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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataaatttgtttgaattttggttacatttggagttcttgtgcatttgaatggatgggctgattgaggtttagtggacagGTTGTCAGTGGGATTGCTTTGCCATCCGGGTCTGATAAGCTATATACTGGGAGCAAAGATGAAACTGTGAGGATTTGGGACTGTCAATCTGGTCAG

Basic information

species Vitis vinifera
transcript Vv16s0100g00320.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0100g00320.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA09G27300.1 (Glycine max), 3'ss of exon 1
-----gtaataaatt-tgtttga-attttggttaca----tttg-gagttcttg-----tgcatttgaatggatgggctg-attgaggtttagtggacagGTTGTCAGTGGGATTGCTTTGCCATCCGGGTCTGATAAGCTATATACTGGGAGCAAAGATGAAACTGTGAGGATTTGGGACTGTCAATCTGGTCAG
     || | || |  | ||||| |    | |||||    | || | ||  |||     || | |||| ||||||  |||   |   ||| | || ||||| ||| ||||  ||||| || || || || ||||||||||| |||||||| ||||  ||||| ||||  |||||||||||||| || | |||  ||
actctgtgaaaattgatatttgatagcacgtttacaagagtgtgtgggtgtttggtgattggagttgactggatgaactgtggttttgttgaatgaacagGCTGTGAGTGCAATTGCCTTTCCCTCTGGTTCTGATAAGCTGTATACTGGAAGCACTGATGAGACTGCAAGGATTTGGGACTGCCAGTGTGGAAAG
















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|351049271|gb|FQ429014.1|FQ429014
EST:     GTGTTGGTGATTGTTTCTCGAGTTTGACACAGCTTGAAGGGCATCAGAAG                         GTTGTCAGTGGGATTGCTTTGCCATCCGGGTCTGATAAGCTATATACTGGG
genomic: GTGTTGGTGATTGTTTCTCGAGTTTGACACAGCTTGAAGGGCATCAGAAGgtaataaatt ... tagtggacagGTTGTCAGTGGGATTGCTTTGCCATCCGGGTCTGATAAGCTATATACTGGG
EST: gi|349829433|gb|FQ419965.1|FQ419965
EST:     GTGTTGGTGATTGTTTCTCGAGTTTGACACAGCTTGAAGGGCATCAGAAG                         GTTGTCAGTGGGATTGCTTTGCCATCCGGGTCTGATAAGCTATATACTGGG
genomic: GTGTTGGTGATTGTTTCTCGAGTTTGACACAGCTTGAAGGGCATCAGAAGgtaataaatt ... tagtggacagGTTGTCAGTGGGATTGCTTTGCCATCCGGGTCTGATAAGCTATATACTGGG
EST: gi|161721021|gb|FC069636.1|FC069636
EST:     GTGTTGGTGATTGTTTCTCGAGTTTGACACAGCTTGAAGGGCATCAGAAG                         GTTGTCAGTGGGATTGCTTTGCCATCCGGGTCTGATAAGCTATATACTGGG
genomic: GTGTTGGTGATTGTTTCTCGAGTTTGACACAGCTTGAAGGGCATCAGAAGgtaataaatt ... tagtggacagGTTGTCAGTGGGATTGCTTTGCCATCCGGGTCTGATAAGCTATATACTGGG
EST: gi|110698131|gb|EE075789.1|EE075789
EST:     GTGTTGGTGATTGTTTCTCGAGTTTGACACAGCTTGAAGGGCATCAAAAG                         GTTGTCAGTGGGATTGCTTTTGC-ATCCGGGTCTGATAAGCTATATACTGG
genomic: GTGTTGGTGATTGTTTCTCGAGTTTGACACAGCTTGAAGGGCATCAGAAGgtaataaatt ... tagtggacagGTTGTCAGTGGGATTGCTTT-GCCATCCGGGTCTGATAAGCTATATACTGG
EST: gi|30305654|gb|CB982448.1|CB982448
EST:     GTGTTGGCGATTGTTTCTCGAGATTGACACAGCTTGAAGGGCATCAGAAG                         GTTGGCAGTGTGATTGCTTTGCCATCCGGGTCTGATAAGCTATATACTGGG
genomic: GTGTTGGTGATTGTTTCTCGAGTTTGACACAGCTTGAAGGGCATCAGAAGgtaataaatt ... tagtggacagGTTGTCAGTGGGATTGCTTTGCCATCCGGGTCTGATAAGCTATATACTGGG
EST: gi|33409918|gb|CF215545.1|CF215545
EST:     GTGTTGGTGATTGTTTCTCGAGTTTGACACAGCTTGAAGGGCATCAGATC                         GTTGTCAGTGGGATTGCTTTGCCATCCGGGTCT
genomic: GTGTTGGTGATTGTTTCTCGAGTTTGACACAGCTTGAAGGGCATCAGAAGgtaataaatt ... tagtggacagGTTGTCAGTGGGATTGCTTTGCCATCCGGGTCT
EST: gi|34550256|gb|CF518474.1|CF518474
EST:     GTGTTGGTGATTGTTTCTCGAGTTTGACACAGCTTGAAGGGCATCAGAAG                         GTTGTCAGGTGGGAGAT-CTTTGCCATCCGGGTCTGATAAGCTATATACTG
genomic: GTGTTGGTGATTGTTTCTCGAGTTTGACACAGCTTGAAGGGCATCAGAAGgtaataaatt ... tagtggacagGTTGTCAG-TGGGAT-TGCTTTGCCATCCGGGTCTGATAAGCTATATACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttggagttcttgtgcatttgaatggatgggctgattgaggtttagtggacagGTTGTCAGTGGGATTGCTTTGCCATCCGGGTCTGATAAGCTATATACTGGGAGCAAAGATGAAACTGTGAGGATTTGGGACTGTCAATCTGGTCAG
                               ggctgat  putative branch site (score: 4)
                  atttgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaataaatttgtttgaattttggttacatttggagttcttgtgcatttgaatggatgggctgattgaggtttagtggacagGTTGTCAGTGGGATTGCTTTGCCATCCGGGTCTGATAAGCTATATACTGGGAGCAAAGATGAAACTGTGAGGATTTGGGACTGTCAATCTGGTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT