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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgtcttctattacaatgacaccattttattttgtattaggaaggctaaaagtctaaattcaggttcttacataatgcttaactccctctaaatttcagATCCTGCTGCAAGTGCTGATTTAGCAGTGGTTTTGATGCAAGAAGGATTAGCACATGTTATCCTCATTGGTAGAAG

Basic information

species Vitis vinifera
transcript Vv04s0023g00140.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g00140.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os04g56480.1 (Oryza sativa), 3'ss of exon 5
-----tatgtcttctattacaatgacaccattttattttgtattaggaaggctaaaagtctaaattcaggttcttacataatgcttaactccctctaaatttcagATCCTGCTGCAAGTGCTGATTTAGCAGTGGTTTTGATGCAAGAAGGATTAGCACATGTTATCCTCATTGGTAGAAG
     |    ||| | ||  |   ||   ||  |||||| | |||  |    |    |   ||    | ||||| ||  | ||| |     ||||||    | ||| ||  |||||||||||||| |||||||  || | |||||||||||| | |||||| |  ||||||||||||||||
taaacttctacttttgttttatcaac-ttatcatattttctgttattattctttcttgagaaatgcaatgttctaactgagtgcatctaaacctcta----ttagACCCAACTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTGCACATTTGTTCCTCATTGGTAGAAG

upper sequence: Vv04s0023g00140.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G044011_T01 (Zea mays), 3'ss of exon 6
tatgtcttctattacaa--tgacaccattttattttgtattaggaaggctaaaagtctaaattcaggttcttacataatgcttaactccctctaaatttcagATCCTGCTGCAAGTGCTGATTTAGCAGTGGTTTTGATGCAAGAAGGATTAGCACATGTTATCCTCATTGGTAGAAG
|   | ||||   |  |  |    |    |    |  |  |        ||   || | ||      |  ||  ||   |  | ||     |||  ||  |||||||||||||||||||||| |||||||  || | |||||||||||| | || ||  |  |||||||||| | |||
tccattttctgagattagttttttctgaatcgcctcatcctctattatttatctgtatgaaacatactgatttaattgagtctgaccaaaccta--ttgtagATCCTGCTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAG

upper sequence: Vv04s0023g00140.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA10G31310.1 (Glycine max), 3'ss of exon 6
--tatgtcttctattacaatgacaccattttattttgtattaggaaggctaaaagtctaaattcaggttcttacataatgcttaactccctctaaattt--cagATCCTGCTGCAAGTGCTGATTTAGCAGTGGTTTTGATGCAAGAAGGATTAGCACATGTTATCCTCATTGGTAGAAG
  |||       |  |       |  |||     |    | ||   |  ||||  | |  | |||   |  |  ||||     || ||| |  | ||||  ||||||||| ||||||||||||| |||||||||| |||||||||||||||||||| ||| |  ||||  ||||||||||
tttataaagcaaaaaatggaattaatattcctcatctggtcagttggtgtaaatttttgtagtcaaaatggtgaataaa----aattccatgcacattttgcagATCCTGGTGCAAGTGCTGATCTAGCAGTGGTGTTGATGCAAGAAGGATTAGCCCATATCCTCCTTGTTGGTAGAAG

upper sequence: Vv04s0023g00140.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA20G36200.1 (Glycine max), 3'ss of exon 6
--tatgtcttctattacaatgacaccattttattttgtattaggaaggctaaaagtctaaattcaggttcttacataatgcttaactccctctaaatttcagATCCTGCTGCAAGTGCTGATTTAGCAGTGGTTTTGATGCAAGAAGGATTAGCACATGTTATCCTCATTGGTAGAAG
    |    | ||| |     | |    |||| | |   | ||   |  ||||  | |  | |||   |  |  ||||   |  |        |  || ||||||||| ||||||||||||| |||| ||||| |||||||||||||||||||| ||| |  ||||  ||||||||||
acagtcatatttataaagcaaaaatggatttaatattcctcagttggtgtaaatttttgtaatcaaaatggtgaataaaaat--atcatgcacattttgcagATCCTGGTGCAAGTGCTGATCTAGCCGTGGTGTTGATGCAAGAAGGATTAGCCCATATCCTCCTTGTTGGTAGAAG

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|71861191|gb|DT010246.1|DT010246
EST:     GTGGTTTGGGACTCGTTCGCTTTAGATACACTCAATCAGGCCTCTG                         ATCCTGCTGCAAGTGCTGATTTAGCAGTGGTTTTGATGCAAGAAGGATTAG
genomic: GTGGTTTGGGACTCATTGGCTTTAGATACACTCAATCAGGCCTCTGgtatgtcatc ... taaatttcagATCCTGCTGCAAGTGCTGATTTAGCAGTGGTTTTGATGCAAGAAGGATTAG
EST: gi|110356881|gb|EC920025.1|EC920025
EST:     GTGGTTTGGGACTCGTTCGCTTTAGATACACTCAATCAGGCCTCTG                         ATCCTGCTGCAAGTGCTGATTTAGCAGTGGTTTTGATGCAAGAAGGATTAG
genomic: GTGGTTTGGGACTCATTGGCTTTAGATACACTCAATCAGGCCTCTGgtatgtcatc ... taaatttcagATCCTGCTGCAAGTGCTGATTTAGCAGTGGTTTTGATGCAAGAAGGATTAG
EST: gi|110724761|gb|EE100872.1|EE100872
EST:     GTGGTTTGGGACTCGTTCGCTTTAGATACACTCAATCAGGCCTCTG                         ATCCTGCTGCAAGTGCTGATTTAGCAGTGGTTTTGATGCAAGAAGGATTAG
genomic: GTGGTTTGGGACTCATTGGCTTTAGATACACTCAATCAGGCCTCTGgtatgtcatc ... taaatttcagATCCTGCTGCAAGTGCTGATTTAGCAGTGGTTTTGATGCAAGAAGGATTAG
EST: gi|110712695|gb|EE087976.1|EE087976
EST:     GTGGTTTGGGACTCGTTCGCTTTAGATACACTCAATCAGGCCTCTG                         ATCCTGCTGCAAGTGCTGATTTAGCAGTGGTTTTGATGCAAGAAGGATTAG
genomic: GTGGTTTGGGACTCATTGGCTTTAGATACACTCAATCAGGCCTCTGgtatgtcatc ... taaatttcagATCCTGCTGCAAGTGCTGATTTAGCAGTGGTTTTGATGCAAGAAGGATTAG
EST: gi|71865271|gb|DT014326.1|DT014326
EST:     GTGGTTTGGGACTCGTTCGCTTTAGATACACTCAATCAGGCCTCTG                         ATCCTGCTGCAAGTGCTGATTTAGCAGTGGTTTTGATGCAAGAAGGATTAG
genomic: GTGGTTTGGGACTCATTGGCTTTAGATACACTCAATCAGGCCTCTGgtatgtcatc ... taaatttcagATCCTGCTGCAAGTGCTGATTTAGCAGTGGTTTTGATGCAAGAAGGATTAG
EST: gi|161715809|gb|FC065164.1|FC065164
EST:     GTGGTTTGGGACTCGTTCGCTTTAGATACACTCAATCAGGCCTCTG                         ATCCTGCTGCAAGTGCTGATTTAGCAGTGGTTTTGATGCAAGAAGGATTAG
genomic: GTGGTTTGGGACTCATTGGCTTTAGATACACTCAATCAGGCCTCTGgtatgtcatc ... taaatttcagATCCTGCTGCAAGTGCTGATTTAGCAGTGGTTTTGATGCAAGAAGGATTAG
EST: gi|30135371|gb|CB920709.1|CB920709
EST:     GTGGTTTGGGACTCGTTCGCTTTAGATACACTCAATCAGGCCTCTG                         ATCCTGCTGCAAGTGCTGATTTAGCAGTGGTTTTGATGCAAGAAGGATTAG
genomic: GTGGTTTGGGACTCATTGGCTTTAGATACACTCAATCAGGCCTCTGgtatgtcatc ... taaatttcagATCCTGCTGCAAGTGCTGATTTAGCAGTGGTTTTGATGCAAGAAGGATTAG
EST: gi|30129653|gb|CB914992.1|CB914992
EST:     GTGGTTTGGGACTCGTTCGCTTTAGATACACTCAATCAGGCCTCTG                         ATCCTGCTGCAAGTGCTGATTTAGCAGTGGTTTTGATGCAAGAAGGATTAG
genomic: GTGGTTTGGGACTCATTGGCTTTAGATACACTCAATCAGGCCTCTGgtatgtcatc ... taaatttcagATCCTGCTGCAAGTGCTGATTTAGCAGTGGTTTTGATGCAAGAAGGATTAG
EST: gi|161719832|gb|FC065768.1|FC065768
EST:     GTGGTTTGGGACTCGTTCGCTTTAGATACACTCAATCAGGCCTCTG                         ATCCTGCTGCAAGTGCTGATTTAGCAGTGGTTTTGATGCAAGAAGGATTAG
genomic: GTGGTTTGGGACTCATTGGCTTTAGATACACTCAATCAGGCCTCTGgtatgtcatc ... taaatttcagATCCTGCTGCAAGTGCTGATTTAGCAGTGGTTTTGATGCAAGAAGGATTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctaaaagtctaaattcaggttcttacataatgcttaactccctctaaatttcagATCCTGCTGCAAGTGCTGATTTAGCAGTGGTTTTGATGCAAGAAGGATTAGCACATGTTATCCTCATTGGTAGAAG
                                      ctccctct  CT-rich tract
                       ttacataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatgtcttctattacaatgacaccattttattttgtattaggaaggctaaaagtctaaattcaggttcttacataatgcttaactccctctaaatttcagATCCTGCTGCAAGTGCTGATTTAGCAGTGGTTTTGATGCAAGAAGGATTAGCACATGTTATCCTCATTGGTAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- tgtcttc
- - - - - - - - - gacacca
- - - - - - - - - - - - - - - - - - - - ggaaggc