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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagataggataaaattggaaagttatgttttagatctggattttttttctttttataaaagtattttattcacttcttttccatttgatgttctatccagATATTTGGAGGGGTTGGTATTGCTTGTTTGCCATTGGGACTTATATTTTCATTCATTCGGCGTCCCAAGGCTGTTATCACACGTTCACAGTATATCAAG

Basic information

species Vitis vinifera
transcript Vv08s0007g02270.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g02270.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 4
--gagataggataaaattggaaagtta--tgttttagatctggattttttttctttttataaaagtattttattcacttcttttccatttgatgttctatccagATATTTGGAGGGGTTGGTATTGCTTGTTTGCCATTGGGACTTATATTTTCATTCATTCGGCGTCCCAAGGCTGTTATCACACGTTCACAGTATATCAAG
  |   ||| |  || ||| ||  |      |||   |  |  | || |  |    | ||    || | || || ||  |||| | |||   ||||   |  |||||||||| || ||||| ||||||||  | ||||||||||||||||| |||||  | ||||| || || ||||| || ||||| ||||| ||||| |||
ctgtactagaaacaatttgaaatatggatcctttccaacatccaattctgctgcaatcatgctggtttctt-tttacaactttcctattcc-tgtttggt--agATATTTGGTGGTGTTGGAATTGCTTGCCTTCCATTGGGACTTATATTCTCATTTGTCCGGCGCCCAAAAGCTGTCATTACACGCTCACAATATATAAAG

upper sequence: Vv08s0007g02270.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM5G871262_T02 (Zea mays), 3'ss of exon 4
gagataggataaaattggaaagttatgttttagatctggattttttttctttttataaaagtattttattcacttcttttccatttgatgttctatcc---agATATTTGGAGGGGTTGGTATTGCTTGTTTGCCATTGGGACTTATATTTTCATTCATTCGGCGTCCCAAGGCTGTTATCACACGTTCACAGTATATCAAG
    | |  |   |||    | |  |||      ||   ||  | |      || |  |  | || | |     |  |  | ||    | |||| |     |||||||||| || || || ||||| ||  | ||||||||||||||||| |||||  |||||||||| || ||||| || ||||| ||||| ||||| |||
---ttcgcctgccatttagtactcctgtaacttgtcatcatgctgtcatcaattctgcattttttctttcattctgctaactataccttattctttttggtagATATTTGGTGGTGTCGGAATTGCCTGCCTTCCATTGGGACTTATATTCTCATTTGTTCGGCGTCCAAAAGCTGTAATTACACGCTCACAATATATAAAG

upper sequence: Vv08s0007g02270.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G012284_T01 (Zea mays), 3'ss of exon 2
gagataggataaaatt--ggaaagttatgttttagatctggattttttttctttttataaaagtattttattcacttcttt---tccatttgatgttctatccagATATTTGGAGGGGTTGGTATTGCTTGTTTGCCATTGGGACTTATATTTTCATTCATTCGGCGTCCCAAGGCTGTTATCACACGTTCACAGTATATCAAG
  | |    |   |||  | |  | |||    |  | |     | |  |  || |     || | |||  |||| |    |   |  |  |  | || |    |||||||||| || || || ||||| ||  | ||||||||||||||||| |||||  |||| ||||| || ||||| || ||||| ||||| ||||| |||
--gctcacctgtcatttagtactgctataacctgtaaccatgctgtaatcgttct---gcaattttttctttcattctgctaactataccttttctttttggtagATATTTGGTGGTGTCGGAATTGCCTGCCTTCCATTGGGACTTATATTCTCATTTGTTCGTCGTCCAAAAGCTGTAATTACACGCTCACAATATATAAAG

upper sequence: Vv08s0007g02270.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA01G30400.1 (Glycine max), 3'ss of exon 4
gagataggataaaattggaa--agttatgttttagatc-tggattttttttctttttataaaagtattttattcacttcttttccatttgatgttctatccagATATTTGGAGGGGTTGGTATTGCTTGTTTGCCATTGGGACTTATATTTTCATTCATTCGGCGTCCCAAGGCTGTTATCACACGTTCACAGTATATCAAG
 | |  | | ||||   |||  | |||  |   || || |   |  ||||  |||| |||  |||  | |   || || |||||  |      ||| |||||||||||||| || ||||||||||||||| | ||||||||||||||||||||||||||||||||||| |||||||||||||| ||||||||||||||||||
taaactgtacaaaagaagaatcaattacttcccaggtcatatttacttttatttttcatattagtgatattaacaattgttttctttcca---ttcaatccagATATTTGGTGGTGTTGGTATTGCTTGTCTTCCATTGGGACTTATATTTTCATTCATTCGGCGTCCAAAGGCTGTTATCACTCGTTCACAGTATATCAAG

upper sequence: Vv08s0007g02270.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA03G07890.1 (Glycine max), 3'ss of exon 4
gagataggataaaattggaaagttat--gttttagatctggattttttttctttttataaaagtattttattcacttcttttccatttgatgttctatccagATATTTGGAGGGGTTGGTATTGCTTGTTTGCCATTGGGACTTATATTTTCATTCATTCGGCGTCCCAAGGCTGTTATCACACGTTCACAGTATATCAAG
 |  |   ||||  ||  |||||  |   |   || ||   ||||  |||  ||||  | |    |  |||  |||  | ||   |||    ||| |||||||||||||| || ||||||||||||||| | ||||||||||||||||||||||||||||| ||||| |||||||||||||| ||||||||||||||||||
tacttgtaataactttctaaagtcttcaatcccaggtc-acatttacttttatttttcatattagtgatatcaactattgttttctttc-cattcaatccagATATTTGGTGGTGTTGGTATTGCTTGTCTTCCATTGGGACTTATATTTTCATTCATTCGACGTCCAAAGGCTGTTATCACTCGTTCACAGTATATCAAG

upper sequence: Vv08s0007g02270.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA18G43020.1 (Glycine max), 3'ss of exon 4
gagataggataaaattggaaag--ttatgttttagatctggattttttttctttttataaaagtattttattcacttcttttccatttgatgttctatccagATATTTGGAGGGGTTGGTATTGCTTGTTTGCCATTGGGACTTATATTTTCATTCATTCGGCGTCCCAAGGCTGTTATCACACGTTCACAGTATATCAAG
   || |  | |  |    |||  ||   |  || |||   |||   |   | |||    |    |  |||| |    || |    |   ||||| |||||||||||||| || ||||||||||| ||| | ||||| ||||||||||||||||| ||||||||||| |||||||||||||| || |||||||||||||||
-taatggatttatttaaataagcctttcatactaaatc-acattaagtacttcttttcccattcttgatatttaaccattgttttctcactgttcaatccagATATTTGGTGGTGTTGGTATTGCCTGTCTTCCATTAGGACTTATATTTTCATTTATTCGGCGTCCAAAGGCTGTTATCACTCGCTCACAGTATATCAAG

upper sequence: Vv08s0007g02270.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA07G18160.1 (Glycine max), 3'ss of exon 4
gagataggataaaattggaaag--ttatgttttagatc---tggattttttttctttttataaaagtattttattcacttcttttccatttgatgttctatccagATATTTGGAGGGGTTGGTATTGCTTGTTTGCCATTGGGACTTATATTTTCATTCATTCGGCGTCCCAAGGCTGTTATCACACGTTCACAGTATATCAAG
   || |  | |  |  | |||  ||   || || |||   |  |    |  |  |  |||    |   ||||  || |  |||  || |    |||| |||||||||||||| || ||||||||||| ||| | ||||| ||||||||||||||||| ||||||||||| |||||||||||||| || || ||||||||||||
-taatggatttatttaagtaagccttccattctaaatcacattaagcgctagttgtcctattcttgatatttaaccattgttttctcact----gttcaatccagATATTTGGTGGTGTTGGTATTGCCTGTCTTCCATTAGGACTTATATTTTCATTTATTCGGCGTCCAAAGGCTGTTATCACTCGCTCGCAGTATATCAAG

upper sequence: Vv08s0007g02270.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA16G19230.1 (Glycine max), 3'ss of exon 3
gagataggataaaattggaaag--ttatgttttagatc---tggattttttttctttttataaaagtattttattcacttcttttccatttgatgttctatccagATATTTGGAGGGGTTGGTATTGCTTGTTTGCCATTGGGACTTATATTTTCATTCATTCGGCGTCCCAAGGCTGTTATCACACGTTCACAGTATATCAAG
   || |  | |  |  | |||  ||   || || |||   |  |    |  |  |  |||    |   ||||  || |  |||  || |    |||| |||||||||||||| || ||||||||||| ||| | ||||| ||||||||||||||||| ||||||||||| ||||||||||| || || || ||||||||||||
-taatggatttatttaagtaagccttccattctaaatcacattaagcactagttgtcctattcttgatatttaaccattgttttctcact----gttcaatccagATATTTGGTGGTGTTGGTATTGCCTGTCTTCCATTAGGACTTATATTTTCATTTATTCGGCGTCCAAAGGCTGTTATAACTCGCTCGCAGTATATCAAG

upper sequence: Vv08s0007g02270.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 4
gagataggataaaattggaaagttat----gttt-tagatctggattttttttctttttataaaagtattttattcacttcttttccatttgatgttctatccagATATTTGGAGGGGTTGGTATTGCTTGTTTGCCATTGGGACTTATATTTTCATTCATTCGGCGTCCCAAGGCTGTTATCACACGTTCACAGTATATCAAG
     | |||| ||||    |   ||    ||   ||||| |    ||| |   |||   |||||  | | |  | |||  || | |  |  |   | | || |||||||||| || ||||||||||| ||| | ||||| ||||||||   | |||||||  |||| || |||||||||||||| || ||||| ||||| |||
---gcaagatataattctgtatccattgaagtaaatagatgtttgatttatacatttcagtaaaaaaaatctgataactaattgttctctcaaa--tatttctagATATTTGGTGGTGTTGGTATTGCATGTCTACCATTAGGACTTATCACTGCATTCATCAGGCGACCAAAGGCTGTTATCACTCGATCACAATATATAAAG

upper sequence: Vv08s0007g02270.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 4
--------------------------------------------------------------------------------------------gagataggataaaattggaaagttatgttttagatctggattttttttctttttataaaagtattttattcacttcttttccatttgatgttctatccagATATTTGGAGGGGTTGGTATTGCTTGTTTGCCATTGGGACTTATATTTTCATTCATTCGGCGTCCCAAGGCTGTTATCACACGTTCACAGTATATCAAG
                                                                                            | | |    |  | ||  ||   |   |||   | |||   |||||| ||||     |||| ||| |    |  ||||||   |   ||||| ||    ||||||||| || ||||||||||||||  | || ||||| |||||   | |||||||  |||| || |||||||||||||| || ||||||||||| |||
gtatgtacatctctctattaggtgttttgtgttaaaagtttcacctcattgtcttggaaggcatataatctttctcatattaaggcttggttgtgttctcttgcagttaaaagact---tttggtagctgtgattttttgctttcctctaaag-attctgagaaactcttttatctcaaatgttgta----gATATTTGGTGGTGTTGGTATTGCTTGCCTACCCTTGGGCCTTATCACTGCATTCATCAGGCGACCAAAGGCTGTTATCACTCGGTCACAGTATATAAAG

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|110730881|gb|EE108469.1|EE108469
EST:     CAGAATATGTTGTTGCTCTTGCTACCATTGTCGGATCTGTACTTTTCTN-                         ATATTTTGGAAGGGTTG
genomic: CAGAATATGTTGTTGCTCTTGCTACCATTGTCGGATCTGTACTTTTCTCTgtatgttcat ... ttctatccagATATTT-GGAGGGGTTG
EST: gi|71873418|gb|DT022473.1|DT022473
EST:     CAGAATATGTTGTTGCTCTTGCTACCATTGTCGGATCTGTACTTTTCTCT                         ATATTTGGAGGGGTTGGTATTGCTTGTTTGCCATTGGGACTTATATTTTCA
genomic: CAGAATATGTTGTTGCTCTTGCTACCATTGTCGGATCTGTACTTTTCTCTgtatgttcat ... ttctatccagATATTTGGAGGGGTTGGTATTGCTTGTTTGCCATTGGGACTTATATTTTCA
EST: gi|30254542|gb|CB971287.1|CB971287
EST:     CAGAATATGTTGTTGCTCTTGCTACCATTGTCGGATCTGTACTTTTCTCT                         ATATTTGGAGGGGTTGGTATTGCTTGTTTGCCATTGGGACTTATATTTTCA
genomic: CAGAATATGTTGTTGCTCTTGCTACCATTGTCGGATCTGTACTTTTCTCTgtatgttcat ... ttctatccagATATTTGGAGGGGTTGGTATTGCTTGTTTGCCATTGGGACTTATATTTTCA
EST: gi|161716762|gb|FC065585.1|FC065585
EST:     CAGAATATGTTGTTGCTCTTGCTACCATTGTCGGATCTGTACTTTTCTCT                         ATATTTGGAGGGGTGGGTAT
genomic: CAGAATATGTTGTTGCTCTTGCTACCATTGTCGGATCTGTACTTTTCTCTgtatgttcat ... ttctatccagATATTTGGAGGGGTTGGTAT
EST: gi|110372187|gb|EC936337.1|EC936337
EST:     CAGAATATGTTGTTGCTCTTGCTACCATTGTCGGATCTGTACTTTTCTCT                         ATATTTGGAGGGGTTGGTATTGCTTGTTTGCCATTGGGACTTATATTTTCA
genomic: CAGAATATGTTGTTGCTCTTGCTACCATTGTCGGATCTGTACTTTTCTCTgtatgttcat ... ttctatccagATATTTGGAGGGGTTGGTATTGCTTGTTTGCCATTGGGACTTATATTTTCA
EST: gi|110708808|gb|EE086769.1|EE086769
EST:     CAGAATATGTTGTTGCTCTTGCTACCATTGTCAGATCTGTACTTTTCTCT                         ATATTTGAAAGGGTTGGTATTGCCTTGTT-GCAATTGGGACATATATTT
genomic: CAGAATATGTTGTTGCTCTTGCTACCATTGTCGGATCTGTACTTTTCTCTgtatgttcat ... ttctatccagATATTTGGAGGGGTTGGTATTGC-TTGTTTGCCATTGGGACTTATATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctttttataaaagtattttattcacttcttttccatttgatgttctatccagATATTTGGAGGGGTTGGTATTGCTTGTTTGCCATTGGGACTTATATTTTCATTCATTCGGCGTCCCAAGGCTGTTATCACACGTTCACAGTATATCAAG
                                     atttgat  putative branch site (score: 5)
                                             ttctatcc  CT-rich tract
     ttttataaaagtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gagataggataaaattggaaagttatgttttagatctggattttttttctttttataaaagtattttattcacttcttttccatttgatgttctatccagATATTTGGAGGGGTTGGTATTGCTTGTTTGCCATTGGGACTTATATTTTCATTCATTCGGCGTCCCAAGGCTGTTATCACACGTTCACAGTATATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - ggataaa
- - - - - - -attggaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaagta