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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataggcacctgagatcaaattgatgaaattttatatttcttagatgttgtcacctaagaaatatgttattttttccattcagGTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGG

Basic information

species Vitis vinifera
transcript Vv02s0025g03530.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g03530.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os07g27790.1 (Oryza sativa), 3'ss of exon 11
gtataggcacctgagatcaaattgatgaaattttatatttcttagatgttgtcacct------aagaaatatgttattttttccatt-------cagGTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGG
   |  || | | |  |   || | |||    | ||      | ||   ||| | ||      || || ||| |  | ||||  |||       ||||||||||||||| ||||  | || ||||| ||||||||||| || || |||||||| || |||||||||||||||||||||
--gtttgcccttaaatttgtatagctgat-catcatggcatgttgacactgtaagcttaatgtaataactatttgttcttttgtatttggcttgcagGTCAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGCATTTTGG

upper sequence: Vv02s0025g03530.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os05g03820.3 (Oryza sativa), 3'ss of exon 11
----------------gtataggcacctgagatcaaattgatgaaattttatatttcttagatgttgtcacctaagaaatatgttattttttccattcagGTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGG
                ||||||     | |        || ||| | | |||  ||     ||||  | || ||     | | || | |||  | | ||||| ||||||||| ||||  | || ||||| ||||||||||| || || |||||||| || ||||||||||||| |||||||
gtttgcccttcaatttgtatagcacgatcatcatggcatgttgacactgtatgctt----aatgtaataac-tatttgttcttttgtatttggcttgcagGTTAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGTATTTTGG

upper sequence: Vv02s0025g03530.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G111579_T01 (Zea mays), 3'ss of exon 10
gtataggcacctgag-atcaaattgatgaaat-tttatatttcttagatgttgtcacctaagaaatatgttattttttccattcagGTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGG
|| ||  |   |     |  |   ||||  || | | |  ||  ||| | | |  |         | |  |   || | | | ||||| ||||| ||||| ||| | || ||||| ||||||||||| || || |||||||| || ||||| ||||| |||||||||
gtttacccttttatctgtttacacgatggcatatctgtcgttgctaggtatcgcaataactcttgtcttctgcattctgcttgcagGTTAGGCTAAAGAGGTACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGTTGCCTGCATTTTGG

upper sequence: Vv02s0025g03530.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA08G01750.2 (Glycine max), 3'ss of exon 10
--------gtataggcacctgagatcaaattga---tgaaattttata-----tttcttagatgttgtcacctaagaaa--tatgttatttt-ttccattcagGTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGG
         ||| ||   |  |  | || | |    ||    |||  |     |||     |  ||      |  | ||  | |||||  || |||  |||||||||||||||||||||| ||||| ||||| ||||||||||||||||| ||||| |||||||||||||| ||||||||||||
gttagtttctattggtttcacaatttaactggtatctgttgctttgcaatagatttgcagcactttccttgttgtgtaacttgtgttacattattcttttcagGTCAGGCTGAAGAGATATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGGAGAAGGTTATGTGCTTTACCAGCATTTTGG

upper sequence: Vv02s0025g03530.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA05G37850.1 (Glycine max), 3'ss of exon 11
--------gtataggcacctgagatcaaattgatgaaattttatatttcttagat--gttgtcacctaagaaatatgttatt---------ttttccattcagGTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGG
         ||| ||   |  |  |  || || |     ||  | |   || |||  |  |     |      | |||||||         | |||  ||||||||||||||||||| || ||||| ||||| ||||||||||||||||| ||||| || || |||||||| ||||||||||||
gttagtttctattggtttcacaattttaactggtatctgttgctttgcattggatttgcagcactttccttgttgtgttattgtaaaccattattcttttcagGTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGG

upper sequence: Vv02s0025g03530.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT4G23100.3 (Arabidopsis thaliana), 3'ss of exon 11
gtataggcacctgagatcaaattgatgaaattt-tatatttcttagatgttgtcacctaa----gaaatatgttattttttc----cattcagGTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGG
|| ||  || |||     | | |  |  |||     |||  |||  || |      || |    ||| | ||  |   || |    || | ||||  || |||||||||||||||| ||||| |||||||||||||| |||||||||||| | |||||  ||||||| || |||
gt-taatcatctgcctcaagagtctttcaatcagcctatgactttcatttccctgtcttatgttgaagtctgacaacgttccataacact-agGTTCGGTTGAAGAGATACTTGGAGATGAGAGGTGCTGATGGAGGTCCCTGGAGGAGGCTGTGTGCCCTGCCAGCTTTCTGG

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|27580232|gb|CB002927.1|CB002927
EST:     AACAATATTCCCTGAG                         GTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGG
genomic: AACAATATTCCCTGAGgtataggcac ... ttccattcagGTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGG
EST: gi|22009546|gb|BQ794580.1|BQ794580
EST:     TGCCAAACTTCAATGATTGGGAGAATCATCTGACAACAATATTCCCTGAG                         GTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGTAGGGCCCTGG
genomic: TGCCAAACTTCAATGATTGGGAGAATCATCTGACAACAATATTCCCTGAGgtataggcac ... ttccattcagGTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGG
EST: gi|254917830|gb|GR903482.1|GR903482
EST:     TGCCAAACTTCAATGATTGGGAGAATCATCTGACAACAATATTCCCTGAG                         GTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGG
genomic: TGCCAAACTTCAATGATTGGGAGAATCATCTGACAACAATATTCCCTGAGgtataggcac ... ttccattcagGTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGG
EST: gi|110428549|gb|EC995024.1|EC995024
EST:     TGCCAAACTTCAATGATTGGGAGAATCATCTGACAACAATATTCCCTGAG                         GTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGG
genomic: TGCCAAACTTCAATGATTGGGAGAATCATCTGACAACAATATTCCCTGAGgtataggcac ... ttccattcagGTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGG
EST: gi|110725594|gb|EE102275.1|EE102275
EST:     TGCCAAACTTCAATGATTGGGAGAATCATCTGACAACAATATTCCCTGAG                         GTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGG
genomic: TGCCAAACTTCAATGATTGGGAGAATCATCTGACAACAATATTCCCTGAGgtataggcac ... ttccattcagGTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGG
EST: gi|32245737|gb|CD711556.1|CD711556
EST:     TGCCAAACTTCAATGATTGGGAGAATCATCTGACAACAATATTCCCTGAG                         GTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGG
genomic: TGCCAAACTTCAATGATTGGGAGAATCATCTGACAACAATATTCCCTGAGgtataggcac ... ttccattcagGTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGG
EST: gi|30130004|gb|CB915343.1|CB915343
EST:     TGCCAAACTTCAATGATTGGGAGAATCATCTGACAACAATATTCCCTGAG                         GTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGG
genomic: TGCCAAACTTCAATGATTGGGAGAATCATCTGACAACAATATTCCCTGAGgtataggcac ... ttccattcagGTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGG
EST: gi|22009504|gb|BQ794538.1|BQ794538
EST:     TGCCAAACTTCAATGATTGGGAGAATCATCTGACAACAATATTCCCTGAG                         GTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGTAGGGCCCTGG
genomic: TGCCAAACTTCAATGATTGGGAGAATCATCTGACAACAATATTCCCTGAGgtataggcac ... ttccattcagGTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGG
EST: gi|27586164|gb|CB008859.1|CB008859
EST:     TGCCAAACTTCAATGATTGGGAGAATCATCTGACAACAATATTCCCTGAG                         GTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGG
genomic: TGCCAAACTTCAATGATTGGGAGAATCATCTGACAACAATATTCCCTGAGgtataggcac ... ttccattcagGTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGG
EST: gi|30297452|gb|CB974246.1|CB974246
EST:     TGCCAAACTTCAATGATTGGGAGAATCATCTGACAACAATATTCCCTGAG                         GTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGG
genomic: TGCCAAACTTCAATGATTGGGAGAATCATCTGACAACAATATTCCCTGAGgtataggcac ... ttccattcagGTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGG
EST: gi|32246359|gb|CD712178.1|CD712178
EST:     TGCCAAACTTCAATGATTGGGAGAATCATCTGACAACAATATTCCCTGAG                         GTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGG
genomic: TGCCAAACTTCAATGATTGGGAGAATCATCTGACAACAATATTCCCTGAGgtataggcac ... ttccattcagGTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGG
EST: gi|32247869|gb|CD713688.1|CD713688
EST:     TGCCAAACTTCAATGATTGGGAGAATCATCTGACAACAATATTCCCTGAG                         GTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGG
genomic: TGCCAAACTTCAATGATTGGGAGAATCATCTGACAACAATATTCCCTGAGgtataggcac ... ttccattcagGTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGG
EST: gi|30125117|gb|CB910456.1|CB910456
EST:     TGCCAAACTTCAATGATTGGGAGAATCATCTGACAACAATATTCCCTGAG                         GTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGG
genomic: TGCCAAACTTCAATGATTGGGAGAATCATCTGACAACAATATTCCCTGAGgtataggcac ... ttccattcagGTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGG
EST: gi|30322432|gb|CD005694.1|CD005694
EST:     AACAATATTCCCTGAG                         GTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGG
genomic: AACAATATTCCCTGAGgtataggcac ... ttccattcagGTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGG
EST: gi|37187375|gb|CF606728.1|CF606728
EST:     TGCCAAACTTCAATGATTGGGAGAATCATCTGACAACAATATTCCCTGAG                         GTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGG
genomic: TGCCAAACTTCAATGATTGGGAGAATCATCTGACAACAATATTCCCTGAGgtataggcac ... ttccattcagGTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttatatttcttagatgttgtcacctaagaaatatgttattttttccattcagGTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGG
                                      ttattttttccattc  CT-rich tract
                           taagaaatatgttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataggcacctgagatcaaattgatgaaattttatatttcttagatgttgtcacctaagaaatatgttattttttccattcagGTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG