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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gataagtaatttgaaataccctgttaagaatgtttctgttacagtgaaatgccatcctccttcctgtggcactactaatgttgtttggacttctgtgcagGATCCTCTGAGAGGTGGTAAAGATGAGCTGATTGACTATGTGGTTGCTTTCATACACTCAGGAGATGCAGAAGCTCTTGCTAAGGATTCCATGGCACCTC

Basic information

species Vitis vinifera
transcript Vv14s0006g00430.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0006g00430.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT3G02410.1 (Arabidopsis thaliana), 3'ss of exon 10
gataagtaatttgaaataccctgttaagaatgtttctgttacagtgaaatgccatcctccttcctgtggcactactaatgttgtttggacttctgtgca-gGATCCTCTGAGAGGTGGTAAAGATGAGCTGATTGACTATGTGGTTGCTTTCATACACTCAGGAGATGCAGAAGCTCTTGCTAAGGATTCCATGGCACCTC
     ||||    ||| | ||  | ||||   |||    ||||      | |    |||  |  |||    |||   |  ||      ||| |  |||| ||||||||||||||| ||||||||||||||  ||||  || | ||  || | |||||| | |  ||    || ||  |    || ||| |  | || || |
-----gtaagc--aaacaaccattaaagatcattttc--taca------tacatagctcaatgttgt----ctaaacacattac--aaactgcattgcaagGATCCTCTGAGAGGCGGTAAAGATGAGCTATTTGATCATATAGTCTCTATGATACACGCCGATGACAGTGACGCATTGAGAAACGATGCTGTTGCGCCAC
















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|110388405|gb|EC953154.1|EC953154
EST:     CTGAACTTATTTTATATGAAGGAAAAACTCATACAGATTTATTTCTTCAA                         GACCCTCTGAGAGGTGGTAAAGATGAGCTGATTGACTATGTGGTTGCTTTC
genomic: CTGAACTTATTTTATATGAAGGAAAAACTCATACAGATTTATTTCTTCAAgtaagagatg ... ttctgtgcagGATCCTCTGAGAGGTGGTAAAGATGAGCTGATTGACTATGTGGTTGCTTTC
EST: gi|110714548|gb|EE091581.1|EE091581
EST:     CTGAACTTATTTTATATGAAGGAAAAACTCATACAGATTTATTTCTTCAA                         GATCCTCTGAGAGGTGGTAAAGATGAGCTGATTGACTATGTGGTTGCTTTC
genomic: CTGAACTTATTTTATATGAAGGAAAAACTCATACAGATTTATTTCTTCAAgtaagagatg ... ttctgtgcagGATCCTCTGAGAGGTGGTAAAGATGAGCTGATTGACTATGTGGTTGCTTTC
EST: gi|30330044|gb|CD013306.1|CD013306
EST:     CTAAACTTATTTTATATGAAGGAAAAACTCATGCAGATTTATTTCTTCAA                         GACCCTCTGAGAGGTGGTAAAGATGAGCTGATTGACTATGTGGTTGCTTTC
genomic: CTGAACTTATTTTATATGAAGGAAAAACTCATACAGATTTATTTCTTCAAgtaagagatg ... ttctgtgcagGATCCTCTGAGAGGTGGTAAAGATGAGCTGATTGACTATGTGGTTGCTTTC
EST: gi|83275657|gb|DV939665.1|DV939665
EST:     CTGAACTTATTTTATATGAAGGAAAAACTCATACAGATTTATTTCTTCAA                         GACCCTCTGAGAGGTGGTAAAGATGAGCTGATTGACTATGTGGTTGCTTTC
genomic: CTGAACTTATTTTATATGAAGGAAAAACTCATACAGATTTATTTCTTCAAgtaagagatg ... ttctgtgcagGATCCTCTGAGAGGTGGTAAAGATGAGCTGATTGACTATGTGGTTGCTTTC
EST: gi|110411087|gb|EC976788.1|EC976788
EST:     CTGAACTTATTTTATATGAAGGAAAAACTCATACAGATTTATTTCTTCAA                         GATCCTCTGAGAGGTGGTAAAGATGAGCTGATTGACTATGTGGTTGCTTTC
genomic: CTGAACTTATTTTATATGAAGGAAAAACTCATACAGATTTATTTCTTCAAgtaagagatg ... ttctgtgcagGATCCTCTGAGAGGTGGTAAAGATGAGCTGATTGACTATGTGGTTGCTTTC
EST: gi|27582217|gb|CB004912.1|CB004912
EST:     CTGAACTTATTTTATATGAAGGAAAAACTCATACAGATTTATTTCTTCAA                         GACCCTCTGAGAGGTGGTAAAGATGAGCTGATTGACTATGTGGTTGCTTTC
genomic: CTGAACTTATTTTATATGAAGGAAAAACTCATACAGATTTATTTCTTCAAgtaagagatg ... ttctgtgcagGATCCTCTGAGAGGTGGTAAAGATGAGCTGATTGACTATGTGGTTGCTTTC
EST: gi|30328980|gb|CD012242.1|CD012242
EST:     CTGAACTTATTTTATATGAAGGAAAAACTCATACAGATTTATTTCTTCAA                         GACCCTCTGAGAGGTGGTAAAGATGAGCTGATTGACTATGTGGTTGCTTTC
genomic: CTGAACTTATTTTATATGAAGGAAAAACTCATACAGATTTATTTCTTCAAgtaagagatg ... ttctgtgcagGATCCTCTGAGAGGTGGTAAAGATGAGCTGATTGACTATGTGGTTGCTTTC
EST: gi|34364287|gb|CF405872.1|CF405872
EST:     CTGAACTTATTTTATATGAAGGAAAAACTCATACAGATTTATTTCTTCAA                         GACCCTCTGAGAGGTGGTAAAGATGAGCTGATTGACTATGTGGTTGCTTTC
genomic: CTGAACTTATTTTATATGAAGGAAAAACTCATACAGATTTATTTCTTCAAgtaagagatg ... ttctgtgcagGATCCTCTGAGAGGTGGTAAAGATGAGCTGATTGACTATGTGGTTGCTTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaatgccatcctccttcctgtggcactactaatgttgtttggacttctgtgcagGATCCTCTGAGAGGTGGTAAAGATGAGCTGATTGACTATGTGGTTGCTTTCATACACTCAGGAGATGCAGAAGCTCTTGCTAAGGATTCCATGGCACCTC
                           tactaat  putative branch site (score: 1)
                                            cttctgt  putative PPT
                           tactaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gataagtaatttgaaataccctgttaagaatgtttctgttacagtgaaatgccatcctccttcctgtggcactactaatgttgtttggacttctgtgcagGATCCTCTGAGAGGTGGTAAAGATGAGCTGATTGACTATGTGGTTGCTTTCATACACTCAGGAGATGCAGAAGCTCTTGCTAAGGATTCCATGGCACCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - gaaatac
- - - - - - - - - -cctgtta
- - - - - - - - - - - - - - - - - -ctgttac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggcacta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgg