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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctgcacaagttgaccatgggtcataagtattacttggtgccttccaaaataataaatatttaactggtgtcttattgaagcatttggttggttatgcagATCTTAGCCTTAGATGAACGCTACAGGCTATCGGAGTCAAAGGATTATGAGGTGAAGGTGGCATTTCTCCAACTGGCCATCTTAGCTGGGTGCAAAGATT

Basic information

species Vitis vinifera
transcript Vv13s0067g03300.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0067g03300.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA20G38780.1 (Glycine max), 3'ss of exon 3
cctgcacaagttgaccatgggtcataagtattacttggtgccttccaaa-ataataaatatttaactggtgtcttat--tgaagcatttggttg------gttatgcagATCTTAGCCTTAGATGAACGCTACAGGCTATCGGAGTCAAAGGATTATGAGGTGAAGGTGGCATTTCTCCAACTGGCCATCTTAGCTGGGTGCAAAGATT
       |  ||     ||   | | | | | |   |   | || || | ||| |   | ||||    ||||   ||  | |  | ||||  |       || |||||| || ||| ||| |||  |||||||| |||||| |||||||| ||||| ||||| |||||| |||||||||||  ||| || | |  ||| ||||||  ||
-------acatttgt--tgaaactttaatgtcatacgcctcattgcacatatattgcctgtttactgtgtgttccatcttaattcttttgtataatacatgtcatgcagGTCATAGACTTGGATTCACGCTACAAGCTATCTGAGTCAAAAGATTACGAGGTAAAGGTGTCATTTCTCCAAAGGGCTATTTCATGTGGATGCAAAACTT
















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|110684727|gb|EE062338.1|EE062338
EST:     AATGGGAGCTCTACTTGGAGAACCTCCCAAAATCTGTAGAAGCTTCCCAG                         ATCTTAGCCTTAGATGAACGCTACAGGCTATCGGAGTCAAAGGATTATGAG
genomic: AATGGGAGCTCTACTTGGAGAACCTCCCAAAATCTGTAGAAGCTTCCCAGgtatggtttt ... ggttatgcagATCTTAGCCTTAGATGAACGCTACAGGCTATCGGAGTCAAAGGATTATGAG
EST: gi|34415539|gb|CF414293.1|CF414293
EST:     GAGCTCTACTTGGAGAACCTCCCCAAATCTGTAGAAGCTTCCCAG                         ATCTTAGCCTTAGATGAACGCTACAGGCTATCGGAGTCAAAGGATTATGAG
genomic: GAGCTCTACTTGGAGAACCTCCCAAAATCTGTAGAAGCTTCCCAGgtatggtttt ... ggttatgcagATCTTAGCCTTAGATGAACGCTACAGGCTATCGGAGTCAAAGGATTATGAG
EST: gi|110685534|gb|EE062336.1|EE062336
EST:     A-TGGGAGCTCTACTTGGAGAACCTCCCAAAATCTGTAGAAGCTTCCCAG                         ATCTTAGCCTTAGATGAACGCTACAGGCTATTGGAGTCAAAGGATTATGAG
genomic: AATGGGAGCTCTACTTGGAGAACCTCCCAAAATCTGTAGAAGCTTCCCAGgtatggtttt ... ggttatgcagATCTTAGCCTTAGATGAACGCTACAGGCTATCGGAGTCAAAGGATTATGAG
EST: gi|110426221|gb|EC992622.1|EC992622
EST:     AATGGGAGCTCTACTTGGAGAACCTCCCAAAATCTGTAGAAGCTTCCCAG                         ATCTTAGCCTTAGATGAACGCTACAGGCTATCGGAGTCAAAGGATTATGAG
genomic: AATGGGAGCTCTACTTGGAGAACCTCCCAAAATCTGTAGAAGCTTCCCAGgtatggtttt ... ggttatgcagATCTTAGCCTTAGATGAACGCTACAGGCTATCGGAGTCAAAGGATTATGAG
EST: gi|110362378|gb|EC925908.1|EC925908
EST:     AATGGGAGCTCTACTTGGAGAACCTCCCAAAATCTGTAGAAGCTTCCCAG                         ATCTTAGCCTTAGATGAACGCTACAGGCTATCGGAGTCAAAGGATTATGAG
genomic: AATGGGAGCTCTACTTGGAGAACCTCCCAAAATCTGTAGAAGCTTCCCAGgtatggtttt ... ggttatgcagATCTTAGCCTTAGATGAACGCTACAGGCTATCGGAGTCAAAGGATTATGAG
EST: gi|29782758|gb|CB348337.2|CB348337
EST:     AATGGGAGCTCTACTTGGAGAACCTCCCAAAATCTGTAGAAGCTTCCCAG                         ATCTTAGCCTTAGATGAACGCTACAGGCTATCGGAGTCAAAGGATTATGAG
genomic: AATGGGAGCTCTACTTGGAGAACCTCCCAAAATCTGTAGAAGCTTCCCAGgtatggtttt ... ggttatgcagATCTTAGCCTTAGATGAACGCTACAGGCTATCGGAGTCAAAGGATTATGAG
EST: gi|29782793|gb|CB348418.2|CB348418
EST:     AATGGGAGCTCTACTTGGAGAACCTCCCAAAATCTGTAGAAGCTTCCCAG                         ATCTTAGCCTTAGATGAACGCTACAGGCTATCGGAGTCAAAGGATTATGAG
genomic: AATGGGAGCTCTACTTGGAGAACCTCCCAAAATCTGTAGAAGCTTCCCAGgtatggtttt ... ggttatgcagATCTTAGCCTTAGATGAACGCTACAGGCTATCGGAGTCAAAGGATTATGAG
EST: gi|352776634|gb|FQ465432.1|FQ465432
EST:     AATGGGAGCTCTACTTGGAGAACCTCCCAAAATCTGTAGAAGCTTCCCAG                         ATCTTAGCCTTAGATGAACGCTACAGGCTATCGGAGTCAAAGGATTATGAG
genomic: AATGGGAGCTCTACTTGGAGAACCTCCCAAAATCTGTAGAAGCTTCCCAGgtatggtttt ... ggttatgcagATCTTAGCCTTAGATGAACGCTACAGGCTATCGGAGTCAAAGGATTATGAG
EST: gi|352781911|gb|FQ469208.1|FQ469208
EST:     AATGGGAGCTCTACTTGGAGAACCTCCCAAAATCTGTAGAAGCTTCCCAG                         ATCTTAGCCTTAGATGAACGCTACAGGCTATCGGAGTCAAAGGATTATGAG
genomic: AATGGGAGCTCTACTTGGAGAACCTCCCAAAATCTGTAGAAGCTTCCCAGgtatggtttt ... ggttatgcagATCTTAGCCTTAGATGAACGCTACAGGCTATCGGAGTCAAAGGATTATGAG
EST: gi|352781501|gb|FQ468345.1|FQ468345
EST:     AATGGGAGCTCTACTTGGAGAACCTCCCAAAATCTGTAGAAGCTTCCCAG                         ATCTTAGCCTTAGATGAACGCTACAGGCTATCGGAGTCAAAGGATTATGAG
genomic: AATGGGAGCTCTACTTGGAGAACCTCCCAAAATCTGTAGAAGCTTCCCAGgtatggtttt ... ggttatgcagATCTTAGCCTTAGATGAACGCTACAGGCTATCGGAGTCAAAGGATTATGAG
EST: gi|30125077|gb|CB910416.1|CB910416
EST:     AATGGGAGCTCTACTTGGAGAACCTCCCAAAATCTGTAGAGGCTTCCCAG                         ATCTTAGCCTTAGATGAACGCTACAGGCTATCGGAGTCAAAGGATTATGAG
genomic: AATGGGAGCTCTACTTGGAGAACCTCCCAAAATCTGTAGAAGCTTCCCAGgtatggtttt ... ggttatgcagATCTTAGCCTTAGATGAACGCTACAGGCTATCGGAGTCAAAGGATTATGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaaataataaatatttaactggtgtcttattgaagcatttggttggttatgcagATCTTAGCCTTAGATGAACGCTACAGGCTATCGGAGTCAAAGGATTATGAGGTGAAGGTGGCATTTCTCCAACTGGCCATCTTAGCTGGGTGCAAAGATT
             atttaac  putative branch site (score: 3)
     taataaatatttaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctgcacaagttgaccatgggtcataagtattacttggtgccttccaaaataataaatatttaactggtgtcttattgaagcatttggttggttatgcagATCTTAGCCTTAGATGAACGCTACAGGCTATCGGAGTCAAAGGATTATGAGGTGAAGGTGGCATTTCTCCAACTGGCCATCTTAGCTGGGTGCAAAGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
cctgcac
- - - - - - -accatgg
- - - - - - - - - - - - - - - -tacttgg
- - - - - - - - - - - - - - - - - - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatttg