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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtcttttgttggccaactagctaactaggaagtgaaaactccatgtggcagctctttatttattttttcatttttcttagccggtcacttttacaacagGGAGAGGATTTGATACGGGAAAGTGGAGTGCCTTATGCAATTGTGAGGCCTTGTGCATTAACTGAGGAGCCTGCTGGAGCTGATCTCATTTTTGATCAAG

Basic information

species Vitis vinifera
transcript Vv10s0003g01640.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g01640.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os02g13970.2 (Oryza sativa), 3'ss of exon 13
tgtcttttgttggccaactagctaactaggaagtgaaaactccatgtggcagctctttatttattttttcatttttcttagccggtcacttttacaacagGGAGAGGATTTGATACGGGAAAGTGGAGTGCCTTATGCAATTGTGAGGCCTTGTGCATTAACTGAGGAGCCTGCTGGAGCTGATCTCATTTTTGATCAAG
       | |  ||||  |  |    |    | ||   | |   ||||     |  ||    ||  | ||    | |||| |   |  | |||    ||||| |||||||| || |||||||||||  | || ||| | |||||| |||| |||||  |||| ||||| || ||||||||||| ||||| ||||| || |
------gtatgcgccatttttcc--tttattattgtgcatt---tgtgcttattgatt-cacatcatgtctaaatgcttatcgcatgtccttt----cagGGTGAGGATTTAATCCGGGAAAGTGGCATTCCATATACTATTGTGCGGCCATGTGCTCTAACAGAGGAACCAGCTGGAGCTGACCTCATATTTGACCAGG

upper sequence: Vv10s0003g01640.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G019358_T03 (Zea mays), 3'ss of exon 11
tgtcttttgttggccaactagctaactaggaagtgaaaactccatgtggcagctctttatttattttttcatttttcttagccggtcacttttaca--acagGGAGAGGATTTGATACGGGAAAGTGGAGTGCCTTATGCAATTGTGAGGCCTTGTGCATTAACTGAGGAGCCTGCTGGAGCTGATCTCATTTTTGATCAAG
  |||   ||     ||       |||    | ||    ||||   |     |   ||  |||| ||   |   || |     |       |  |    |||||||||||||| || |||||||| ||  | || ||  | ||||| ||||| ||||||||||||||||| || |||||||| |||||||| ||||| || |
catctaa-gtactttaagatatagactgaacaatggtg-ctcctcattttgtcatgttggttatcttggaaccattatataatgtctgaggtggcctttcagGGAGAGGATTTAATTCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCATGTGCATTAACTGAGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGG

upper sequence: Vv10s0003g01640.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA08G12480.1 (Glycine max), 3'ss of exon 13
--tgtcttttgttggccaactagctaactaggaagt-gaaaactccatgtggcagctctttatttattttttcatttttcttagccggtcacttttacaacagGGAGAGGATTTGATACGGGAAAGTGGAGTGCCTTATGCAATTGTGAGGCCTTGTGCATTAACTGAGGAGCCTGCTGGAGCTGATCTCATTTTTGATCAAG
     ||  |  | ||  || |   | |||   |||  |  | |  || |  |  |   | |  || || |||||||     |   ||| | | || |||||||| ||||||||  |  | ||||||||  | || |||||||| ||||||||||||||||||||||||||||||||||| ||  |||| |||||||||||||
ggaacctccttattgcttacca-taacctatttagttaaggaattgatatttc--cctgtcacataattgttcatttgctaaaagtggttaatgttgcaacagGGCGAGGATTTACTTAGAGAAAGTGGCATTCCCTATGCAATCGTGAGGCCTTGTGCATTAACTGAGGAGCCTGCTGGTGCCAATCTTATTTTTGATCAAG

upper sequence: Vv10s0003g01640.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA05G29330.2 (Glycine max), 3'ss of exon 13
------tgtcttttgttggccaactagctaactaggaagtgaaaactccatgtggcagctctttatttattttttcatttttcttagccggtcacttttacaacagGGAGAGGATTTGATACGGGAAAGTGGAGTGCCTTATGCAATTGTGAGGCCTTGTGCATTAACTGAGGAGCCTGCTGGAGCTGATCTCATTTTTGATCAAG
      |   | ||| | ||||  ||||  | |  |   || ||  | ||| |  |  |     |  || || |||||||     |   |||   | || |||||||| ||||||||  |  | ||||||||  | || |||| ||| ||||||||||||||||||||||||||||||||||| || ||||| |||||||||||||
ggaacctccttattgcttgcca--tagcctatttagttatgcaa--ttcatatttc--cctgccacatacttgttcatttgctaaaagtggtttatgttgcaacagGGCGAGGATTTACTTAGAGAAAGTGGCATTCCCTATGTAATCGTGAGGCCTTGTGCATTAACTGAGGAGCCTGCTGGTGCCGATCTTATTTTTGATCAAG

upper sequence: Vv10s0003g01640.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT4G18810.1 (Arabidopsis thaliana), 3'ss of exon 13
tgtcttttgttggccaactagctaactaggaagtgaaaactccatgtggcagctctttatttattttttcatttttcttagccggtcacttttacaacagGGAGAGGATTTGATACGGGAAAGTGGAGTGCCTTATGCAATTGTGAGGCCTTGTGCATTAACTGAGGAGCCTGCTGGAGCTGATCTCATTTTTGATCAAG
     |||||    | |    ||  ||     |   ||| |       |    | |  |   |||||     | ||  |      | |||        ||||||||||| ||||||| || || ||  | || | |||||||||  |||| ||||| ||||| || |||||||| ||||||||||||||||| || ||||
----gtttgtctctctat--actctctgcttcgcagaaaattggaaaagtcattttcaaaagattttaaagctcttacttttgaatgact--------agGGAGAGGATCTGATACGCGACAGCGGGATTCCATTTGCAATTGTACGGCCATGTGCTTTAACAGAAGAGCCTGCCGGAGCTGATCTCATTTTCGAACAAG

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|30329616|gb|CD012878.1|CD012878
EST:     CTGTTCGCTTGAACAAGGAATTGGGCTTCATTCTCACATTCAAGTTGAAG                         GGAGAGGATTTGATACGGGAAAGTGGAGTGTCTTATGCAATTGTGAGGCCT
genomic: CTGTTCGCTTGAACAAGGAATTGGGCTTCATTCTCACATTCAAGTTGAAGgtttcatact ... tttacaacagGGAGAGGATTTGATACGGGAAAGTGGAGTGCCTTATGCAATTGTGAGGCCT
EST: gi|351013609|gb|FQ429750.1|FQ429750
EST:     CTGTTCGCTTGAACAAGGAATTGGGCTTCATTCTCACATTCAAGTTGAAG                         GGAGAGGATTTGATACGGGAAAGTGGAGTGCCTTATGCAATTGTGAGGCCT
genomic: CTGTTCGCTTGAACAAGGAATTGGGCTTCATTCTCACATTCAAGTTGAAGgtttcatact ... tttacaacagGGAGAGGATTTGATACGGGAAAGTGGAGTGCCTTATGCAATTGTGAGGCCT
EST: gi|110724595|gb|EE100559.1|EE100559
EST:     AAGGAATTGGGCTTCATTCTCACATTCAAGTTGAAG                         GGAGAGGATTTGATACGGGAAAGTGGAGTGCCTTATGCAATTGTGAGGCCT
genomic: AAGGAATTGGGCTTCATTCTCACATTCAAGTTGAAGgtttcatact ... tttacaacagGGAGAGGATTTGATACGGGAAAGTGGAGTGCCTTATGCAATTGTGAGGCCT
EST: gi|161721461|gb|FC070452.1|FC070452
EST:     CTGTTCGCTTGAACAAGGAATTGGGCTTCATTCTCACATTCAAGTTGAAG                         GGAGAGGATTTGATACGGGAAAGTGGAGTGCCTTATGCAATTGTGAGGCCT
genomic: CTGTTCGCTTGAACAAGGAATTGGGCTTCATTCTCACATTCAAGTTGAAGgtttcatact ... tttacaacagGGAGAGGATTTGATACGGGAAAGTGGAGTGCCTTATGCAATTGTGAGGCCT
EST: gi|351019257|gb|FQ429417.1|FQ429417
EST:     CTGTTCGCTTGGACAAGGAATTGGGCTTCATTCTCACATTCAAGTTGAAG                         GGAGAGGATTTGATACGGGAAAGTGGAGTGCCTTATGCAATTGTGAGGCCT
genomic: CTGTTCGCTTGAACAAGGAATTGGGCTTCATTCTCACATTCAAGTTGAAGgtttcatact ... tttacaacagGGAGAGGATTTGATACGGGAAAGTGGAGTGCCTTATGCAATTGTGAGGCCT
EST: gi|110361661|gb|EC925153.1|EC925153
EST:     CTGTTCGCTTGAACAAGGAATTGGGCTTCATTCTCACATTCAAGTTGAAG                         GGAGAGGATTTGATACGGGAAAGTGGAGTGCCTTATGCAATTGTGAGGCCT
genomic: CTGTTCGCTTGAACAAGGAATTGGGCTTCATTCTCACATTCAAGTTGAAGgtttcatact ... tttacaacagGGAGAGGATTTGATACGGGAAAGTGGAGTGCCTTATGCAATTGTGAGGCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtggcagctctttatttattttttcatttttcttagccggtcacttttacaacagGGAGAGGATTTGATACGGGAAAGTGGAGTGCCTTATGCAATTGTGAGGCCTTGTGCATTAACTGAGGAGCCTGCTGGAGCTGATCTCATTTTTGATCAAG
                                        tcactttt  CT-rich tract
        tctttatttatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtcttttgttggccaactagctaactaggaagtgaaaactccatgtggcagctctttatttattttttcatttttcttagccggtcacttttacaacagGGAGAGGATTTGATACGGGAAAGTGGAGTGCCTTATGCAATTGTGAGGCCTTGTGCATTAACTGAGGAGCCTGCTGGAGCTGATCTCATTTTTGATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - ttgttgg
- - - - - - -ccaacta
- - - - - - - - - - - - - - - aagtgaaa
- - - - - - - - - - - - - - - - - - - -ctccatg