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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcgtgtgttcagtggttacactgccttattttgagtgtctatatggccaatgatgtactattttccaaaaccattataacaaacatcactcttgtaacagTTGATGGATATTAATGAAAGCCCTGTCTATGTTCTTCTCAATCCGTCAATCAATCATGCACAAAAGGATCTCCCTGTGACTATCTATGAAAGTG

Basic information

species Vitis vinifera
transcript Vv19s0015g01950.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0015g01950.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G080652_T01 (Zea mays), 3'ss of exon 2
gcgtgtgttcagtggttacactgccttattttgagtgtctatatggccaatgatgtac-tattttccaaaaccattataacaaacatc-actcttgtaac-agTTGATGGATATTAATGAAAGCCCTGTCTATGTTCTTCTCAATCCGTCAATCAATCATGCACAAAAGGATCTCCCTGTGACTATCTATGAAAGTG
  | | ||| ||   ||   |||||  | | |     | | | ||  |  ||  |||  ||||      |  |   |||||   | |  | |  | |  | |||||||||||||||| ||||||||||| ||| | ||  | |||||  ||||||| |   | ||||| ||||||||||||||||||||||| ||||
aggagagttgagaaattgt-ctgcc--agtatatacatttgtttgatctgtgtagtatatattcatttgactccacataaccttcttttatttgtatttccagTTGATGGATATTAACGAAAGCCCTGTTTATCTCCTATTAAATCCTACAATCAACCTCTCCCAAAAAGATCTCCCTGTGACTATCTATGAGAGTG

upper sequence: Vv19s0015g01950.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA04G12890.1 (Glycine max), 3'ss of exon 2
-gcgtgtgttcagtggttacactgccttattttgagtgtctatatggccaatgatgtactattttccaaaacc-attataacaaacatcactcttgtaacagTTGATGGATATTAATGAAAGCCCTGTCTATGTTCTTCTCAATCCGTCAATCAATCATGCACAAAAGGATCTCCCTGTGACTATCTATGAAAGTG
  | | ||        || || ||  |||||  ||      |||    ||| | |  |  || ||      |  |||||| |    | | ||  ||||||||||||||||||| |||||||| || || ||||||||||||||||| || ||||||||| | || |||||||| ||||| | ||| | ||||||||
ttcatctgaaattctctttcagtgatttattcagaaatcaaatacattcaa-gttcaagaatctttagtttctgattatatctgg-acctctgctgtaacagTTGATGGATATCAATGAAAGTCCAGTTTATGTTCTTCTCAATCCTTCTATCAATCATTCTCAGAAGGATCTACCTGTCAGTATTTTTGAAAGTG

upper sequence: Vv19s0015g01950.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G47850.1 (Glycine max), 3'ss of exon 2
-gcgtgtgttcagtggttacactgccttattttgagtgtctatatggccaatgatgtactattttccaaaaccattataacaaacatcactcttgtaacagTTGATGGATATTAATGAAAGCCCTGTCTATGTTCTTCTCAATCCGTCAATCAATCATGCACAAAAGGATCTCCCTGTGACTATCTATGAAAGTG
  | | ||        || || ||  |||||  ||      |||    |||        || |||        ||| || |    | | ||  ||||||||||||||||||| |||||||| || || ||||||||||||||||| || ||||| ||| | || |||||||| ||||| | ||| | ||||||||
ttcatctgaaattctcttccagtgatttattcagaagtcgaatacattcaaattcaagttactttagtttctgattttatctgg-acctctgctgtaacagTTGATGGATATCAATGAAAGTCCAGTTTATGTTCTTCTCAATCCTTCTATCAACCATTCTCAGAAGGATCTACCTGTCAGTATTTTTGAAAGTG

upper sequence: Vv19s0015g01950.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT4G26430.1 (Arabidopsis thaliana), 3'ss of exon 2
gcgtgtgttcagtggttacactgccttattttgagtgtctatatggccaatgatgtactattttccaaaaccattataacaaacatcactcttgtaacagTTGATGGATATTAATGAAAGCCCTGTCTATGTTCTTCTCAATCCGTCAATCAATCATGCACAAAAGGATCTCCCTGTGACTATCTATGAAAGTG
  ||| ||   || | |  | ||  ||| | | | | |  ||       | ||| |   ||| | |  |    ||        ||||         |||| ||||||| |||||||||   ||||| ||||||||| | |||||  | |||||||||||||| |||||||| |||||||||||||| ||||| |
--gtgagtagtgtagctttaatgt-ttaatataaat-ttaattgaatttaggat-tctcattgtactgatttgttgaggttttcatct--------acagCTGATGGACATTAATGAATCTCCTGTGTATGTTCTTTTAAATCCTGCTATCAATCATGCACAGAAGGATCTTCCTGTGACTATCTACGAAAGCG

upper sequence: Vv19s0015g01950.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G56280.1 (Arabidopsis thaliana), 3'ss of exon 2
gcgtgtgttcagtggttacactgccttattttgagtgtctatatggccaatgatgtactattttccaaaaccattataacaaacatcactcttg-taacagTTGATGGATATTAATGAAAGCCCTGTCTATGTTCTTCTCAATCCGTCAATCAATCATGCACAAAAGGATCTCCCTGTGACTATCTATGAAAGTG
           |||  | || |||  | | | |  | | | |||     | |||    |  | || ||||   |  |           |||||| | ||||||||||||||| ||||||   ||||| ||||| ||| | || ||  | ||||||||  |||| |||||||| || |||||||| ||||||||||
-----------gtgagtccaatgctctctctagtatttttgtataattga-gat---ttggtctctaaaagtgtggtttttgtgtctgctcttggtgacagTTGATGGATATCAATGAATCTCCTGTTTATGTGCTTTTAAACCCTGCTATCAATCACACACAGAAGGATCTTCCAGTGACTATTTATGAAAGTG

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|110713432|gb|EE089350.1|EE089350
EST:     ACTCCACCGGAAGTGATGCCCAAGAATCAGATATGCATATTCATAAAGCT                         TTGATGGATATTAATGAAAGCCCTGTCTATGTTCTTCTCAATCCGTCAATC
genomic: ACTCCACCGGAAGTGATGCCCAAGAATCAGATATGCATATTCATAAAGCTgtaagttcac ... cttgtaacagTTGATGGATATTAATGAAAGCCCTGTCTATGTTCTTCTCAATCCGTCAATC
EST: gi|71855098|gb|DT004153.1|DT004153
EST:     ACTCCACCGGAAGTGATGCCCAAGAATCAGATATGCATATTCATAAAGCT                         TTGATGGATATTAATGAAAGCCCTGTCTATGTTCTTCTCAATCCGTCAATC
genomic: ACTCCACCGGAAGTGATGCCCAAGAATCAGATATGCATATTCATAAAGCTgtaagttcac ... cttgtaacagTTGATGGATATTAATGAAAGCCCTGTCTATGTTCTTCTCAATCCGTCAATC
EST: gi|26261888|gb|CA812951.1|CA812951
EST:     ACTCCACCGGAAGTGATGCCCAAGAATCAGATATGCATATNCATAAAGCT                         TTGATGGATATAAATGAAAGCCCTGTCTATGTTCTTCTCAATCCGTCAATC
genomic: ACTCCACCGGAAGTGATGCCCAAGAATCAGATATGCATATTCATAAAGCTgtaagttcac ... cttgtaacagTTGATGGATATTAATGAAAGCCCTGTCTATGTTCTTCTCAATCCGTCAATC
EST: gi|71856758|gb|DT005813.1|DT005813
EST:     ACTCCACCGGAAGTGATGCCCAAGAATCAGATATGCATATTCATAAAGCT                         TTGATGGATATTAATGAAAGCCCTGTCTATGTTCTTCTCAATCCGTCAATC
genomic: ACTCCACCGGAAGTGATGCCCAAGAATCAGATATGCATATTCATAAAGCTgtaagttcac ... cttgtaacagTTGATGGATATTAATGAAAGCCCTGTCTATGTTCTTCTCAATCCGTCAATC
EST: gi|110363635|gb|EC927237.1|EC927237
EST:     CATATTCATAAAGCT                         TTGATGGATATTAATGAAAGCCCTGTCTATGTTCTTCTCAATCCGTCAATC
genomic: CATATTCATAAAGCTgtaagttcac ... cttgtaacagTTGATGGATATTAATGAAAGCCCTGTCTATGTTCTTCTCAATCCGTCAATC
EST: gi|110368023|gb|EC931983.1|EC931983
EST:     ACTCCACCGGAAGTGATGCCCAAGAATCAGATATGCATATTCATAAAGCT                         TTGATGGATATTAATGAAAGCCCTGTCTATGTTCTTCTCAATCCGTCAATC
genomic: ACTCCACCGGAAGTGATGCCCAAGAATCAGATATGCATATTCATAAAGCTgtaagttcac ... cttgtaacagTTGATGGATATTAATGAAAGCCCTGTCTATGTTCTTCTCAATCCGTCAATC
EST: gi|110404227|gb|EC968960.1|EC968960
EST:     ACTCCACCGGAAGTGATGCCCAAGAATCAGATATGCATATTCATAAAGCT                         TTGATGGATATTAATGAAAGCCCTGTCTATGTTCTTCTCAATCCGTCAATC
genomic: ACTCCACCGGAAGTGATGCCCAAGAATCAGATATGCATATTCATAAAGCTgtaagttcac ... cttgtaacagTTGATGGATATTAATGAAAGCCCTGTCTATGTTCTTCTCAATCCGTCAATC
EST: gi|349818410|gb|FQ409185.1|FQ409185
EST:     ACTCCACCGGAAGTGATGCCCAAGAATCAGATATGCATATTCATAAAGCT                         TTGATGGATATTAATGAAAGCCCTGTCTATGTTCTTCTCAATCCGTCAATC
genomic: ACTCCACCGGAAGTGATGCCCAAGAATCAGATATGCATATTCATAAAGCTgtaagttcac ... cttgtaacagTTGATGGATATTAATGAAAGCCCTGTCTATGTTCTTCTCAATCCGTCAATC
EST: gi|110684768|gb|EE062427.1|EE062427
EST:     ACTCCACCGGAAGTGATGCCCAAGAATCAGATATGCATATTCATAAAGCT                         TTGATGGATATTAATGAAAGCCCTGTCTATGTTCTTCTCAATCCGTCAATC
genomic: ACTCCACCGGAAGTGATGCCCAAGAATCAGATATGCATATTCATAAAGCTgtaagttcac ... cttgtaacagTTGATGGATATTAATGAAAGCCCTGTCTATGTTCTTCTCAATCCGTCAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccaatgatgtactattttccaaaaccattataacaaacatcactcttgtaacagTTGATGGATATTAATGAAAGCCCTGTCTATGTTCTTCTCAATCCGTCAATCAATCATGCACAAAAGGATCTCCCTGTGACTATCTATGAAAGTG
                            ttataac  putative branch site (score: 2)
                                        tcactctt  putative PPT
                           attataacaaacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcgtgtgttcagtggttacactgccttattttgagtgtctatatggccaatgatgtactattttccaaaaccattataacaaacatcactcttgtaacagTTGATGGATATTAATGAAAGCCCTGTCTATGTTCTTCTCAATCCGTCAATCAATCATGCACAAAAGGATCTCCCTGTGACTATCTATGAAAGTG

- -tgtgttc
- - - - - - - - - cactgcc
- - - - - - - - - - - - - - - -tgagtgt
- - - - - - - - - - - - - - - - - - - - - - - ccaatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaccat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaacat