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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgaacaatagcatgtggagttttcaatactttatagtttctttgatgcgtcactgtaagtttgaatttatatctgtctgattattttcaatttttcagCAAAGAAGGGCTGGTCCCCTTGGTTGAATACAATGAAAAGAAGATCTTTGAGGTGAAACTGAAGGAAATGAAATCTGCATTAACAACCCAGATTGCAGAT

Basic information

species Vitis vinifera
transcript Vv04s0023g00670.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g00670.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os11g21990.1 (Oryza sativa), 3'ss of exon 5
tgtgaacaatagcatgtggagttttcaatactttatagtttctttgatgcgtcactgtaagtttgaatttatatctgtctgattattttcaatttttcagCAAAGAAGGGCTGGTCCCCTTGGTTGAATACAATGAAAAGAAGATCTTTGAGGTGAAACTGAAGGAAATGAAATCTGCATTAACAACCCAGATTGCAGAT
              |  |  ||| |||  | ||| |  |       |   || |    |  ||   | || ||  ||| | |||||  ||   | ||||| |||||||| |||       | ||||| ||||||||||||||||| |||||||| ||||| ||||| || || |   || | |||||   |||    || 
-------------gtaagttgttatcatgattttttgctgaacagaagtagttaaatgatattctgagttctag-tgtttcattatgctc---tcttcagTAAAGAAGGTCTGACAAGTCTTGTTGAGTACAATGAAAAGAAGATGTTTGAGGTTAAACTTAAGGAGATAAAGTTAACACTGACAACAATGATCAATGAA

upper sequence: Vv04s0023g00670.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA09G38530.1 (Glycine max), 3'ss of exon 5
tgtgaacaatagcatgtggagttt--tcaatactttatagtttctttgatgcgtcactgtaagtttgaattt-----atatctgtctgattattttcaatttttcagCAAAGAAGGGCTGGTCCCCTTGGTTGAATACAATGAAAAGAAGATCTTTGAGGTGAAACTGAAGGAAATGAAATCTGCATTAACAACCCAGATTGCAGAT
     | | | | || |  ||||     | ||   | | |||| | | || |   | |||    || | | |     | |  | | | |  ||| | || |||| ||||| ||||| |||||  ||||||| || || ||||||||||| |  |||||||||||||| ||||||||||| ||| | |||||| | ||| |  |||| 
-----atagttggatatttagttagactagtatactgt-gtttttgtcattccctattgttcagttaactatggtggaaacttatgtaac-attgttaactttttagCAAGGAAGGACTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAAATTTTGAGGTGAAACTTAAGGAAATGAAGTCTTCTTTAACAGCACAGTTAACAGAC

upper sequence: Vv04s0023g00670.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA18G47780.1 (Glycine max), 3'ss of exon 5
tgtgaacaatagcatgtggagttt--tcaatactttatagtttctttgatgcgtcactgtaagtttgaatttat----atctgtctgattattttcaatttttcagCAAAGAAGGGCTGGTCCCCTTGGTTGAATACAATGAAAAGAAGATCTTTGAGGTGAAACTGAAGGAAATGAAATCTGCATTAACAACCCAGATTGCAGAT
     | | | | || |  ||||     | ||   | | |||| | | || |   | |||    || | | |      | ||     || ||| | || |||| ||||| |||||  ||||  ||||||| || || ||||||||||| || |||||||||||||| ||||||||||| ||| | |||||| | |||||  |||| 
-----atagttggatatttagttagactagtatactgt-gtttttgtcattccctattgttcagttaactatgatggaaactaatatatcattgttaactttttagCAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGAGGTGAAACTTAAGGAAATGAAGTCTTCTTTAACAGCACAGATAACAGAG

upper sequence: Vv04s0023g00670.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G65220.1 (Arabidopsis thaliana), 3'ss of exon 5
tgtgaacaatagcatgtggagttttcaatactttatagtttctttgatgcgtcactgtaagtttgaattt---atatctgtctgattatt--ttcaatttttcagCAAAGAAGGGCTGGTCCCCTTGGTTGAATACAATGAAAAGAAGATCTTTGAGGTGAAACTGAAGGAAATGAAATCTGCATTAACAACCCAGATTGCAGAT
        ||    | |    || ||| |  | | |  | ||| || |   | | ||||  | | || ||   |||||||    | | ||  |||   |||| || || | |||  ||    |  |||| || |||||||||| ||| || ||||||||||| ||||||||||| ||| | |   | || | |||  |  |||| 
---ttctgattctgtattcgattatcacttgtcttt--tatctctgctttcttattgtatatgtaaaattgatatatctgctatacttttccttctgattttaagTAAGGCAGGATTGACAGCTCTGGTAGAGTACAATGAAAGGAAAATATTTGAGGTGAAGCTGAAGGAAATCAAAGCGGTCCTTACGAGCCAAGTGACAGAG

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|27580317|gb|CB003012.1|CB003012
EST:     TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAGGTTTCTCTGAGCATTTCAC                         CAAAGAAGGGCTGGTCCCCTTGGTTGAATACAATGAAAAGAAGATCTTTGA
genomic: TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAGGTTTCTCTGAGCATTTCACgtgagtgttt ... aatttttcagCAAAGAAGGGCTGGTCCCCTTGGTTGAATACAATGAAAAGAAGATCTTTGA
EST: gi|110721235|gb|EE098001.1|EE098001
EST:     TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAGGTTTCTCTGAGCATTTCAC                         -AAAGAAGGGCTGGTCCCCTTGGTTGAAT-CAATGAAAAGA
genomic: TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAGGTTTCTCTGAGCATTTCACgtgagtgttt ... aatttttcagCAAAGAAGGGCTGGTCCCCTTGGTTGAATACAATGAAAAGA
EST: gi|351054991|gb|FQ440330.1|FQ440330
EST:     TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAGGTTTCTCTGAGCATTTCAC                         CAAAGAAGGGCTGGTCCCCTTGGTTGAATACAATGAAAA
genomic: TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAGGTTTCTCTGAGCATTTCACgtgagtgttt ... aatttttcagCAAAGAAGGGCTGGTCCCCTTGGTTGAATACAATGAAAA
EST: gi|351032388|gb|FQ461641.1|FQ461641
EST:     TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAGGTTTCTCTGAGCATTTCAC                         CAAAGAAAGGCTGGTCCCCTTGGTTGAATACAAT
genomic: TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAGGTTTCTCTGAGCATTTCACgtgagtgttt ... aatttttcagCAAAGAAGGGCTGGTCCCCTTGGTTGAATACAAT
EST: gi|110730299|gb|EE107223.1|EE107223
EST:     TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAAGTTTCTCTGAGCATTTCAC                         CAAAGAGGGGCTGGGTCCC-TTGGTTGAAATACA-TGAAAAAGA-GATCTT
genomic: TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAGGTTTCTCTGAGCATTTCACgtgagtgttt ... aatttttcagCAAAGAAGGGCTGG-TCCCCTTGGTTGAA-TACAATGAAAA-GAAGATCTT
EST: gi|351026516|gb|FQ428528.1|FQ428528
EST:     TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAGGTTTCTCTGAGCATTTCAC                         CAAAGAAGGGCTGGTCCCCTTGGTTGAATAACA-TGAAAAGAAGATCTTTG
genomic: TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAGGTTTCTCTGAGCATTTCACgtgagtgttt ... aatttttcagCAAAGAAGGGCTGGTCCCCTTGGTTGAATA-CAATGAAAAGAAGATCTTTG
EST: gi|33407242|gb|CF212869.1|CF212869
EST:     TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAGGTTTCTCTGAGCATTTCAC                         CAAAGAAGGGCTGGTCCCCTTGGTTGAATACAATGAAAAGAAGATCTTTGA
genomic: TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAGGTTTCTCTGAGCATTTCACgtgagtgttt ... aatttttcagCAAAGAAGGGCTGGTCCCCTTGGTTGAATACAATGAAAAGAAGATCTTTGA
EST: gi|110732894|gb|EE108581.1|EE108581
EST:     TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAGGTTTCTCTGAGCATTTCAC                         CAAAGAAGGGCTGGTCCCCTTGGTTGAATACAATGAAAAGAAGATCTTTGA
genomic: TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAGGTTTCTCTGAGCATTTCACgtgagtgttt ... aatttttcagCAAAGAAGGGCTGGTCCCCTTGGTTGAATACAATGAAAAGAAGATCTTTGA
EST: gi|349829918|gb|FQ422231.1|FQ422231
EST:     TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAGGTTTCTCTGAGCATTTCAC                         CAAAGAAGGGCTGGTCCCCTTGGTTGAATACAATGAAAAGAAGATCTTTGA
genomic: TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAGGTTTCTCTGAGCATTTCACgtgagtgttt ... aatttttcagCAAAGAAGGGCTGGTCCCCTTGGTTGAATACAATGAAAAGAAGATCTTTGA
EST: gi|34542615|gb|CF510847.1|CF510847
EST:     TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAGGTTTCTCTGAGCATTTCAC                         CAAAGAAGGGCTGGTCCCCTTGGTTGAATACAATGAAAAGAAGATCTTTGA
genomic: TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAGGTTTCTCTGAGCATTTCACgtgagtgttt ... aatttttcagCAAAGAAGGGCTGGTCCCCTTGGTTGAATACAATGAAAAGAAGATCTTTGA
EST: gi|110700927|gb|EE078011.1|EE078011
EST:     TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAGGTTTCTCTGAGCATTTCAC                         CAAAGAAAGGCTGATCCCC
genomic: TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAGGTTTCTCTGAGCATTTCACgtgagtgttt ... aatttttcagCAAAGAAGGGCTGGTCCCC
EST: gi|110417271|gb|EC983312.1|EC983312
EST:     TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAGGTTTCTCTGAGCATTTCAC                         CAAAGAAGGGCTGGTCCCCTTGGTTGAATACAATGAAAAGAAGATCTTTGA
genomic: TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAGGTTTCTCTGAGCATTTCACgtgagtgttt ... aatttttcagCAAAGAAGGGCTGGTCCCCTTGGTTGAATACAATGAAAAGAAGATCTTTGA
EST: gi|110688422|gb|EE066958.1|EE066958
EST:     TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAGGTTTCTCTGAGCATTTCAC                         CAAAGAAGGGCTGGTCCCCTTGGTTGAATACAATGAAAAGAAGATCTTTGA
genomic: TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAGGTTTCTCTGAGCATTTCACgtgagtgttt ... aatttttcagCAAAGAAGGGCTGGTCCCCTTGGTTGAATACAATGAAAAGAAGATCTTTGA
EST: gi|110685192|gb|EE063331.1|EE063331
EST:     TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAGGTTTCTCTGAGCATTTCAC                         CAAAGAAGGGCTGGTCCCCTTGGGTGAAATACA-TGAAA-GAAGATCTTTG
genomic: TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAGGTTTCTCTGAGCATTTCACgtgagtgttt ... aatttttcagCAAAGAAGGGCTGGTCCCCTTGGTTGAA-TACAATGAAAAGAAGATCTTTG
EST: gi|110715301|gb|EE093198.1|EE093198
EST:     TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAGGTTTCTCTGAGCATTTCAC                         CAAAGAAGGGCTGGTCCCCTTGGTTGAATACAATGAAAAGAAGATCTTTGA
genomic: TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAGGTTTCTCTGAGCATTTCACgtgagtgttt ... aatttttcagCAAAGAAGGGCTGGTCCCCTTGGTTGAATACAATGAAAAGAAGATCTTTGA
EST: gi|351046957|gb|FQ454567.1|FQ454567
EST:     TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAAGTTTCTCTGAGCATTTCAC                         CAAAGAAGGGCTGG
genomic: TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAGGTTTCTCTGAGCATTTCACgtgagtgttt ... aatttttcagCAAAGAAGGGCTGG
EST: gi|294964249|gb|GW838052.1|GW838052
EST:     TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAGGTTTCTCTGAGCATTTCAC                         CAAAGAAGGGCTGGTCCCCTTGGTTGAATACAATGAAAAGAAGATCTTTGA
genomic: TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAGGTTTCTCTGAGCATTTCACgtgagtgttt ... aatttttcagCAAAGAAGGGCTGGTCCCCTTGGTTGAATACAATGAAAAGAAGATCTTTGA
EST: gi|110699539|gb|EE076636.1|EE076636
EST:     TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAGGTTTCTCTGAGCATTTCAC                         CAAAGAAGGGCTGGTCCCCTTGGTTGAATANCA-TGAAAAGAAGATCTTTG
genomic: TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAGGTTTCTCTGAGCATTTCACgtgagtgttt ... aatttttcagCAAAGAAGGGCTGGTCCCCTTGGTTGAATA-CAATGAAAAGAAGATCTTTG
EST: gi|349811233|gb|FQ406221.1|FQ406221
EST:     TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAGGTTTCTCTGAGCATTTCAC                         CAAAGAAGGGCTGGTCC
genomic: TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAGGTTTCTCTGAGCATTTCACgtgagtgttt ... aatttttcagCAAAGAAGGGCTGGTCC
EST: gi|110689548|gb|EE065870.1|EE065870
EST:     TCTTCCCTTCTGCTAAGCGTTCTGCTGAANGGTT-CTCTGAGCATTTCAC                         CAAAGAAGGGCTGGTCCCCCTTGG
genomic: TCTTCCCTTCTGCTAAGCGTTCTGCTGAA-GGTTTCTCTGAGCATTTCACgtgagtgttt ... aatttttcagCAAAGAAGGGCTGGTCCCC-TTGG
EST: gi|33404953|gb|CF210580.1|CF210580
EST:     TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAGGTTTCTCTGAGCATTTCAC                         CAAAAGAAGGGCTGGTCCCCTTGGTTGAATACAAT
genomic: TTCTTCCCTTCTGCTAAGCGTTCTGCTGAAGGTTTCTCTGAGCATTTCACgtgagtgttt ... aatttttcagCAAA-GAAGGGCTGGTCCCCTTGGTTGAATACAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgcgtcactgtaagtttgaatttatatctgtctgattattttcaatttttcagCAAAGAAGGGCTGGTCCCCTTGGTTGAATACAATGAAAAGAAGATCTTTGAGGTGAAACTGAAGGAAATGAAATCTGCATTAACAACCCAGATTGCAGAT
                               gtctgat  putative branch site (score: 4)
                                               tttttc  putative PPT
                                  tgattattttcaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgaacaatagcatgtggagttttcaatactttatagtttctttgatgcgtcactgtaagtttgaatttatatctgtctgattattttcaatttttcagCAAAGAAGGGCTGGTCCCCTTGGTTGAATACAATGAAAAGAAGATCTTTGAGGTGAAACTGAAGGAAATGAAATCTGCATTAACAACCCAGATTGCAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - aacaata
- - - - - - catgtgg
- - - - - - - - - - - - - - - - - - - - - -ttgatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - cactgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtctga