |||||| ||  ||||||||| ||||||||||| |||||||||||||| || |||||| | ||| ||||||
gtatagccttcaactgttattaaatgttattaacttatttggggtgtacatttactatatctttttgtgaataaactatcctggatttctctgtcataggagaaagttgatgattcttattctcttgaaaattgtagATCCCTTTCTGTGTGGTTGTTGGATGGTGCATGGGAAAAGAAATGGACTTAAATTTTCAACTATTTGAGACTGCCACACTTTTTATCACTGTGTTAGTAG

upper sequence: Vv09s0018g01840.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA13G44960.1 (Glycine max), 3'ss of exon 8
--------------------------------------------------------------------------------------------gggtccttg-agatcagttctatgataaatatatagcatggtgtt--tttcttat-tagtgaatattgag--aggcttaagaatcttgtgctgttgatgattgcagATTCCCTTCTGTGTGGTTGTTGGTTGGATTATGGGACAACCAATGGACTTGAATTTTCAACTCTTTGAGACTGCCACTCTCTTTATCGCGGTGCTAGTAG
                                                                                              ||| | | ||  || ||||    |  ||  |     |    ||  ||  | |  |  |||  ||||    | | | | |  |||||  || ||||  |||| |||| || |||||||| |||||||| |||   |||||| ||  ||||||||||||||||||||| || ||||||||||| || |||||| | ||| ||||||
gtatggcctcgaactgttattaaatgttattaagttgtttggggtatacatttaccatatctttttgtgattaaactatcctgaatttcttcttgtcataggaggacatttcttgagtttattaactttttaaaattagttaatcagatgatgatcattggagaaagttgatggttcttgatctcttgaaaattgtagATCCCTTTCTGTGTAGTTGTTGGATGGTGCATGGGAAAAGAAATGGACTTGAATTTTCAACTATTCGAGACTGCCACGCTTTTTATCACTGTGTTAGTAG

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|351057010|gb|FQ448527.1|FQ448527
EST:     TCACAATCGGAGTTGCAATTGGTTCATCTACACAAATAGCAATGTTTGTG                         ATTCCCTTCTGTGTGGTTGTTGGTTGGATTATGGGACAACCAATGGACTTG
genomic: TCACAATCGGAGTTGCAATTGGTTCATCTACACAAATAGCAATGTTTGTGgtaagtcttc ... atgattgcagATTCCCTTCTGTGTGGTTGTTGGTTGGATTATGGGACAACCAATGGACTTG
EST: gi|349830905|gb|FQ418189.1|FQ418189
EST:     TCACAATCGGAGTTGCAATTGGTTCATCTACACAAATAGCAATGTTTGTG                         ATTCCCTTCTGTGTGGTTGTTGGTTGGATTATGGGACAACCAATGGACTTG
genomic: TCACAATCGGAGTTGCAATTGGTTCATCTACACAAATAGCAATGTTTGTGgtaagtcttc ... atgattgcagATTCCCTTCTGTGTGGTTGTTGGTTGGATTATGGGACAACCAATGGACTTG
EST: gi|351033483|gb|FQ462134.1|FQ462134
EST:     TCACAATCGGAGTTGCAATTGGTTCATCTACACAAATAGCAATGTTTGTG                         ATTCCCTTCTGTGTGGTTGTTGGTTGGATTATGGGACAACCAATGGACTTG
genomic: TCACAATCGGAGTTGCAATTGGTTCATCTACACAAATAGCAATGTTTGTGgtaagtcttc ... atgattgcagATTCCCTTCTGTGTGGTTGTTGGTTGGATTATGGGACAACCAATGGACTTG
EST: gi|349830995|gb|FQ418279.1|FQ418279
EST:     TCACAATCGGAGTTGCAATTGGTTCATCTACACAAATAGCAATGTTTGTG                         ATTCCCTTCTGTGTGGTTGTTGGTTGGATTATGGGACAACCAATGGACTTG
genomic: TCACAATCGGAGTTGCAATTGGTTCATCTACACAAATAGCAATGTTTGTGgtaagtcttc ... atgattgcagATTCCCTTCTGTGTGGTTGTTGGTTGGATTATGGGACAACCAATGGACTTG
EST: gi|77581344|gb|DV219604.1|DV219604
EST:     TCACAATCGGAGTTGCAATTGGTTCATCTACACAAATAGCAATGTTTGTG                         ATTCCCTTCTGTGTGGTTGTTGGTTGGATTATGGGACAACCAATGGACTTG
genomic: TCACAATCGGAGTTGCAATTGGTTCATCTACACAAATAGCAATGTTTGTGgtaagtcttc ... atgattgcagATTCCCTTCTGTGTGGTTGTTGGTTGGATTATGGGACAACCAATGGACTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttattagtgaatattgagaggcttaagaatcttgtgctgttgatgattgcagATTCCCTTCTGTGTGGTTGTTGGTTGGATTATGGGACAACCAATGGACTTGAATTTTCAACTCTTTGAGACTGCCACTCTCTTTATCGCGGTGCTAGTAG
                                        tgttgat  putative branch site (score: 4)
          tgaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gggtccttgagatcagttctatgataaatatatagcatggtgtttttcttattagtgaatattgagaggcttaagaatcttgtgctgttgatgattgcagATTCCCTTCTGTGTGGTTGTTGGTTGGATTATGGGACAACCAATGGACTTGAATTTTCAACTCTTTGAGACTGCCACTCTCTTTATCGCGGTGCTAGTAG

- - ccttgag
- - - - - - - - - - - - -aaatata
- - - - - - - - - - - - - - - - - gcatggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttgtgc