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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaattttttttaaaagagacaaaaatgaaatttggtctttaggaccttttttttttttttttctcgtaatgtttctcgactaatttaaaatgtatattagGGGGTTCAATGATGCTGTTAATGGGTTTGCGGATGATGGTTGGTCGCTCATGGGTAGTGATGGGGTGGAGGACGTAACCATTGTGATTAACTCATCTCCA

Basic information

species Vitis vinifera
transcript Vv10s0003g04670.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G423337_T01 (Zea mays), 3'ss of exon 3
----gaattttttttaaaagagacaaaaatgaaatttg-gtctttaggaccttttttttttttttttctcgtaatgtttctcgactaatttaaaatgtatattagGGGGTTCAATGATGCTGTTAATGGGTTTGCGGATGATGGTTGGTCGCTCATGGGTAGTGATGGGGTGGAGGACGTAACCATTGTGATTAACTCATCTCCA
    |   |  | || |      |  |  |   ||||| |   || | |  | ||           || | |     ||||  |||  |||||  |   |   ||||| |||||||||||||| ||||||||| | ||||| |||||||| || ||| | ||||| || |  ||||| || || ||||  || ||||| ||||||
gtttgtggtcgtgttcatgtgttctcatttaccatttgtgctgtttgaatttattgccaggacccatcacatggcacttct-aacttctttaatgtaatttacagGGGTTTCAATGATGCTGTCAATGGGTTTCCAGATGACGGTTGGTCACTGATGAGCAGTGACGGTGCTGAGGATGTTACTATTGCTATCAACTCTTCTCCA

upper sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA05G30000.1 (Glycine max), 3'ss of exon 10
--gaattttttttaaaagagacaaaaatgaaatttggtctttag--gaccttttttttttttttttctcgtaatgtttctcgactaatttaaaatgtatattagGGGGTTCAATGATGCTGTTAATGGGTTTGCGGATGATGGTTGGTCGCTCATGGGTAGTGATGGGGTGGAGGACGTAACCATTGTGATTAACTCATCTCCA
   |     ||| | |   |          | || |   |||     | |  ||| | ||  |     | |  ||  |    | |  |||||||| |   |||| ||||||||||||||||| || ||||||| ||||||||||||||| || ||||||| |||||||||||| || || ||||| |  || ||||| ||||| 
gtaaggccctttcatatttggtggttgcatagttggacatttgattaatcactttgtcttcatcaatccttgctgactaataattt-tttaaaatttgatttagAGGGTTCAATGATGCTGTCAACGGGTTTGTGGATGATGGTTGGTCACTGATGGGTAATGATGGGGTGGAAGATGTGACCATAGCCATAAACTCGTCTCCC

upper sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA08G13110.1 (Glycine max), 3'ss of exon 10
--gaattttttttaaaagagacaaaaatgaaatttggtctttag--gaccttttttttttttttttctcgtaatgtttctcgactaatttaaaatgtatattagGGGGTTCAATGATGCTGTTAATGGGTTTGCGGATGATGGTTGGTCGCTCATGGGTAGTGATGGGGTGGAGGACGTAACCATTGTGATTAACTCATCTCCA
   |     ||| | |   |          | || ||  |||     | |  | | | ||  |     | || ||       | |  |||||||| ||| |||| ||||||||||||||||| || ||||||| |||||||||||||||  | ||||||| ||||||||| || || || ||||| |  || ||||||||||| 
gtaaggccctttcatatttggtggttgcatagttgggcatttgcttaatcactctatcttcatcaatccttattgaccaataatttttttaaaatttat-ttagAGGGTTCAATGATGCTGTCAACGGGTTTGTGGATGATGGTTGGTCATTGATGGGTAATGATGGGGTTGAAGATGTGACCATAGGCATAAACTCATCTCCC

upper sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA09G02750.1 (Glycine max), 3'ss of exon 10
------------------------------------------------------------------------------gaattttttttaaaagagacaaaaatgaaatttggtctt--taggaccttttttttttttttttc------tcgtaatgtttctcgactaatttaaaatgtata--ttagGGGGTTCAATGATGCTGTTAATGGGTTTGCGGATGATGGTTGGTCGCTCATGGGTAGTGATGGGGTGGAGGACGTAACCATTGTGATTAACTCATCTCCA
                                                                              || |   |   |   ||  ||  ||| |   ||  ||||  ||  | |   | || ||  |  ||      || ||||  ||      | ||  ||| || ||   ||||||| || ||||||||||| ||||| ||||  |||||||| ||||| || ||||||| |||||||||||| || || || || |  || ||||||||||||
gtaaggccttagtgtcctttgtatgtcaaaccatgcattgtgcattttaattattggctgggtacttttttttcatgtgattaagtagcagttgattcattaatcattcttattcttgctaaaatccaatcttgttcataatcacaacatcataattattaatattttatcgaaattgcattgtttagGGGCTTTAATGATGCTGTGAATGGATTTGTTGATGATGGCTGGTCACTGATGGGTACTGATGGGGTGGAAGATGTGACAATAGCCATAAACTCATCTCCA

upper sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA15G13640.1 (Glycine max), 3'ss of exon 10
-----------------------------------------------------------------------------------------------gaattttttttaaaagagacaaaaatgaaatttggtctttaggaccttttttttttttttttctcgtaatgtttctcgactaatttaaaatgtat--attagGGGGTTCAATGATGCTGTTAATGGGTTTGCGGATGATGGTTGGTCGCTCATGGGTAGTGATGGGGTGGAGGACGTAACCATTGTGATTAACTCATCTCCA
                                                                                               | | ||| || |  |   |     ||      |    || | | | | |   || |   |   |||||||   |      | ||| ||| || ||   ||||||| || ||||||||||| ||||||||||  |||||||| ||||| || ||||||| |||||| ||||| || || || || |  || ||||||||||||
gtaaggcaggcattaatgtccttggtagttctaacatatgctttgtgcattttagttattgacttggcacattttaaacttgatgtgattaagtagcagtttgttcattaatcattcttattcttgctaaaattcaag-cttgtccattatcactgcatcgtaattgctaagtttttattgaaattgcattccttagGGGCTTTAATGATGCTGTGAATGGGTTTGTTGATGATGGCTGGTCACTGATGGGTACTGATGGAGTGGAAGATGTGACTATAGCCATAAACTCATCTCCA

upper sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT2G34710.1 (Arabidopsis thaliana), 3'ss of exon 9
gaattttttttaaaagagacaaaaatgaaatttggtctttaggaccttttttttttttttttctcgtaatgtttctcgactaatttaaaatgtata-----ttagGGGGTTCAATGATGCTGTTAATGGGTTTGCGGATGATGGTTGGTCGCTCATGGGTAGTGATGGGGTGGAGGACGTAACCATTGTGATTAACTCATCTCCA
                    ||  ||  | |||   ||| |   | || |         |||||  || | ||  || | |  || || ||| ||      | ||||| |||||||||||||||||||| |||| ||||||||| ||||| |  |||||||| ||||| |  ||||| || ||  |  |||| ||||  || || 
------------------gtaagtatctacttta--cttaatagctttatcaccaagaatttcttttattcttattctaattgttcaatatggatgaactttcagGGGTTTCAATGATGCTGTTAATGGTTTTGTGGATGATGGATGGTCACCAATGGGTAGCGATGGTGCAGAGGATGTTACTGTAATGATAAACTTGTCCCCT

upper sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT1G30490.1 (Arabidopsis thaliana), 3'ss of exon 10
gaattttttttaaaagagacaaaaatgaaatttggtctttaggaccttttttttttttttttctcgtaatgtttctcgactaatttaaaatgtatattagGGGGTTCAATGATGCTGTTAATGGGTTTGCGGATGATGGTTGGTCGCTCATGGGTAGTGATGGGGTGGAGGACGTAACCATTGTGATTAACTCATCTCCA
                         | | |  |   ||| |  | |||  |||| |||| |      |   ||  || | |   ||    || |  | ||||| |||||||||||||| ||||| ||||  |||||||| ||||| |  ||| |||||||||| |  |||||  | || ||  |||||||||| ||  | 
------------------------gtaatacatttccttgataagcttagttttattttct----aaagcattgttctaattgcttttcttgaaattcagGGGTTTCAATGATGCTGTAAATGGTTTTGTCGATGATGGATGGTCTCCAATGAGTAGTGATGGAGGAGAGGATATTACGATCATGATTAACTCTTCCTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttttttttttttttctcgtaatgtttctcgactaatttaaaatgtatattagGGGGTTCAATGATGCTGTTAATGGGTTTGCGGATGATGGTTGGTCGCTCATGGGTAGTGATGGGGTGGAGGACGTAACCATTGTGATTAACTCATCTCCA
                                gactaat  putative branch site (score: 2)
                                 actaatttaaaatgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaattttttttaaaagagacaaaaatgaaatttggtctttaggaccttttttttttttttttctcgtaatgtttctcgactaatttaaaatgtatattagGGGGTTCAATGATGCTGTTAATGGGTTTGCGGATGATGGTTGGTCGCTCATGGGTAGTGATGGGGTGGAGGACGTAACCATTGTGATTAACTCATCTCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - -aaaagag
- - - - - - - - - acaaaaa