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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctctgtgctgcattgggctcgattggataatttcttacttattccgatattattataactgttgaccaagtgtttgatatatttttctttgttcatgaagGGAGATGTTTATCCAGTGGAACCATCTGATGGGTTCTTATTCAATAAAGTTCTTGATGCTCACTGGGGTGTTCTCTATGATGAAGAT

Basic information

species Vitis vinifera
transcript Vv05s0094g01110.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0094g01110.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G007647_T01 (Zea mays), 3'ss of exon 6
ctctgtgctgcattgggctcgattggata-atttcttact-tattccgatattattataactgttgaccaagtgtttgatatattttt--ctttgt--tcatgaagGGAGATGTTTATCCAGTGGAACCATCTGATGGGTTCTTATTCAATAAAGTTCTTGATGCTCACTGGGGTGTTCTCTATGATGAAGAT
      | ||    |   |  ||  |||  ||||  |||  |||| |  | |    |  | |  || |   || |   || || ||||  |||||      |  |||| ||||||||||| ||||||   ||| | | |  || |   ||  |||| |||||||||||||||||||||||  ||||||| |||
-----agttgttcagactttcatcagatgcatttgatacagtattacagtctgcacactagtcctggctc-gtataacatgtagttttgactttggaactgtccagGGTGATGTTTATCCTGTGGAA---TCTTACGAGAGCTCAGCTAACCAAGTACTTGATGCTCACTGGGGTGTTCTGGATGATGATGAT
















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|29782147|gb|CB347237.2|CB347237
EST:     TGGAAACCAGAACTAAAACACTCAATAGTGAATCTGATGCATCTGTTGGA                         GGAGATGTTTATCCAGTGGAACCATCTGATGGGTTCTTATTCAATAAAGCT
genomic: TGGAAACCAGAACTAAAACACTCAATAGTGAATCTGATGCATCTGTTGGAgtaggcattt ... gttcatgaagGGAGATGTTTATCCAGTGGAACCATCTGATGGGTTCTTATTCAATAAAGTT
EST: gi|30301279|gb|CB978073.1|CB978073
EST:     ACTAAAACACTCAATAGTGAATCTGATGCATCTGTTGGA                         GGAGATGTTTATCCAGTGGAACCATCTGATGGGTTCTTATTCAATAAAGTT
genomic: ACTAAAACACTCAATAGTGAATCTGATGCATCTGTTGGAgtaggcattt ... gttcatgaagGGAGATGTTTATCCAGTGGAACCATCTGATGGGTTCTTATTCAATAAAGTT
EST: gi|110690986|gb|EE068568.1|EE068568
EST:     TGGAAACCAGAACTAAAACACTCAATAGTGAATCTGATGCATCTGTTGGA                         GGAGATGTTTATCCAGTGGAACCATCTGATGGGTTCTTAT-CAATAAAGTT
genomic: TGGAAACCAGAACTAAAACACTCAATAGTGAATCTGATGCATCTGTTGGAgtaggcattt ... gttcatgaagGGAGATGTTTATCCAGTGGAACCATCTGATGGGTTCTTATTCAATAAAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatattattataactgttgaccaagtgtttgatatatttttctttgttcatgaagGGAGATGTTTATCCAGTGGAACCATCTGATGGGTTCTTATTCAATAAAGTTCTTGATGCTCACTGGGGTGTTCTCTATGATGAAGAT
                                  tatttttctttgttc  CT-rich tract
                           tttgatatatttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctctgtgctgcattgggctcgattggataatttcttacttattccgatattattataactgttgaccaagtgtttgatatatttttctttgttcatgaagGGAGATGTTTATCCAGTGGAACCATCTGATGGGTTCTTATTCAATAAAGTTCTTGATGCTCACTGGGGTGTTCTCTATGATGAAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - -ctgcatt
- - - - - - - gggctcg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaagtg