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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtgacttcagatttgtgtttgtttatttatttttccttttagatttggcttagtaacaatagattctaagctatcctgagttgtcttgcagATCCTACATACATGATCCGTGCTATTCCAGGCAATGCATCTGACAATGTGTACTGCACACTCCTTGCTCAAAGTGCTGTTCATGGAGCAATGGCAGGTTA

Basic information

species Vitis vinifera
transcript Vv04s0008g00520.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os05g44922.1 (Oryza sativa), 3'ss of exon 12
gtcagtgacttcagatttgtgtttgtttat-ttatttttccttttag-atttggcttagtaacaatagattctaagctatcctgagttgtcttgcagATCCTACATACATGATCCGTGCTATTCCAGGCAATGCATCTGACAATGTGTACTGCACACTCCTTGCTCAAAGTGCTGTTCATGGAGCAATGGCAGGTTA
   |   |  |  | ||       | | |  || ||   | | |||  | | | ||   |   | ||  || | |  |  |||    |   ||||||||||||| ||||||||||| ||||||||| |||||||||| |||||||| |||||||| || || || || |||||| ||||||| |||||||| || ||
-gtaactatgtttgcttcacacaggataaggttgttacacatcttattactggtctctattgtactaagttgtgaagttccctattattatttgcagATCCTACCTACATGATCCGAGCTATTCCAAGCAATGCATCAGACAATGTCTACTGCACGCTGCTGGCCCACAGTGCTATTCATGGTGCAATGGCCGGCTA

upper sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os06g05860.1 (Oryza sativa), 3'ss of exon 12
gtcagtgacttcagatttgtgtttgtttatttatttttccttttagatttggcttagtaacaatagattctaagctatcctgagttgtcttgcagATCCTACATACATGATCCGTGCTATTCCAGGCAATGCATCTGACAATGTGTACTGCACACTCCTTGCTCAAAGTGCTGTTCATGGAGCAATGGCAGGTTA
||||||  | ||    || | ||    | ||    |  |    |    |||  ||      || | | ||| || | |  ||  || | |||||||||||||||||||||| ||||| |||||  |||||||||||||||||||||| ||||||||  | || || ||||  ||||||||||| ||||| || ||
gtcagtcgcctc----ttttattctacttttagcatcccaagctttgcttgatttcactgtaacaaaatctcagatcttatgc-ttctattgcagATCCTACATACATGATACGTGCCATTCCTAGCAATGCATCTGACAATGTGTATTGCACACTGTTGGCACACAGTGTGGTTCATGGAGCCATGGCTGGATA

upper sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 12
-------------------------------------gtcagtgacttcagatttgtgtttgtttatttatttttccttttagatttggcttagtaacaatagattctaagctatcctgagttgtcttgcagATCCTACATACATGATCCGTGCTATTCCAGGCAATGCATCTGACAATGTGTACTGCACACTCCTTGCTCAAAGTGCTGTTCATGGAGCAATGGCAGGTTA
                                      |  |       || ||   ||     | ||||| | |   |    || |  ||  | ||   |  | |   |||  |  |   |    | |||||||| || |||||||||||||| |||||| |||||||||| |||||||| ||||||||||| || || || |||||  ||||||| |||||||| || ||
gtaaagatcttgtttttatgttcaattctcgatgcacatgcggagtgctagtttgaagtactactttttatatgtatctgagtatctccctatggaatgttgcaataacagcc-tgttatttctaatggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA

upper sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G004932_T01 (Zea mays), 3'ss of exon 12
------gtcagtgact-tcagatttg-tgtttgtttatttatttttccttttagatttggcttagtaacaatagattctaagctatcctgagttgtcttgcagATCCTACATACATGATCCGTGCTATTCCAGGCAATGCATCTGACAATGTGTACTGCACACTCCTTGCTCAAAGTGCTGTTCATGGAGCAATGGCAGGTTA
       |  || ||| | |  |||| | ||  | || || |    | |||     ||||  | || ||||||  ||| |       | || |||    |||||||||||||||||| |||||||||||||| |||||||||| |||||||| ||||| ||||| || || || |||||| | ||||| |||||||| || ||
gtagccatttgtaactcttatttttgctattgatatagttgtaacacatttctagattggtct-gtgacaata--ttcca------tcggaattg----gcagATCCTACATACATGGTCCGTGCTATTCCAAGCAATGCATCAGACAATGTCTACTGTACACTTCTAGCCCACAGTGCTATCCATGGTGCAATGGCGGGGTA

upper sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 12
gtcagtgacttcagatttgtgtttgtttatttatttttccttttagatttggcttagtaacaatagattc--taagctatc--ctgagttgtcttgcagATCCTACATACATGATCCGTGCTATTCCAGGCAATGCATCTGACAATGTGTACTGCACACTCCTTGCTCAAAGTGCTGTTCATGGAGCAATGGCAGGTTA
|| |  | ||||   |||   || ||  |   | | ||  |||   ||||     | |  |||   ||    | |  |  |  |    || |  || |||||| || ||||||||||||||||||||| |||||||||| |||||||| || ||||| || || || || |||||  ||||||| |||||||| || ||
gtaatcgtcttcttttttac-ttggtgaacgcagtgttagtttgtaatttatagca-tgtcaaggaatctgatgaagtgcctgccatttttttatgtagATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCTATTGCACCCTGCTCGCACATAGTGCCATTCATGGTGCAATGGCGGGATA

upper sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 12
gtcagtgacttcagatttgtgtttgtttatttatttttccttttagatttggcttagtaacaatagat-tctaagctatcctgagttgtcttgcagATCCTACATACATGATCCGTGCTATTCCAGGCAATGCATCTGACAATGTGTACTGCACACTCCTTGCTCAAAGTGCTGTTCATGGAGCAATGGCAGGTTA
|||||||| ||    | | || |       | ||  || ||||  |    |  ||  || ||  | || ||| || |    | | |  |  ||||||||| || |||||||| ||||| |||||  |||| || ||||| ||||| ||||||||||| || ||||| ||||  || |||||||| ||||| || ||
gtcagtgattt----tctctggta------tcatgcttgctttacggcaagaattgctagcatcaaatatctcagatgctgtta-tcctactgcagATCCAACGTACATGATACGTGCCATTCCTAGCAACGCCTCTGATAATGTCTACTGCACACTGCTAGCTCACAGTGTGGTCCATGGAGCCATGGCTGGATA

upper sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 10
----------------------------------------------------------------------------------gtcagtgacttcagatttgtgtt-tgtttatttatttttccttttagatttggcttagtaacaatagattctaagctatcctgagttgtcttgcagATCCTACATACATGATCCGTGCTATTCCAGGCAATGCATCTGACAATGTGTACTGCACACTCCTTGCTCAAAGTGCTGTTCATGGAGCAATGGCAGGTTA
                                                                                      ||   || | |||||  |     |||| |  ||||  ||      |  || ||||   |  ||| | |  | | |  |    | |||  ||||||| || |||||||| || || |||||| |||||||||| |||||||| ||||| ||||| |||||||| ||||| || ||||| ||||||||||| ||
gtcagtttctcttacagcattctcctcttcctttttgacctatttatttcttacttagtctttcatttttatttcggatttgaaaggttttttaaaatttgactgacaattatctcattttaattgagttatctgcctagtgggataagacttt--gttgttattg--tatctgccagATCCAACTTACATGATTCGGGCAATTCCAAGCAATGCATCAGACAATGTCTACTGTACACTTCTTGCTCAGAGTGCAGTCCATGGTGCAATGGCAGGGTA

upper sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA04G09180.1 (Glycine max), 3'ss of exon 11
--------------------------------------------------gtcagtgacttcagatttgtgttt-----gtttatttattttt-----ccttttagatttggcttagtaa-caata----gattctaagctatcctga-gttg--tcttgcagATCCTACATACATGATCCGTGCTATTCCAGGCAATGCATCTGACAATGTGTACTGCACACTCCTTGCTCAAAGTGCTGTTCATGGAGCAATGGCAGGTTA
                                                  |||  | | ||    || |  |||     |||| || |  |||        | ||  |||  |  ||| | | | |    |     | ||| |  ||  ||||  |||  ||||||| || ||||||||||| || || | | |||||||||| || ||||| ||||| ||||| |||||||| ||||| || ||||| ||||||||||| ||
gtcagtttctcttacagcattctcttcctttttgacctatttatttcttggtctttcatttttatttcggatttcaaaggttttttaaaatttgacaattatctaattttaaccaagttatctacatcgtgggataaggctttgttgttgttgtatctgccagATCCAACTTACATGATCCGGGCAATCCAAAGCAATGCATCAGATAATGTCTACTGTACACTTCTTGCTCAGAGTGCAGTCCATGGTGCAATGGCAGGGTA

upper sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT4G32840.1 (Arabidopsis thaliana), 3'ss of exon 11
gtcagtgacttcagatttgtgtttgtttatttatttttccttttagatttggcttagtaa--caatagattctaagc-tatcctgagttgtcttgcagATCCTACATACATGATCCGTGCTATTCCAGGCAATGCATCTGACAATGTGTACTGCACACTCCTTGCTCAAAGTGCTGTTCATGGAGCAATGGCAGGTTA
                    ||  |||| |   |       || |  |   |||   ||     ||  |||  ||   |  |   |    | || ||||||| |||||||||||||| |||||||||| ||||||||||||||| || ||||  || |||||||| ||||| || || ||||| |||||||| || ||
--------------------gtacgtttgtcc-tccccaaattcaagtcgagctacatagattcatgaattagaaatatgactcaaaccatgtttcagATCCGACATACATGATCCGAGCTATTCCAGCCAATGCATCTGACAACGTCTACTCAACTCTCCTTGCCCAAAGCGCAGTCCATGGTGCAATGGCTGGCTA

upper sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
---------------gtcagtgacttcagatttgtgtttgtttatttatttttc---cttttagatttg---gcttagtaacaatagattctaagct--atcctgagttgtc-----------ttgcagATCCTACATACATGATCCGTGCTATTCCAGGCAATGCATCTGACAATGTGTACTGCACACTCCTTGCTCAAAGTGCTGTTCATGGAGCAATGGCAGGTTA
               ||     ||||  | ||| |  ||   |  ||  || ||   ||| || |||       ||  |   | | | || || |||  |   |||||  ||            ||||||||| || |||||||| || ||| ||||| ||||||| |||||||| |||||||||||  | |||||||| || ||  | |||||||| |||||||| ||
gtggccatatgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgcttctatattcatgaaattccttttagtcgtttttaggcttgaatatgagtactcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA

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|110710754|gb|EE087164.1|EE087164
EST:     GATCATTTTGCAAGACAGGGTAAGATTGCCATTAATCTGAAGTATATAG                         ATCCTACATACATGATCCGTGCTATTCCAGGCAATGCATCTGACAATGTGT
genomic: GATCATTTTGCAAGACAGCGTAAGATTGCCATTAATCTGAAGTATATAGgtcagtgact ... tgtcttgcagATCCTACATACATGATCCGTGCTATTCCAGGCAATGCATCTGACAATGTGT
EST: gi|34544030|gb|CF512262.1|CF512262
EST:     GATCATTTTGCAAGACAGCGTAAGATTGCCATTAATCTGAAGTATATAG                         ATCCTACATACATGATCCGTGCTATTCCAGGCAATGCATCTGACAATGTGT
genomic: GATCATTTTGCAAGACAGCGTAAGATTGCCATTAATCTGAAGTATATAGgtcagtgact ... tgtcttgcagATCCTACATACATGATCCGTGCTATTCCAGGCAATGCATCTGACAATGTGT
EST: gi|110417232|gb|EC983271.1|EC983271
EST:     GATCATTTTGCAAGACAGCGTAAGATTGCCATTAATCTGAAGTATATAG                         ATCCTACATACATGATCCGTGCTATTCCAGGCAATGCATCTGACAATGTGT
genomic: GATCATTTTGCAAGACAGCGTAAGATTGCCATTAATCTGAAGTATATAGgtcagtgact ... tgtcttgcagATCCTACATACATGATCCGTGCTATTCCAGGCAATGCATCTGACAATGTGT
EST: gi|110406376|gb|EC971947.1|EC971947
EST:     GATCATTTTGCAAGACAGCGTAAGATTGCCATTAATCTGAAGTATATAG                         ATCCTACATACATGATCCGTGCTATTCCAGGCAATGCATCTGACAATGTGT
genomic: GATCATTTTGCAAGACAGCGTAAGATTGCCATTAATCTGAAGTATATAGgtcagtgact ... tgtcttgcagATCCTACATACATGATCCGTGCTATTCCAGGCAATGCATCTGACAATGTGT
EST: gi|110717627|gb|EE093647.1|EE093647
EST:     GATTATTTTGCAAGACAGCGTAAGATTGCCATTAATCTGAAGTATATAG                         ATCCTACATACATGATCCGTGCTATTCCAGGCAATGCATCTGACAATGTGT
genomic: GATCATTTTGCAAGACAGCGTAAGATTGCCATTAATCTGAAGTATATAGgtcagtgact ... tgtcttgcagATCCTACATACATGATCCGTGCTATTCCAGGCAATGCATCTGACAATGTGT
EST: gi|34543942|gb|CF512174.1|CF512174
EST:     GATCATTTTGCAAGACAGCGTAAGATTGCCATTAATCTGAAGTATATAG                         ATCCTACATACATGATCCGTGCTATTCCAGGCAATGCATCTGACAATGTGT
genomic: GATCATTTTGCAAGACAGCGTAAGATTGCCATTAATCTGAAGTATATAGgtcagtgact ... tgtcttgcagATCCTACATACATGATCCGTGCTATTCCAGGCAATGCATCTGACAATGTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttagatttggcttagtaacaatagattctaagctatcctgagttgtcttgcagATCCTACATACATGATCCGTGCTATTCCAGGCAATGCATCTGACAATGTGTACTGCACACTCCTTGCTCAAAGTGCTGTTCATGGAGCAATGGCAGGTTA
              tagtaac  putative branch site (score: 1)
                                            ttgtctt  putative PPT
                 taacaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtgacttcagatttgtgtttgtttatttatttttccttttagatttggcttagtaacaatagattctaagctatcctgagttgtcttgcagATCCTACATACATGATCCGTGCTATTCCAGGCAATGCATCTGACAATGTGTACTGCACACTCCTTGCTCAAAGTGCTGTTCATGGAGCAATGGCAGGTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA