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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgggccatccttataacttctactttactgtatagatatctccataaagtggactgtagacaatagtttggattaatcactgaattttctgttcgcagGTACGTATAGCACGGATTTTCAATACATATGGGCCTCGTATGTGTATTGATGATGGGCGTGTGGTTAGCAATTTTGTTGCACAG

Basic information

species Vitis vinifera
transcript Vv08s0040g02710.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0040g02710.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g62020.1 (Oryza sativa), 3'ss of exon 3
aatgggccatccttataacttctactttactgtatagatatctccataaagtgg--actgtagacaatagtttggattaatcactgaattttctgtt-cgcagGTACGTATAGCACGGATTTTCAATACATATGGGCCTCGTATGTGTATTGATGATGGGCGTGTGGTTAGCAATTTTGTTGCACAG
  ||   ||    | ||  |  || | ||   |   |  |  || | |   | |  ||| |||  | |   |  |||   |  || | |    | ||  |||||| || || || || ||||||||||||||||| ||||| |||||| | |||||||| ||||||||||||||||||||||| |||
-ttgctgcaatactgtagttcgtattgtagcattatgtgacttcaacatcttagtaactatagctatt--ctacgatcttttgctaactgacttattatgcagGTGCGCATTGCTCGCATTTTCAATACATATGGCCCTCGAATGTGTCTAGATGATGGCCGTGTGGTTAGCAATTTTGTTGCCCAG

upper sequence: Vv08s0040g02710.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os03g17230.1 (Oryza sativa), 3'ss of exon 3
aatgggccatccttataacttctactttactgtatagatatctccataaagtggactgtagacaatagtttgga---ttaatcactgaattttctgttcgcagGTACGTATAGCACGGATTTTCAATACATATGGGCCTCGTATGTGTATTGATGATGGGCGTGTGGTTAGCAATTTTGTTGCACAG
  |   |||    | |   || |   ||     | |    |  | |   | |||  |  |   | ||    | |   || |  |   ||| ||   | | |||||  | || || || || ||||| |||||||| |||||||||||| | ||||||||||| || |||||||| || || || |||
--tttaccacatgttttgtttatgtgttgagtaacatcattgcctactgaatggtttccatttattaaagagaaaacttgactaacaaatgtttc-tcctcagGTGAGAATTGCGCGAATATTCAACACATATGGCCCTCGTATGTGTTTAGATGATGGGCGAGTTGTTAGCAACTTCGTCGCTCAG

upper sequence: Vv08s0040g02710.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G370048_T01 (Zea mays), 3'ss of exon 4
------aatgggccatccttataacttctactttactgtatagatatctccataaagtggactgtagacaatagtttggattaatcactgaattttctgttcgcagGTACGTATAGCACGGATTTTCAATACATATGGGCCTCGTATGTGTATTGATGATGGGCGTGTGGTTAGCAATTTTGTTGCACAG
        ||||  |       || |  | |    || |||   || |   | |   ||   | |   |   | | ||  ||  | |||  | |    |||  ||||| ||||| || || ||||||||||||||||| |||||||||||| | |||||||| |||||||| ||||||||||||||||||
tcttctggtgggataaaaaacaaaataatgcagctctttat---tagccttagattttgttatctctccttgaatatgttttcctaacttgaata---gttaacagGTGCGTATTGCCCGCATTTTCAATACATATGGTCCTCGTATGTGTCTCGATGATGGCCGTGTGGTCAGCAATTTTGTTGCACAG

upper sequence: Vv08s0040g02710.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G359234_T03 (Zea mays), 3'ss of exon 3
-aatgggccatccttataacttctactttactgtatagatatctccataaagtggactgtagacaatagtttggattaatcactgaattttct-gttcgcagGTACGTATAGCACGGATTTTCAATACATATGGGCCTCGTATGTGTATTGATGATGGGCGTGTGGTTAGCAATTTTGTTGCACAG
 |||   |       ||||     |          |   |||   | |||| |    | |      | |  |   ||  | ||| |  |   | |||  ||||| ||||| || || ||||||||||||||||| |||||||||||  | || ||||| |||||||| ||||||||||||||||||
taatattctggtggaataaaacaaaacactgcagctccttattagcttaaaatttgttatcactccttgaatatgtt--ttactaacctgaatagttaacagGTGCGTATTGCCCGTATTTTCAATACATATGGTCCTCGTATGTGCCTCGACGATGGTCGTGTGGTCAGCAATTTTGTTGCACAG

upper sequence: Vv08s0040g02710.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G347717_T01 (Zea mays), 3'ss of exon 3
--------aatgggccatccttataacttctactttactgtatagat-atctccataaagtggactgtagacaatagtttggattaatcactgaattttctgttcgcagGTACGTATAGCACGGATTTTCAATACATATGGGCCTCGTATGTGTATTGATGATGGGCGTGTGGTTAGCAATTTTGTTGCACAG
         ||  |      | ||   | | | ||  |||| |   | ||||  ||    |    || |||  | | ||||   ||    |||   || |    | |||||  | || ||||| || || || |||||||| ||||| |||||| | |||||||| || || |||||||| ||||||||||||
tctttgtttatatgttgcaatgatgcttacgagttgtctgtgtgctttatctttattctcttc-ttgaagagcaaactttgacata----ctgtgcttcc----ctcagGTGAGAATTGCACGCATATTTAACACATATGGCCCTCGAATGTGTTTAGATGATGGCCGAGTTGTTAGCAACTTTGTTGCACAG

upper sequence: Vv08s0040g02710.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G19640.1 (Glycine max), 3'ss of exon 3
aatgggccatccttataacttctactttactgtatagatatctccataaagtggactgtagacaatagtttggattaa---tcactgaattttctg-ttcgcagGTACGTATAGCACGGATTTTCAATACATATGGGCCTCGTATGTGTATTGATGATGGGCGTGTGGTTAGCAATTTTGTTGCACAG
         |  |  | | |   || | | || |     | || | ||  ||  | | |  | | ||  |   ||| |   | |     | |  || ||   |||| ||||| || || ||||||||||||||||| || || |||||| | |||||||||||||| |||||||||||||||||||||
----aaaattagtagttaatcacacataagtgaaatttaaactacctatggtaaattttgcaaattaaatgctattgagactgatctggtgtgatggtttatagGTTCGTATTGCTCGAATTTTCAATACATATGGACCCCGCATGTGTTTGGATGATGGGCGTGTCGTTAGCAATTTTGTTGCACAG

upper sequence: Vv08s0040g02710.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G05260.1 (Glycine max), 3'ss of exon 3
------aatgggccatcctt-ataact----tctactttactgtatagatatctccataaagtggactgtagacaatagtttggattaatcactgaattttctgttcgcagGTACGTATAGCACGGATTTTCAATACATATGGGCCTCGTATGTGTATTGATGATGGGCGTGTGGTTAGCAATTTTGTTGCACAG
      ||| |   ||| |  |||| |    | ||   |||| ||| || |  ||   ||| |  |   ||        ||  ||   ||   ||  ||    |||   |||| ||||| || || |||||||| |||||||| || || |||||| | |||||||||||||| |||||||||||||||||||||
aaaacaaatagttaatcatagataagtggaatttaaactact-tatggaaaattctgcaaattacatgtta--------ttgagaccgatt--tggtttgatggtttatagGTTCGTATTGCTCGAATTTTCAACACATATGGACCCCGCATGTGTTTGGATGATGGGCGTGTTGTTAGCAATTTTGTTGCACAG

upper sequence: Vv08s0040g02710.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G53520.4 (Arabidopsis thaliana), 3'ss of exon 3
aatgggccat-ccttataacttctact-ttactgtatagatatctccataaagtggactgtagacaatagtttggattaatcactgaattttctgttcgcagGTACGTATAGCACGGATTTTCAATACATATGGGCCTCGTATGTGTATTGATGATGGGCGTGTGGTTAGCAATTTTGTTGCACAG
  |   | ||   ||  ||  | ||    |  ||  ||  ||| |||| |    ||| | ||    |||     |||   | |||| ||||||  ||  |||||  | || || || |||||||| |||||||||||  | |||||  |||||||||||||||| ||||| || |||||||| |||
-gtttccaatgttttggaatgtttagaactgatgactatttatgtccaaatcacgga-tataacttataagagtgatctctaactgcattttcaattttcagGTTAGAATTGCTCGTATTTTCAACACATATGGGCCCAGAATGTGCCTTGATGATGGGCGTGTTGTTAGTAACTTTGTTGCCCAG

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|110691835|gb|EE070393.1|EE070393
EST:     GTACAGCTGAAACTTTGACAATGGATTATCATAGAGGTGCTGATGTTGAG                         GTACGTATAGCACGAATTTTCAATACATATGGGCCTCGTATGTGTATTGAT
genomic: GTACAGCTGAAACTTTGACAATGGATTATCATAGAGGTGCTGAAGTTGAGgtaactggtc ... ctgttcgcagGTACGTATAGCACGGATTTTCAATACATATGGGCCTCGTATGTGTATTGAT
EST: gi|110387086|gb|EC951729.1|EC951729
EST:     GTACAGCTGAAACTTTGACAATGGATTATCATAGAGGTGCTGATGTTGAG                         GTACGTATAGCACGAATTTTCAATACATATGGGCCTCGTATGTGTATTGAT
genomic: GTACAGCTGAAACTTTGACAATGGATTATCATAGAGGTGCTGAAGTTGAGgtaactggtc ... ctgttcgcagGTACGTATAGCACGGATTTTCAATACATATGGGCCTCGTATGTGTATTGAT
EST: gi|22010887|gb|BQ795921.1|BQ795921
EST:     GTACAGCTGAAACTTTGACAATGGATTATCATAGAGGTGCTGAAGTTGAG                         GTACGTATAGCACGGATTTTCAATACATATGGGCCTCGTATGTGTATTGAT
genomic: GTACAGCTGAAACTTTGACAATGGATTATCATAGAGGTGCTGAAGTTGAGgtaactggtc ... ctgttcgcagGTACGTATAGCACGGATTTTCAATACATATGGGCCTCGTATGTGTATTGAT
EST: gi|30128347|gb|CB913686.1|CB913686
EST:     GTACAGCTGAAACTTTGACAATGGATTATCATAGAGGTGCTGAAGTTGAG                         GTACGTATAGCACGGATTTTCAATACATATGGGCCTCGTATGTGTATTGAT
genomic: GTACAGCTGAAACTTTGACAATGGATTATCATAGAGGTGCTGAAGTTGAGgtaactggtc ... ctgttcgcagGTACGTATAGCACGGATTTTCAATACATATGGGCCTCGTATGTGTATTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataaagtggactgtagacaatagtttggattaatcactgaattttctgttcgcagGTACGTATAGCACGGATTTTCAATACATATGGGCCTCGTATGTGTATTGATGATGGGCGTGTGGTTAGCAATTTTGTTGCACAG
                           gattaat  putative branch site (score: 3)
                                         ttttctgttc  putative PPT
                  aatagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgggccatccttataacttctactttactgtatagatatctccataaagtggactgtagacaatagtttggattaatcactgaattttctgttcgcagGTACGTATAGCACGGATTTTCAATACATATGGGCCTCGTATGTGTATTGATGATGGGCGTGTGGTTAGCAATTTTGTTGCACAG

- - - ccatcct
- - - - - - - - - cttctac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agacaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cactgaa