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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgccaactttcccatacatgttttagctttttgtcctttttttcttgttcgttgttatcactgtgccttgctgtttgtttctgacatacagAGCCCAACATAGAGAGTCCTCTCAACAGCTATGCTGCATCATTATGGAACAACCAAGAAG

Basic information

species Vitis vinifera
transcript Vv13s0019g04090.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g04090.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G35630.1 (Glycine max), 3'ss of exon 4
gtatgccaactttcccatacatgttttagctttttgtcctttttttcttgttcgttgttatcactgtgcctt-gctgtttgtttctgacatacagAGCCCAACATAGAGAGTCCTCTCAACAGCTATGCTGCATCATTATGGAACAACCAAGAAG
    | |   |||     |  |  |||   | | | |  |   |||    |||  | ||       || ||  || ||||  ||   |   |||||||| ||| | ||||||||||| ||||||||||||||| || | |||||  |  | ||||
----gtctgttttttttaattttatttttatatatattttgagttttgcattcacttttgcatgcttgtctgagcagtttactttctaataacagAGCCTAACCTGGAGAGTCCTCTAAACAGCTATGCTGCAGCACTTTGGAATGATAAGGAAG

upper sequence: Vv13s0019g04090.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G31920.2 (Glycine max), 3'ss of exon 4
gtatgccaactttcccatacatgttttagctttttgtcctttttttcttgttcgttgttatcactgtgccttgctgtttgtttctgacatacagAGCCCAACATAGAGAGTCCTCTCAACAGCTATGCTGCATCATTATGGAACAACCAAGAAG
                     |||| | | | | | |    |||| | |   | ||    |   ||| |   ||  |||  ||   |   |||||||| ||| | ||||||||||| ||||||||||||||| || | |||||  || | ||||
------------------gtctgttctcgatatcttttgagttttgcattcacctttcagtgcttgt-ctgagcaatttactttctaataacagAGCCTAACCTGGAGAGTCCTCTAAACAGCTATGCTGCAGCACTTTGGAATGACAAGGAAG
















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|161712977|gb|FC062103.1|FC062103
EST:     TGCCTATGATTGCAAAACCGTTCTTTTATC-ATTCAAAGTCTATTGGGAG                         AAACCA-CATAGAGAGTCCTCTCA-CAGCTATGCTGCATCAT-ATGGAACA
genomic: TGCCTATGATTGCAAAACCGTTCTTTTATCCATTCAAAGTCTATTGGGAGgtatgccaac ... tgacatacagAGCCCAACATAGAGAGTCCTCTCAACAGCTATGCTGCATCATTATGGAACA
EST: gi|110426829|gb|EC993253.1|EC993253
EST:     TGCCTATGATTGCAAAACCGTTCTTTTATCCATTCAAAGTCTATTGGGAG                         AGCCCAACATAGAGAGTCCTCTCAACAGCTATGCTGCATCATTATGGAACA
genomic: TGCCTATGATTGCAAAACCGTTCTTTTATCCATTCAAAGTCTATTGGGAGgtatgccaac ... tgacatacagAGCCCAACATAGAGAGTCCTCTCAACAGCTATGCTGCATCATTATGGAACA
EST: gi|161720059|gb|FC065103.1|FC065103
EST:     TGCCTATGATTGCAAA-CCGTTCTTTTATC-ATTCAA-GTCTATTGGGAG                         AACC-AACATAG
genomic: TGCCTATGATTGCAAAACCGTTCTTTTATCCATTCAAAGTCTATTGGGAGgtatgccaac ... tgacatacagAGCCCAACATAG
EST: gi|110711177|gb|EE087407.1|EE087407
EST:     TGCCTATGATTGCAAAACCGTTCTTTTATC-ATTCAAAGTCTATTGGGA-                         AGACCCAACATAGAGAGTCCTCTCAACAGCTATGCTGCATCATTATGGGAA
genomic: TGCCTATGATTGCAAAACCGTTCTTTTATCCATTCAAAGTCTATTGGGAGgtatgccaac ... tgacatacagAG-CCCAACATAGAGAGTCCTCTCAACAGCTATGCTGCATCATTATGG-AA
EST: gi|28961969|gb|CB341008.1|CB341008
EST:     TGCCTATGATTGCAAAACCGTTCCTTTATCCATTCAAAGTCTATTGGGAG                         AACCCAACATAGAGAGTCCTCTCAACAGCTATGCTGCATCATTATGGAACA
genomic: TGCCTATGATTGCAAAACCGTTCTTTTATCCATTCAAAGTCTATTGGGAGgtatgccaac ... tgacatacagAGCCCAACATAGAGAGTCCTCTCAACAGCTATGCTGCATCATTATGGAACA
EST: gi|110686046|gb|EE063296.1|EE063296
EST:     TGCCTATGATTGCAAAACCGTTCTTTTATCCATTCAAAGTCTATTGGGAG                         AACCCAACATAGAGAGTCCTCTCAACAGCTATGCTGCATCATTATGGAACA
genomic: TGCCTATGATTGCAAAACCGTTCTTTTATCCATTCAAAGTCTATTGGGAGgtatgccaac ... tgacatacagAGCCCAACATAGAGAGTCCTCTCAACAGCTATGCTGCATCATTATGGAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttttcttgttcgttgttatcactgtgccttgctgtttgtttctgacatacagAGCCCAACATAGAGAGTCCTCTCAACAGCTATGCTGCATCATTATGGAACAACCAAGAAG
                                          ttctgac  putative branch site (score: 2)
                                     tttgtttct  CT-rich tract
               ttgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgccaactttcccatacatgttttagctttttgtcctttttttcttgttcgttgttatcactgtgccttgctgtttgtttctgacatacagAGCCCAACATAGAGAGTCCTCTCAACAGCTATGCTGCATCATTATGGAACAACCAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG