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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttcttgaaggtgtatagcttgttggatttagttgtgatattgttgatcctcacatctcctttccattacttagcaaaatcctttttttctgcttgacagGGTATTAGTTTAATGATAACAGTTTTGCAGATAGCTCGATTGCCTAATATCAAG

Basic information

species Vitis vinifera
transcript Vv05s0062g01250.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0062g01250.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA20G39260.1 (Glycine max), 3'ss of exon 7
gttcttgaaggtgtatagcttgttggatttagttgtgatattgttgatcctcacatctcctttccattacttagcaaaatcctttttttctgcttgacagGGTATTAGTTTAATGATAACAGTTTTGCAGATAGCTCGATTGCCTAATATCAAG
||| |   |  |||     ||        | | ||  | | |||| ||  |  | | |  |||     | |||    ||   |   ||| | |||||||||| ||| |||| ||||||||||| || ||| | ||||| ||||||||||| |||
gttgtctcaattgtggttgttaccattcatcgatgataaactgtttattttatcttttattttatgcaatttacttgaaatatggctttattcttgacagGGCATTGGTTTGATGATAACAGTCTTACAGTTGGCTCGGTTGCCTAATATTAAG
















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|110688633|gb|EE067409.1|EE067409
EST:     GGGCGATAACTCGTAAGGCATCATTTTCGTGGATCGGACAAGATGTGCTT                         GGTATTAGTTTAATGATAACAGTTTTGCAGATAGCTCGATTGCCTAATATC
genomic: GGGCGATAACTCGTAAGGCATCATTTTCGTGGATCGGACAAGATGTGCTTgtaagttctt ... tgcttgacagGGTATTAGTTTAATGATAACAGTTTTGCAGATAGCTCGATTGCCTAATATC
EST: gi|294965259|gb|GW838946.1|GW838946
EST:     GGGCGATAACTCGGAAGGCATCATTTTCGCGGATCGGACAAGATGTGCTT                         GGTATTAGTTTAATGATAACAGTTTTGCAGATAGCTCGATTGCCTAATATC
genomic: GGGCGATAACTCGTAAGGCATCATTTTCGTGGATCGGACAAGATGTGCTTgtaagttctt ... tgcttgacagGGTATTAGTTTAATGATAACAGTTTTGCAGATAGCTCGATTGCCTAATATC
EST: gi|110731688|gb|EE106318.1|EE106318
EST:     GGGCGATAACTCGTAAGGCATCATTTTCGTGGATCGGACAAGATGTGCTT                         GGTATTAGTTTAATGATAACAGTTTTGCAGATAGCTCGATTGCCTAATATC
genomic: GGGCGATAACTCGTAAGGCATCATTTTCGTGGATCGGACAAGATGTGCTTgtaagttctt ... tgcttgacagGGTATTAGTTTAATGATAACAGTTTTGCAGATAGCTCGATTGCCTAATATC
EST: gi|110687402|gb|EE064779.1|EE064779
EST:     GGGCGATAACTCGTAAGGCATCATTTTCGTGGATCGGACAAGATGTGCTT                         GGTATTAGTTTAATGATAACAGTTTTGCAGATAGCTCGATTGCCTAATATC
genomic: GGGCGATAACTCGTAAGGCATCATTTTCGTGGATCGGACAAGATGTGCTTgtaagttctt ... tgcttgacagGGTATTAGTTTAATGATAACAGTTTTGCAGATAGCTCGATTGCCTAATATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatcctcacatctcctttccattacttagcaaaatcctttttttctgcttgacagGGTATTAGTTTAATGATAACAGTTTTGCAGATAGCTCGATTGCCTAATATCAAG
  tcctcac  putative branch site (score: 2)
                                  tcctttttttctgctt  putative PPT
                              aaaatccttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcttgaaggtgtatagcttgttggatttagttgtgatattgttgatcctcacatctcctttccattacttagcaaaatcctttttttctgcttgacagGGTATTAGTTTAATGATAACAGTTTTGCAGATAGCTCGATTGCCTAATATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - cttgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaatcc