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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagttttcttttttagaacttaatcatcactaactgatccataaataggattattttttaagccttttatgaatataatcttaatgcttttacttctacttcttcctgatataatagatcgttggtttcattttctagGCAGAAAATCTTATGCTGGAGAGAGGAGAAAATAAAGAG

Basic information

species Vitis vinifera
transcript Vv04s0008g06040.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g06040.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM5G836910_T01 (Zea mays), 3'ss of exon 3
gtcagttttcttttttagaacttaatcatcactaactgatccataaataggattattttttaagccttttatgaatataatcttaatgcttttacttctacttcttcctgatataatagatcgttggtttcattttctagGCAGAAAATCTTATGCTGGAGAGAGGAGAAAATAAAGAG
                                                            | |||||  |  |||    |  |||      ||| |  | |   |||||| | | ||      ||       || | ||||| |||||||||||| |||||| ||||||||| ||||||
-----------------------------------------------------------gtgagcctaatcggaagcagaattta-----cttaataatccaggttcctgttttcatgttctcttttgcatgttatatagGCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG

upper sequence: Vv04s0008g06040.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA14G13480.2 (Glycine max), 3'ss of exon 3
----------gtcagttt---tcttttttagaacttaatcatcactaactgat-------ccataaataggattattttttaagcct--tttatgaatataatcttaa---tgcttttacttctacttcttcctgatataatagatcgttggtttcattttctagGCAGAAAATCTTATGCTGGAGAGAGGAGAAAATAAAGAG
           | | |||   | | |  |   |  | |    | |||  |           | |   |    ||   |  |||   |  || ||||  | || |||||   | |||||   |  | ||  | ||||| ||   ||   |   ||   |||  |||||||| |||||||||||||||||||| || || ||||||
gtctttgttccttactttatgtgtctgctgtgatctgagtgcccctagtttgcatagttctcctgtcttatgtttgctcctaattttgcttcatgatcacaaacttaagactacttttggattgagttaatgctgatttagatgaaattc--ttatttttcttagGCAGAGAATCTTATGCTGGAGAGAGGGGATAACAAAGAG

upper sequence: Vv04s0008g06040.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA17G33050.4 (Glycine max), 3'ss of exon 3
------------------gtcagttttctttt-ttagaacttaatcatcactaactgatc-cataaataggattattttttaagcct--tttatgaatataatcttaa--tgcttttacttctacttcttcctgatataatagatcgttggtttcattttctagGCAGAAAATCTTATGCTGGAGAGAGGAGAAAATAAAGAG
                   |  || |||| |  || ||  ||    |      | |  || | |   |    ||  ||  |||   |  || |||   | || | ||   |  ||||   |  | ||  |  |||| ||   ||   |    |||  ||| |||||||| |||||||||||||||||||| || || ||||||
gtctttgttccgtattttatgtgtcttctgtgatttgagtttccctagtttgcattattctcctgtctcatgtttgttcctaattttgcttcatgttcacaaacctagactatttttggattcagttaatgttgatttagatgaaattcttattc--tttttagGCAGAGAATCTTATGCTGGAGAGAGGGGATAACAAAGAG

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|294965358|gb|GW837073.1|GW837073
EST:     CCTACCGAACAGAAGAACTCCAACCTTATGTGCTTAATGTTGTCAAGAAG                         GCAGAAAATCTTATGCTGGAGAGAGGAGAAAATAAAGAG
genomic: CCTACCGAACAGAAGAACTCCAACCTTATGTGCTTAATGTTGTCAAGAAGgtcagttttc ... cattttctagGCAGAAAATCTTATGCTGGAGAGAGGAGAAAATAAAGAG
EST: gi|161712612|gb|FC062214.1|FC062214
EST:     CCTACCGAACAGAAGAACTCCAACCTTATGTGCTTAATGTTGTCAAGAAG                         GCAGAAAATCTTATGCTGGAGAGAGGAGAAAATAAAGAG
genomic: CCTACCGAACAGAAGAACTCCAACCTTATGTGCTTAATGTTGTCAAGAAGgtcagttttc ... cattttctagGCAGAAAATCTTATGCTGGAGAGAGGAGAAAATAAAGAG
EST: gi|352787010|gb|FQ476043.1|FQ476043
EST:     CCTACCGAACAGAAGAACTCCAACCTTATGTGCTTAATGTTGTCAAGAAG                         GCAGAAAATCTTATGCTGGAGAGAGGAGAAAATAAAGAG
genomic: CCTACCGAACAGAAGAACTCCAACCTTATGTGCTTAATGTTGTCAAGAAGgtcagttttc ... cattttctagGCAGAAAATCTTATGCTGGAGAGAGGAGAAAATAAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcttttacttctacttcttcctgatataatagatcgttggtttcattttctagGCAGAAAATCTTATGCTGGAGAGAGGAGAAAATAAAGAG
                    tcctgat  putative branch site (score: 3)
                                          tttcattttct  putative PPT
                         atataatagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagttttcttttttagaacttaatcatcactaactgatccataaataggattattttttaagccttttatgaatataatcttaatgcttttacttctacttcttcctgatataatagatcgttggtttcattttctagGCAGAAAATCTTATGCTGGAGAGAGGAGAAAATAAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA