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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtatccacttgttaagtagtcatttacttgttttgggaaatgcaattcaagcttttgtattaaaccctgtagacattggttaaaacttggactgctgcagGTTCATCTTATTGAGGGCATCATTGATCAAGTTGAAGGGACAGTTCATGTGTCGTGGGTGCAGCCAAGAGTTTTGGGTATTCCACAGATCAAATCGTTGC

Basic information

species Vitis vinifera
transcript Vv02s0012g02660.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0012g02660.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G083076_T01 (Zea mays), 3'ss of exon 5
-gtatccacttgttaagtagtcatttacttgttttgggaaatgcaattcaagcttttgtattaaaccctgtagacattggttaaaacttggact--gctgcagGTTCATCTTATTGAGGGCATCATTGATCAAGTTGAAGGGACAGTTCATGTGTCGTGGGTGCAGCCAAGAGTTTTGGGTATTCCACAGATCAAATCGTTGC
||| | | ||| | | || | || | | | | || | | | | | || ||| | |||||||||||||||||||||| || |||||| |||| || | ||||||||||| |||||||| ||||| ||||| | || || |||||| | || | ||||
tgtaatc-ttggtttgacgtgtttgtggttccatcatttcatatgact--gccctacgtctggcaatccatttgtaacatttctgctttgtttttaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTTTCGTGGGTCCAGCCCAGAGTGCTTGGAATCCCACAGGTTAAGGCTTTGC

upper sequence: Vv02s0012g02660.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM5G868757_T04 (Zea mays), 3'ss of exon 6
---gtatccacttgttaagtagtcatttacttgttttgggaaatg-caattcaagcttttgtattaaaccctgtagacattggttaaaacttggactgctgcagGTTCATCTTATTGAGGGCATCATTGATCAAGTTGAAGGGACAGTTCATGTGTCGTGGGTGCAGCCAAGAGTTTTGGGTATTCCACAGATCAAATCGTTGC
|| | || | | || | | | || | | || | | | ||| | || | | || | | | | |||||||||||||||||||||| || |||||| |||| || | |||||||| || || ||||| ||||| ||||| | || ||||||||| | || | ||||
tgagtctttggttttgacgtgtttgtgtttccattgtttcatttgactgccttgcgtctggtaatccacttgtaacatttttgctttgtttcaaa----tgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTATCATGGGTCCAGCCTAGAGTGCTTGGAATTCCACAGGTTAAGGCTTTGC

upper sequence: Vv02s0012g02660.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA09G34310.1 (Glycine max), 3'ss of exon 5
------gtatccacttgttaagtagtcatttacttgttttgggaaatgcaattcaagcttttgtattaaaccctgtagacattggttaaaacttggactgctgcagGTTCATCTTATTGAGGGCATCATTGATCAAGTTGAAGGGACAGTTCATGTGTCGTGGGTGCAGCCAAGAGTTTTGGGTATTCCACAGATCAAATCGTTGC
|||| | | || || | | || || || | | || ||| || ||||| | | | | || | | | ||||||||||| |||||||| || |||||||||||||| || ||||| ||||| || |||||||||||||||||| ||||||||| |||||||||||| || |
ttttgaatatctgcat-ttgagaacttgatt-tttattgtcattgaggctggacaa--caccgtcttaaaatttaaggcttgtaactgaattctt--ttattacagGTTCATCTAATTGAGGGTATAATTGATCAAGTTGAGGGCACAGTGCATGTTTCCTGGGTGCAGCCAAGAGTTCTGGGTATTCAACAGATCAAATCCTTAC

upper sequence: Vv02s0012g02660.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA01G01460.1 (Glycine max), 3'ss of exon 5
gtatccacttgttaagtagtcatttacttgttttggga--aatgcaattcaagcttttgtattaaaccctgtagacattggttaaaacttggactgctgcagGTTCATCTTATTGAGGGCATCATTGATCAAGTTGAAGGGACAGTTCATGTGTCGTGGGTGCAGCCAAGAGTTTTGGGTATTCCACAGATCAAATCGTTGC
|||| || | | ||||| || | | || |||| | ||||| | || | | || || ||||||||||||| |||||||| || |||||||||||||| || ||||| || || || |||||||||||||||||| ||||||||| |||||||||||| || |
-tatcttttttgaatttctgcatttgagaacttgagttttattgtcattcttaacaacattttaaaatttaaagcttgtaagtgaattttttga-attgcagGTTCATCTAATTGAGGGTATAATTGATCAAGTTGAGGGCACAGTCCACGTTTCTTGGGTGCAGCCAAGAGTTCTGGGTATTCAACAGATCAAATCCTTAC

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|110694606|gb|EE071858.1|EE071858
EST:     CCAAACTTTCTGTGGAGGATGTGGAGTATCTTCTTATGAAGAGCCTTTCT                         GTTCATCTTATTGAGGGCATCATTGATCAAGTTGAAGGGACAGTTCATGTG
genomic: CCAAACTTTCTGTGGAGGATGTGGAGTATCTTCTCATGAAGAGCCTTTCTgtaagtcctt ... actgctgcagGTTCATCTTATTGAGGGCATCATTGATCAAGTTGAAGGGACAGTTCATGTG
EST: gi|110702107|gb|EE080439.1|EE080439
EST:     CCAAACTTTCTGTGGAGGATGTGGAGTATCTTCTCATGAAGAGCCTTTCT                         GTTCATCTTATTGAGGGCATCATTGATC
genomic: CCAAACTTTCTGTGGAGGATGTGGAGTATCTTCTCATGAAGAGCCTTTCTgtaagtcctt ... actgctgcagGTTCATCTTATTGAGGGCATCATTGATC
EST: gi|351019814|gb|FQ439631.1|FQ439631
EST:     CCAAACTTTCTGTGGAGGATGTGGAGTATCTTCTCATGAAGAGCCTTTCT                         GTTCATCTTATTGAGGGCATCATTGATCAAGTTGAAGGGACAGTTCATGTG
genomic: CCAAACTTTCTGTGGAGGATGTGGAGTATCTTCTCATGAAGAGCCTTTCTgtaagtcctt ... actgctgcagGTTCATCTTATTGAGGGCATCATTGATCAAGTTGAAGGGACAGTTCATGTG
EST: gi|110694939|gb|EE072388.1|EE072388
EST:     CCAAACTTTCTGTGGAGGATGTGGAGTATCTTCTCATGAAGAGCCTTTCT                         GTTCATCTTATTGAGGGCATCATTGATCAAGTTGAAGGGACAGTTCATGTG
genomic: CCAAACTTTCTGTGGAGGATGTGGAGTATCTTCTCATGAAGAGCCTTTCTgtaagtcctt ... actgctgcagGTTCATCTTATTGAGGGCATCATTGATCAAGTTGAAGGGACAGTTCATGTG
EST: gi|110426954|gb|EC993383.1|EC993383
EST:     CATGAAGAGCCTTTCT                         GTTCATCTTATTGAGGGCATCATTGATCAAGTTGAAGGGACAGTTCATGTG
genomic: CATGAAGAGCCTTTCTgtaagtcctt ... actgctgcagGTTCATCTTATTGAGGGCATCATTGATCAAGTTGAAGGGACAGTTCATGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaagcttttgtattaaaccctgtagacattggttaaaacttggactgctgcagGTTCATCTTATTGAGGGCATCATTGATCAAGTTGAAGGGACAGTTCATGTGTCGTGGGTGCAGCCAAGAGTTTTGGGTATTCCACAGATCAAATCGTTGC
       ttttgtattaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatccacttgttaagtagtcatttacttgttttgggaaatgcaattcaagcttttgtattaaaccctgtagacattggttaaaacttggactgctgcagGTTCATCTTATTGAGGGCATCATTGATCAAGTTGAAGGGACAGTTCATGTGTCGTGGGTGCAGCCAAGAGTTTTGGGTATTCCACAGATCAAATCGTTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - ccacttg
- - - - - - - - - - catttac
- - - - - - - - - - - - - - - ttttggg
- - - - - - - - - - - - - - - - - - - aatgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaccct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaactt