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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtaaaaatggttgtattcagcattctttggtggcaggattaggtttttctcactgttcttgtcttataatggacgttctgtttctcttatgtgttgcagGTGGACATGATAGTGATAACAGATGGCAGTCGTATTCTTGGTCTGGGTGACCTTGGAGTTCAGGGAATTGGAATTCCTATTGGGAAACTTGATATGTATG

Basic information

species Vitis vinifera
transcript Vv15s0046g03670.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0046g03670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os10g35960.2 (Oryza sativa), 3'ss of exon 4
agtaaaaatggttgtattcagcatt----ctttg-gtggcaggattaggtttttctcactgttcttgtcttataatggacgttctgttt--ctcttatgtgttgcagGTGGACATGATAGTGATAACAGATGGCAGTCGTATTCTTGGTCTGGGTGACCTTGGAGTTCAGGGAATTGGAATTCCTATTGGGAAACTTGATATGTATG
   | ||||  || ||   | ||||    |||   |  |||  ||| | |   | ||    | ||||| ||  |        |||| ||  |  ||   | || ||||| |||||||||||  | || ||||| || |||||||| ||||| ||||| |||||||||||||| || || || ||||| || ||||||||| | ||||
---ataaatatttctacaaaccattgaaacttcatgcagcataattggttccatttc----tgcttgtgttgaacctctgcatctgattggccgttgcttatttcagGTTGACATGATAGTTGTGACTGATGGGAGCCGTATTCTAGGTCTAGGTGATCTTGGAGTTCAGGGCATAGGTATACCTATCGGTAAACTTGATGTTTATG

upper sequence: Vv15s0046g03670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA03G01680.1 (Glycine max), 3'ss of exon 5
-----agtaaaaatggttgtattcagcattctttggtggcaggattaggtttttctcactgttcttgtcttataatggacgttctgtttctcttatgtgttgcagGTGGACATGATAGTGATAACAGATGGCAGTCGTATTCTTGGTCTGGGTGACCTTGGAGTTCAGGGAATTGGAATTCCTATTGGGAAACTTGATATGTATG
       | |   ||||  | ||  |  || ||  |||  |  ||  |    ||     ||||| |   ||||  | |    ||   || |  | | |||||||||| |||||||| ||  |||||||||| ||||| ||||||||  | ||||||||||||||||||||||||||||| || || || ||||||||| ||||||
aattcgatgactttggt-atgttttggtttattgagtgataaaatagg---cttgcagttgttcattcattatgtttggttatcatcttattct-tctgttgcagGTAGACATGATTGTCTTAACAGATGGAAGTCGAATTCTTGGCTTAGGTGACCTTGGAGTTCAGGGAATTGGAATCCCCATAGGAAAACTTGATGTGTATG

upper sequence: Vv15s0046g03670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA07G08110.1 (Glycine max), 3'ss of exon 4
-----agtaaaaatggttgtattcagcattctttggtggcaggattaggtttttctcactgttcttgtcttataatggacgttctgtttctcttatgtgttgcagGTGGACATGATAGTGATAACAGATGGCAGTCGTATTCTTGGTCTGGGTGACCTTGGAGTTCAGGGAATTGGAATTCCTATTGGGAAACTTGATATGTATG
       | |   ||||  | ||  |  |  ||  ||| ||  ||  |    ||   | ||||| |   ||||  | | |  ||   || |  | | |||||||||| |||||||| ||  |||||||||| ||||| ||||||||  | ||||||||||||||||||||||||||||| || || || ||||||||| ||||||
aattccatgactttggt-atgttttggttcattaagtgacaaaatagg---cttgcaattgttcattcattatgtttggctatcatcttattct-tctgttgcagGTAGACATGATTGTCTTAACAGATGGAAGTCGAATTCTTGGCTTAGGTGACCTTGGAGTTCAGGGAATTGGAATCCCCATAGGAAAACTTGATGTGTATG

upper sequence: Vv15s0046g03670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA09G39870.1 (Glycine max), 3'ss of exon 4
agtaaaaatggttgta--ttcagcattctttggtggcaggattag--gtttttctcactgttcttgtcttataatggacgtt-ctgtttctcttatgtgttgcagGTGGACATGATAGTGATAACAGATGGCAGTCGTATTCTTGGTCTGGGTGACCTTGGAGTTCAGGGAATTGGAATTCCTATTGGGAAACTTGATATGTATG
        | |   ||  ||  |   | ||||||     || |||     || |||  ||  ||  | |  || |||   |  || | |   ||   |||| ||||| |||||||| ||  | |||||||| ||||||||||||||  |||||||||||||||||||||| |||||||| ||||| || |||||||| |||||||
-----gccttgccataatttaggagctttttggttcagtgagtagcaaacttgctccttgccctgatttattattggttataactatcttgtttccttgtttcagGTAGACATGATTGTCTTGACAGATGGTAGTCGTATTCTTGGCTTGGGTGACCTTGGAGTTCAGGGCATTGGAATACCTATAGGAAAACTTGACATGTATG

upper sequence: Vv15s0046g03670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA18G46340.1 (Glycine max), 3'ss of exon 4
agtaaaaatggttgta--ttcagcattctttggtggcaggattag--gtttttctcactgttcttgtcttataatggacgttctg-tttctcttatgtgttgcagGTGGACATGATAGTGATAACAGATGGCAGTCGTATTCTTGGTCTGGGTGACCTTGGAGTTCAGGGAATTGGAATTCCTATTGGGAAACTTGATATGTATG
        | | | ||  ||  |   | ||||||     || |||     || ||| |||   |  | |  |  |||   |  |  | ||| ||   |||| ||||| |||||||| ||  | |||||||| ||||||||||||||  |||||||||||||||||||||| |||||||| ||||| || |||||||| |||||| 
----tgccttgctataattttggagctttttggttcagtgagtagcaaacttgctccctggcttcatttatttttggttataataatctcttttccttgtttcaGGTAGACATGATTGTCTTGACAGATGGTAGTCGTATTCTTGGCTTGGGTGACCTTGGAGTTCAGGGCATTGGAATACCTATAGGAAAACTTGACATGTAT-

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|110711032|gb|EE087769.1|EE087769
EST:     AGGATAAAGGAGAGATGATGTCCATGATCTACAACTGGCCAGCTCACCAG                         GTGGACATGATAGTGATAACAGATGGCAGTCGTATTCTTGGTCTGGGTGAC
genomic: AGGATAAAGGAGAGATGATGTCCATGATCTACAACTGGCCAGCTCACCAGgtactgtgtg ... tgtgttgcagGTGGACATGATAGTGATAACAGATGGCAGTCGTATTCTTGGTCTGGGTGAC
EST: gi|110685703|gb|EE062665.1|EE062665
EST:     AGGATAAAGGAGAGATGATGTCCATGATCTACAACTGGCCAGCTCACCAG                         TTGGACATGATAGTGATAACAGATGGCAGTCGTATTCTTGGTCTGGGTGAC
genomic: AGGATAAAGGAGAGATGATGTCCATGATCTACAACTGGCCAGCTCACCAGgtactgtgtg ... tgtgttgcagGTGGACATGATAGTGATAACAGATGGCAGTCGTATTCTTGGTCTGGGTGAC
EST: gi|110711784|gb|EE088657.1|EE088657
EST:     AGGATAAAGGAGAGATGATGTCCATGATCTACAACTGGCCAGCTCACCAG                         GTGGACATGATTGTGATAACAGATGGCAGTCGTATTCTTGGGTCTGGGTGA
genomic: AGGATAAAGGAGAGATGATGTCCATGATCTACAACTGGCCAGCTCACCAGgtactgtgtg ... tgtgttgcagGTGGACATGATAGTGATAACAGATGGCAGTCGTATTCTTGG-TCTGGGTGA
EST: gi|110710958|gb|EE087607.1|EE087607
EST:     AGGATAAAGGAGAGATGATGTCCATGATCTACAACTGGCCAGCTCACCAG                         GTGGACATGATTGTGATAACAGATGGCAGTCGTATTCTTGGTCTGGGTGAA
genomic: AGGATAAAGGAGAGATGATGTCCATGATCTACAACTGGCCAGCTCACCAGgtactgtgtg ... tgtgttgcagGTGGACATGATAGTGATAACAGATGGCAGTCGTATTCTTGGTCTGGGTGAC
EST: gi|110698263|gb|EE075598.1|EE075598
EST:     AGGATAAAGGAGAGATGATGTCCATGATCTACAACTGGCCAGCTCACCAG                         GTGGACATGATAGTGATAACAGATGGCAGTCGTATTCTTGGTCTGGGTGAC
genomic: AGGATAAAGGAGAGATGATGTCCATGATCTACAACTGGCCAGCTCACCAGgtactgtgtg ... tgtgttgcagGTGGACATGATAGTGATAACAGATGGCAGTCGTATTCTTGGTCTGGGTGAC
EST: gi|110711356|gb|EE087746.1|EE087746
EST:     AGGATAAAGGAGAGATGATGTCCATGATCTACAACTGGCCAGCTCACCAG                         GTGGACATGATTGTGATAACAGATGGCAGTCGTATTCTTGGTCTGGGTGAC
genomic: AGGATAAAGGAGAGATGATGTCCATGATCTACAACTGGCCAGCTCACCAGgtactgtgtg ... tgtgttgcagGTGGACATGATAGTGATAACAGATGGCAGTCGTATTCTTGGTCTGGGTGAC
EST: gi|110699671|gb|EE076873.1|EE076873
EST:     AGGATAAAGGAGAGATGATGTCCATGATCTACAACTGGCCAGCTCACCAG                         GTGGACATGATAGTGATAACAGATGGCAGTCGTATTCTTGGTCTGGGTGAC
genomic: AGGATAAAGGAGAGATGATGTCCATGATCTACAACTGGCCAGCTCACCAGgtactgtgtg ... tgtgttgcagGTGGACATGATAGTGATAACAGATGGCAGTCGTATTCTTGGTCTGGGTGAC
EST: gi|110719431|gb|EE094555.1|EE094555
EST:     AGGATAAAGGAGAGATGATGTCCATGATCTACAACTGGCCAGCTCACCAG                         GTGGACATGATTGTGATAACAGATGGCAGTCGTATTCTTGGTCTGGGTGAC
genomic: AGGATAAAGGAGAGATGATGTCCATGATCTACAACTGGCCAGCTCACCAGgtactgtgtg ... tgtgttgcagGTGGACATGATAGTGATAACAGATGGCAGTCGTATTCTTGGTCTGGGTGAC
EST: gi|110712870|gb|EE088292.1|EE088292
EST:     AGGATAAAGGAGAGATGATGTCCATGATCTACAACTGGCCAGCTCACCAG                         GTGGACATGATTGTGATAACAGATGGCAGTCGTATTCTTGGTCTGGGTGAC
genomic: AGGATAAAGGAGAGATGATGTCCATGATCTACAACTGGCCAGCTCACCAGgtactgtgtg ... tgtgttgcagGTGGACATGATAGTGATAACAGATGGCAGTCGTATTCTTGGTCTGGGTGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttctcactgttcttgtcttataatggacgttctgtttctcttatgtgttgcagGTGGACATGATAGTGATAACAGATGGCAGTCGTATTCTTGGTCTGGGTGACCTTGGAGTTCAGGGAATTGGAATTCCTATTGGGAAACTTGATATGTATG
  ttctcac  putative branch site (score: 2)
                               ttctgtttctcttat  putative PPT
                 tcttataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtaaaaatggttgtattcagcattctttggtggcaggattaggtttttctcactgttcttgtcttataatggacgttctgtttctcttatgtgttgcagGTGGACATGATAGTGATAACAGATGGCAGTCGTATTCTTGGTCTGGGTGACCTTGGAGTTCAGGGAATTGGAATTCCTATTGGGAAACTTGATATGTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
-gtaaaaa
- - - - tggttgt
- - - - - - - - - - gcattct
- - - - - - - - - - - - - - - - ggcagga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgtttc