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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttttagctttgctagattaatctaaatgtagtttagcagtatgaatactctcactttctttccttttttttttctttaaaggaacaacactttattgaatttctgtgcttggcagCTATGTTCTGAAGGGTAGATCTCCTTTAACATTGAAGCATGGGAAACCTGATCATGAAGCAACAGAT

Basic information

species Vitis vinifera
transcript Vv05s0102g01110.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0102g01110.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G032222_T03 (Zea mays), 3'ss of exon 13
gtgagttttagctttgctagattaatctaaatgtagtttagcagtatgaatactctcactttctttccttttttttttctttaaaggaacaacactttattgaatttctgtgcttggcagCTATGTTCTGAAGGGTAGATCTCCTTTAACATTGAAGCATGGGAAACCTGATCATGAAGCAACAGAT
||||| |    |  || ||    ||| ||  || || ||||   |    ||| |   | |   ||  ||   |  | |||           | |||||  | | |||           |||||  |  | || || |  || ||||  |||||||||||||||| ||| ||||||||||||||||| 
gtgaggt----ccctgttaagaaaat-tacctg-agattagtcattgatatatttctattccattcactgagtcatgtct-----------atacttt--taactttt----------agCTACATATTCAAAGGGAAGTCACCTTATACATTGAAGCATGGGAGACCCGATCATGAAGCAACAGAC
















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|30251567|gb|CB969300.1|CB969300
EST:     GCATTTGAGTATGGGCTCATTCCTGGTTTGGCTTTAAGTGCTTTAGAACA                         CTATGTTCCGAAGGGTAGATCTCTTTTAACATTGAAGCATGGGAAACCTGA
genomic: GCATTTGAGTATGGGCTCATTCCTGGTTTGGCTTTAAGTGCTTTAGAACAgtgagtttta ... tgcttggcagCTATGTTCTGAAGGGTAGATCTCCTTTAACATTGAAGCATGGGAAACCTGA
EST: gi|18459158|gb|BM437436.1|BM437436
EST:     GCATTTGAGTATGGGCTCATTCCTGGTTTGGCTTTAAGTGCTTTAGAACA                         CTATGTTCTGAAGGGTAGATCTCCTTTAACATTGAAGCATGGGAAACCTGA
genomic: GCATTTGAGTATGGGCTCATTCCTGGTTTGGCTTTAAGTGCTTTAGAACAgtgagtttta ... tgcttggcagCTATGTTCTGAAGGGTAGATCTCCTTTAACATTGAAGCATGGGAAACCTGA
EST: gi|30251648|gb|CB969381.1|CB969381
EST:     GCATTTGAGTATGGGCTCATTCCTGGTTTGGCTTTAAGTGCTTTAGAACA                         CTATGTTCCGAAGGGTAGATCTCTTTTAACATTGAAGCATGGGAAACCTGA
genomic: GCATTTGAGTATGGGCTCATTCCTGGTTTGGCTTTAAGTGCTTTAGAACAgtgagtttta ... tgcttggcagCTATGTTCTGAAGGGTAGATCTCCTTTAACATTGAAGCATGGGAAACCTGA
EST: gi|30251671|gb|CB969404.1|CB969404
EST:     GCATTTGAGTATGGGCTCATTCCTGGTTTGGCTTTAAGTGCTTTAGAACA                         CTATGTTCCGAAGGGTAGATCTCTTTTAACATTGAAGCATGGGAAACCTGA
genomic: GCATTTGAGTATGGGCTCATTCCTGGTTTGGCTTTAAGTGCTTTAGAACAgtgagtttta ... tgcttggcagCTATGTTCTGAAGGGTAGATCTCCTTTAACATTGAAGCATGGGAAACCTGA
EST: gi|110364442|gb|EC924185.1|EC924185
EST:     GCATTTGAGTATGGGCTCATTCCTGGTTTGGCTTTAAGTGCTTTAGAACA                         CTATGTTCTGAAGGGTAGATCTCCTTTAACATTGAAGCATGGGAAACCTGA
genomic: GCATTTGAGTATGGGCTCATTCCTGGTTTGGCTTTAAGTGCTTTAGAACAgtgagtttta ... tgcttggcagCTATGTTCTGAAGGGTAGATCTCCTTTAACATTGAAGCATGGGAAACCTGA
EST: gi|30321185|gb|CD004447.1|CD004447
EST:     GCTTTAAGTGCTTTAGAACA                         CTATGTTCTGAAGGGTAGATCTCCTTTAACATTGAAGCATGGGAAACCTGA
genomic: GCTTTAAGTGCTTTAGAACAgtgagtttta ... tgcttggcagCTATGTTCTGAAGGGTAGATCTCCTTTAACATTGAAGCATGGGAAACCTGA
EST: gi|30251591|gb|CB969324.1|CB969324
EST:     GCATTTGAGTATGGGCTCATTCCTGGTTTGGCTTTAAGTGCTTTAGAACA                         CTATGTTCCGAAGGGTAGATCTCTTTTAACATTGAAGCATGGGAAACCTGA
genomic: GCATTTGAGTATGGGCTCATTCCTGGTTTGGCTTTAAGTGCTTTAGAACAgtgagtttta ... tgcttggcagCTATGTTCTGAAGGGTAGATCTCCTTTAACATTGAAGCATGGGAAACCTGA
EST: gi|30251604|gb|CB969337.1|CB969337
EST:     GCATTTGAGTATGGGCTCATTCCTGGTTTGGCTTTAAGTGCTTTAGAACA                         CTATGTTCCGAAGGGTAGATCTCTTTTAACATTGAAGCATGGGAAACCTGA
genomic: GCATTTGAGTATGGGCTCATTCCTGGTTTGGCTTTAAGTGCTTTAGAACAgtgagtttta ... tgcttggcagCTATGTTCTGAAGGGTAGATCTCCTTTAACATTGAAGCATGGGAAACCTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccttttttttttctttaaaggaacaacactttattgaatttctgtgcttggcagCTATGTTCTGAAGGGTAGATCTCCTTTAACATTGAAGCATGGGAAACCTGATCATGAAGCAACAGAT
                                       tttctgt  CT-rich tract
     ttttttttctttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttttagctttgctagattaatctaaatgtagtttagcagtatgaatactctcactttctttccttttttttttctttaaaggaacaacactttattgaatttctgtgcttggcagCTATGTTCTGAAGGGTAGATCTCCTTTAACATTGAAGCATGGGAAACCTGATCATGAAGCAACAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA