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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttcattttcttttggtctatgatgtgcctcatatcttccttttatctttcatgaacatgttacatttctgaccgatatgctatgttgtgttatgtgcagCCACTGTTTCCTGGGGAAAGTGGTGTTGATCAGCTGGTGGAAATCATTAAG

Basic information

species Vitis vinifera
transcript Vv15s0048g02010.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0048g02010.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os10g37740.1 (Oryza sativa), 3'ss of exon 8
gttcattttcttttggtctatgatgtgcctcatatcttccttttatctttcatgaacatgttacattt---ctgaccgatatgctatgttgtgttatgtgcagCCACTGTTTCCTGGGGAAAGTGGTGTTGATCAGCTGGTGGAAATCATTAAG
|| | |  | || |||     | || |  | |    |   |  | |  | || ||   | |     ||   |||| |  | | |    |   |  |  ||||||| ||||| ||||| ||||||||||||||||| ||||||||||| || |||
gtacttcattttatgg---gggttgggggttaataatggatgctgtgctgcaagactctttcctgctttggctgatcttttttccgaatatggacaattgcagCCTCTGTTCCCTGGAGAAAGTGGTGTTGATCAACTGGTGGAAATAATAAAG

upper sequence: Vv15s0048g02010.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G109624_T01 (Zea mays), 3'ss of exon 8
-----gttcattttcttttggtctatgatgtgcctcat-atcttccttttatctttcatgaacatgttacatttctgaccgatatgctatgttgtgttatgtgcagCCACTGTTTCCTGGGGAAAGTGGTGTTGATCAGCTGGTGGAAATCATTAAG
     |  |||| |  |||| || |      |     | |    | |  |||||      || || ||   ||  || ||  |  ||         ||    ||||||  |||||||||| ||||||||||||||||| |||||||||||||| |||
tttatggacattatgatttgatcaactcccagttaattgagacacttgctatctgctgacaaaatattg--ttgatgtccactgggccccccccaatt----gcagCCTTTGTTTCCTGGTGAAAGTGGTGTTGATCAACTGGTGGAAATCATAAAG

upper sequence: Vv15s0048g02010.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G131853_T01 (Zea mays), 3'ss of exon 8
--gttcattttcttttggtctatgatgtgcctcat-atcttccttttatctttcatgaacatgttacatttctgaccgatatgctatgttgtgttatgtgcagCCACTGTTTCCTGGGGAAAGTGGTGTTGATCAGCTGGTGGAAATCATTAAG
  |  ||||    |||| ||       ||     | |    | | |||||       ||  || |  |  ||  || |     || |        || |||||||  |||||||||| |||||||||||||| || ||||||||||| || |||
atgcacattaggatttgatccgctcactgttgattgagacacttcttatccgatgacaatttggttgacatcc-actgcccccct-tcccccaaaat-tgcagCCTTTGTTTCCTGGTGAAAGTGGTGTTGACCAACTGGTGGAAATAATAAAG

upper sequence: Vv15s0048g02010.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 8
-----------gttcattttc--ttttggtctatgatgtgcc-tcatatcttcctt--ttatctttcatgaacatgttacatttctgaccgatatgcta-----tgttg---tgttatgtgcagCCACTGTTTCCTGGGGAAAGTGGTGTTGATCAGCTGGTGGAAATCATTAAG
            | |||| |    ||| |  |||||||  || |  ||| ||  ||  | |  |||||| |  |  |   | |        || || ||     |||||   |  ||   | ||||||||||||| |||||||||||  |||||||||||||||| || || |||
gtaagtatattatacattgtagagtttcggttatgatgaaccattttattttgattgatcagttttcattattacttcgaaataacatttaatctgataacaactgttgattttctacccgtagCCACTGTTTCCCGGGGAAAGTGGCATTGATCAGCTGGTGGAGATAATCAAG

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|349820373|gb|FQ403989.1|FQ403989
EST:     TTGATATGTGGTCTGCAGGTTGCGTTGTGGCTGAGCTTCTTCTTGGCCAG                         CCACTGTTTCCTGGGGAAAGTGGTGTTGATCAGCTGGTGGAAATCATTAAG
genomic: TTGATATGTGGTCTGCAGGTTGCGTTGTGGCTGAGCTTCTTCTTGGCCAGgtgggtttat ... ttatgtgcagCCACTGTTTCCTGGGGAAAGTGGTGTTGATCAGCTGGTGGAAATCATTAAG
EST: gi|110688693|gb|EE067533.1|EE067533
EST:     TTGATATGTGGTCTGCAGGCTGCGTTGTGGCTGAGCTTCTTCTTGGCCAG                         CCACTGTTTCCTGGGGAAAGTGGTGTTGATCAGCTGGTGGAAATCATTAAG
genomic: TTGATATGTGGTCTGCAGGTTGCGTTGTGGCTGAGCTTCTTCTTGGCCAGgtgggtttat ... ttatgtgcagCCACTGTTTCCTGGGGAAAGTGGTGTTGATCAGCTGGTGGAAATCATTAAG
EST: gi|32249937|gb|CD715756.1|CD715756
EST:     TTGATATGTGGTCTGCAGGTTGCGTTGTGGCTGAGCTTCTTCTTGGCCAG                         CCACTGTTTCCTGGGGAAAGTGGTGTTGATCAGCTGGTGGAAATCATTAAG
genomic: TTGATATGTGGTCTGCAGGTTGCGTTGTGGCTGAGCTTCTTCTTGGCCAGgtgggtttat ... ttatgtgcagCCACTGTTTCCTGGGGAAAGTGGTGTTGATCAGCTGGTGGAAATCATTAAG
EST: gi|110732276|gb|EE107431.1|EE107431
EST:     TTGATATGTGGTCTGCAGGCTGCGTTGTGGCTGAGCTTCTTCTTGGCCAG                         CCACTTTTTCCTGGGGAAAGTGGTGTTGATCAGCTGGTGGAAATCATTAAG
genomic: TTGATATGTGGTCTGCAGGTTGCGTTGTGGCTGAGCTTCTTCTTGGCCAGgtgggtttat ... ttatgtgcagCCACTGTTTCCTGGGGAAAGTGGTGTTGATCAGCTGGTGGAAATCATTAAG
EST: gi|37189535|gb|CF608884.1|CF608884
EST:     TTGATATGTGGTCTGCAGGTTGCGTTGTGGCTGAGCTTCTTCTTGGCCAG                         CCACTGTTTCCTGGGGAAAGTGGTGTTGATCAGCTGGTGGAAATCATTAAG
genomic: TTGATATGTGGTCTGCAGGTTGCGTTGTGGCTGAGCTTCTTCTTGGCCAGgtgggtttat ... ttatgtgcagCCACTGTTTCCTGGGGAAAGTGGTGTTGATCAGCTGGTGGAAATCATTAAG
EST: gi|27579903|gb|CB002598.1|CB002598
EST:     TTGATATGTGGTCTGCAGGCTGCGTTGTGGCTGAGCTTCTTCTTGGCCAG                         CCACTGTTTCCTGGGGAAAGTGGTGTTGATCAGCTGGTGGAAATCATTAAG
genomic: TTGATATGTGGTCTGCAGGTTGCGTTGTGGCTGAGCTTCTTCTTGGCCAGgtgggtttat ... ttatgtgcagCCACTGTTTCCTGGGGAAAGTGGTGTTGATCAGCTGGTGGAAATCATTAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttcatgaacatgttacatttctgaccgatatgctatgttgtgttatgtgcagCCACTGTTTCCTGGGGAAAGTGGTGTTGATCAGCTGGTGGAAATCATTAAG
                     ttctgac  putative branch site (score: 2)
               ttacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcattttcttttggtctatgatgtgcctcatatcttccttttatctttcatgaacatgttacatttctgaccgatatgctatgttgtgttatgtgcagCCACTGTTTCCTGGGGAAAGTGGTGTTGATCAGCTGGTGGAAATCATTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - -cttttgg
- - - - - - - - - - - - -tgcctca
- - - - - - - - - - - - - - - - - - - - - - - - - - -gaacatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttctgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgtg