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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttatcatgttcacttgctcttgttcattctttcgtgtgctgcaacacttgtgctttcttgtgcagaattaggttttaattgttggataatgtgcttgcagCTGGACTTTCAGCTTCCTTCTCGTTTTGATTTGTCTTACTCAGCTGAGGATGAAGCTAAGAGGGAGAGACCTGTCATGATACACCGAGCCATCCTAGGGT

Basic information

species Vitis vinifera
transcript Vv01s0026g00340.t01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0026g00340.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA01G03930.1 (Glycine max), 3'ss of exon 15
gtttatcatgttcacttgctcttgttcattctttcgtgtgctgcaacacttgtgctttcttgtgcagaattaggttttaattgttggataatgtgcttgcagCTGGACTTTCAGCTTCCTTCTCGTTTTGATTTGTCTTACTCAGCTGAGGATGAAGCTAAGAGGGAGAGACCTGTCATGATACACCGAGCCATCCTAGGGT
||||      ||||  ||   ||      || |||   || | ||    || ||  |   | | |||  | | | ||  ||   ||  |  | ||||||||||| ||||| |||||||||  ||||||| | |||   | |||||||||||||||||| || |  ||||||||||| ||||||||| ||||||||||||| |
gtttgcacctttcagctggattt------tcattcacatgattcag---ttttgaataacttttcagc-tgatggttggatgaatg--tggt-tgcttgcagCTTGACTTCCAGCTTCCTGATCGTTTTAAGTTGGAATTCTCAGCTGAGGATGAAGCCAAAATTGAGAGACCTGTAATGATACACAGAGCCATCCTAGGAT

upper sequence: Vv01s0026g00340.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA02G03750.1 (Glycine max), 3'ss of exon 15
gtttatcatgttcacttgctcttgttcattctttcgtgtgctgcaacacttgtgctttcttgtgcagaattaggttttaattgttggataatgtgcttgcagCTGGACTTTCAGCTTCCTTCTCGTTTTGATTTGTCTTACTCAGCTGAGGATGAAGCTAAGAGGGAGAGACCTGTCATGATACACCGAGCCATCCTAGGGT
||||    ||||||  |    |||  |||||  | |  |       || || ||  |   | | |||     ||||  |    |  | |    ||| ||||||| ||||| |||||||||  ||||||| | |||   | |||||||||||||||||| || |  ||||||||||| ||||||||| ||||||| ||||| |
gtttgcactgttcagctagatttg--cattcacttgatt-------cagttttgaataacttttcagctgatggttggatgaatctggt----tgcctgcagCTTGACTTCCAGCTTCCTGATCGTTTTAAGTTGGAATTCTCAGCTGAGGATGAAGCCAAAATTGAGAGACCTGTAATGATACACAGAGCCATTCTAGGAT
















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|30325956|gb|CD009218.1|CD009218
EST:     TTAGTGTTTCTGATGCATTAAGTAGGAAGTTCCAGTGTGCAACATTACAG                         CTGGACTTTCAGCTTCCTTCCCGTTTTGATTTGTCTTACTCAGCTGAGGAT
genomic: TTAGTGTTTCTGATGCATTAAGTAGGAAATTCCAGTGTGCAACATTACAGgtttatcatg ... gtgcttgcagCTGGACTTTCAGCTTCCTTCTCGTTTTGATTTGTCTTACTCAGCTGAGGAT
EST: gi|30325105|gb|CD008367.1|CD008367
EST:     TTAGTGTTTCTGATGCATTAAGTAGGAAGTTCCAGTGTGCAACATTACAG                         CTGGACTTTCAGCTTCCTTCCCGTTTTGATTTGTCTTACTCAGCTGAGGAT
genomic: TTAGTGTTTCTGATGCATTAAGTAGGAAATTCCAGTGTGCAACATTACAGgtttatcatg ... gtgcttgcagCTGGACTTTCAGCTTCCTTCTCGTTTTGATTTGTCTTACTCAGCTGAGGAT
EST: gi|32268540|gb|CD717699.1|CD717699
EST:     TTAGTGTTTCTGATGCATTAAGTAGGAAGTTCCAGTGTGCAACATTACAG                         CTGGACTTTCAGCTTCCTTCCCGTTTTGATTTGTCTTACTCAGCTGAGGAT
genomic: TTAGTGTTTCTGATGCATTAAGTAGGAAATTCCAGTGTGCAACATTACAGgtttatcatg ... gtgcttgcagCTGGACTTTCAGCTTCCTTCTCGTTTTGATTTGTCTTACTCAGCTGAGGAT
EST: gi|30323442|gb|CD006704.1|CD006704
EST:     TTAGTGTTTCTGATGCATTAAGTAGGAAGTTCCAGTGTGCAACATTACAG                         CTGGACTTTCAGCTTCCTTCCCGTTTTGATTTGTCTTACTCAGCTGAGGAT
genomic: TTAGTGTTTCTGATGCATTAAGTAGGAAATTCCAGTGTGCAACATTACAGgtttatcatg ... gtgcttgcagCTGGACTTTCAGCTTCCTTCTCGTTTTGATTTGTCTTACTCAGCTGAGGAT
EST: gi|32249386|gb|CD715205.1|CD715205
EST:     TTAGTGTTTCTGATGCATTAAGTAGGAAGTTCCAGTGTGCAACATTACAG                         CTGGACTTTCAGCTTCCTTCCCGTTTTGATTTGTCTTACTCAGCTGAGGAT
genomic: TTAGTGTTTCTGATGCATTAAGTAGGAAATTCCAGTGTGCAACATTACAGgtttatcatg ... gtgcttgcagCTGGACTTTCAGCTTCCTTCTCGTTTTGATTTGTCTTACTCAGCTGAGGAT
EST: gi|22011637|gb|BQ796671.1|BQ796671
EST:     TTAGTGTTTCTGATGCATTAAGTAGGAAGTTCCAGTGTGCAACATTACAG                         CTGGACTTTCAGCTTCCTTCCCGTTTTGATTTGTCTTACTCAGCTGAGGAT
genomic: TTAGTGTTTCTGATGCATTAAGTAGGAAATTCCAGTGTGCAACATTACAGgtttatcatg ... gtgcttgcagCTGGACTTTCAGCTTCCTTCTCGTTTTGATTTGTCTTACTCAGCTGAGGAT
EST: gi|110360907|gb|EC924350.1|EC924350
EST:     TTAGTGTTTCTGATGCATTAAGTAGGAAATTCCAGTGTGCAACATTACAG                         CTGGACTTTCAGCTTCCTTCTTGTTTTGATTTGTCTTACTCAGCTGAGGAT
genomic: TTAGTGTTTCTGATGCATTAAGTAGGAAATTCCAGTGTGCAACATTACAGgtttatcatg ... gtgcttgcagCTGGACTTTCAGCTTCCTTCTCGTTTTGATTTGTCTTACTCAGCTGAGGAT
EST: gi|22011184|gb|BQ796218.1|BQ796218
EST:     TGCATTAAGTAGGAAATTCCAGTGTGCAACATTACAG                         CTGGACTTTCAGCTTCCTTCTCGTTTTGATTTGTCTTACTCAGCTGAGGAT
genomic: TGCATTAAGTAGGAAATTCCAGTGTGCAACATTACAGgtttatcatg ... gtgcttgcagCTGGACTTTCAGCTTCCTTCTCGTTTTGATTTGTCTTACTCAGCTGAGGAT
EST: gi|156735898|gb|EV240019.1|EV240019
EST:     TAGTGTTTCTGATGCATTAAGTAGGAAGTTCCCGTGTGCAAACATTACAG                         CTGGACTTTTCAGCTT
genomic: TAGTGTTTCTGATGCATTAAGTAGGAAATTCCAGTGTGCAA-CATTACAGgtttatcatg ... gtgcttgcagCTGGACTTT-CAGCTT
EST: gi|30327091|gb|CD010353.1|CD010353
EST:     TTAGTGTTTCTGATGCATTAAGTAGGAAGTTCCAGTGTGCAACATTACAG                         CTGGACTTTCAGCTTCCTTCCCGTTTTGATTTGTCTTACTCAGCTGAGGAT
genomic: TTAGTGTTTCTGATGCATTAAGTAGGAAATTCCAGTGTGCAACATTACAGgtttatcatg ... gtgcttgcagCTGGACTTTCAGCTTCCTTCTCGTTTTGATTTGTCTTACTCAGCTGAGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttgtgctttcttgtgcagaattaggttttaattgttggataatgtgcttgcagCTGGACTTTCAGCTTCCTTCTCGTTTTGATTTGTCTTACTCAGCTGAGGATGAAGCTAAGAGGGAGAGACCTGTCATGATACACCGAGCCATCCTAGGGT
                           ttttaat  putative branch site (score: 3)
                    aattaggttttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttatcatgttcacttgctcttgttcattctttcgtgtgctgcaacacttgtgctttcttgtgcagaattaggttttaattgttggataatgtgcttgcagCTGGACTTTCAGCTTCCTTCTCGTTTTGATTTGTCTTACTCAGCTGAGGATGAAGCTAAGAGGGAGAGACCTGTCATGATACACCGAGCCATCCTAGGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG