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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggaatgtcttttaatgatacttcattcattgaaaagtttgctatatgcagctgtatcatgtggttggacattacaaattttcttctttcatctatatgcaactcacagGACATAGCTGCGGAGGCTGTGAAGAAGAGGCGTCGTGCCACCAAGAAGCCATTCTCCAGATCCATAGTTGGTACTACCTTGGAGGCGATACAGAAGAGGA

Basic information

species Vitis vinifera
transcript Vv13s0074g00140.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0074g00140.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g59990.1 (Oryza sativa), 3'ss of exon 4
gtggaatgt-cttttaatgatacttcattcattgaaaagtttgctatatgcagctgtatcatgtggttggacattacaaattttcttctttcatctatatgcaactcacagGACATAGCTGCGGAGGCTGTGAAGAAGAGGCGTCGTGCCACCAAGAAGCCATTCTCCAGATCCATAGTTGGTACTACCTTGGAGGCGATACAGAAGAGGA
     |||| |  |||       ||  | ||   |   | | |   |       | |||||||   |||     | | | ||||||   ||  || |  |   |||   |||||||   ||| || ||||| ||||||||||||||  ||||||||||||||| |||  | || || |||||| ||||  |||| |  || || |||| ||
----catgtgcagttatccgagttttctgcagcaactggctggaattgctgccttatatcatgcccttg----ctgctatttttctgaatt--tcaacgttgcact-gtagGACATTCATGCTGAAGCTGTCAAGAAGAGGCGTCGCACCACCAAGAAGCCATACTCACGGTCAATTGTTGGTGCTACACTGGAAGTTATCCAAAAGAAGA

upper sequence: Vv13s0074g00140.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G074898_T03 (Zea mays), 3'ss of exon 4
gtggaatgtcttttaatgatacttcattcattgaaaagtttgctatatgcagctgtatcatgtggttggacat-tacaaattttcttctttcatctatatgcaactcac----agGACATAGCTGCGGAGGCTGTGAAGAAGAGGCGTCGTGCCACCAAGAAGCCATTCTCCAGATCCATAGTTGGTACTACCTTGGAGGCGATACAGAAGAGGA
              ||  | ||   |||     || | ||   | |     |||  |  |||  | | ||  | || |   | |  ||||  || ||| ||  | |       |||||||   ||| || ||||| ||||||||||| || |||||||||||||||| ||| || ||||| || ||| || ||||||| | ||| ||||||| ||
------------ccaactagacg--attgcaacaacaattgtttctgccatgcta-acaatggtgctagaagtctagagcctctgatcttaaatgtatttgtcatttgtctgtagGACATCCATGCTGAAGCTGTCAAGAAGAGGCGCCGCGCCACCAAGAAGCCATACTCGAGGTCCATTGTGGGTGCTTCCTTGGAAGTGATCCAGAAGAAGA

upper sequence: Vv13s0074g00140.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G110328_T03 (Zea mays), 3'ss of exon 4
gtggaatgtcttttaatgatacttcattcattgaaaagtttgctatatgcagctgtatcatgtggttggacattacaaattttcttctttcatctat--atgcaactcacagGACATAGCTGCGGAGGCTGTGAAGAAGAGGCGTCGTGCCACCAAGAAGCCATTCTCCAGATCCATAGTTGGTACTACCTTGGAGGCGATACAGAAGAGGA
          | | ||| |  |||    ||   | ||  || || |   ||    ||| |||  | |  |  |    ||  || | | |  ||       | |       |||| ||   ||| |||||||| ||||||||||| || |||||||||||||||| ||| || ||||| || ||| || || | |||| ||| ||||||| ||
--------catctgaataaatctttg--caacaacaa--ttactctcgccacacttattatggcgctaaaagtctagaaccttttacatgtattagccatttctgtctgtagGATATCCATGCTGAGGCTGTCAAGAAGAGGCGCCGCGCCACCAAGAAGCCATACTCGAGGTCCATTGTGGGTGCTTCCCTAGAGGTGATCCAGAAGAAGA

upper sequence: Vv13s0074g00140.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G142640_T02 (Zea mays), 3'ss of exon 5
gtggaatgtcttttaatgatacttcattcattgaaaagtttgctatatgcagctgtatcatgtggttggacattacaaattttcttctttcatctatatgcaactcacagGACATAGCTGCGGAGGCTGTGAAGAAGAGGCGTCGTGCCACCAAGAAGCCATTCTCCAGATCCATAGTTGGTACTACCTTGGAGGCGATACAGAAGAGGA
 | ||    | ||| || ||   ||||   ||| ||| | |            | ||  | ||| |   |   || |  ||   | ||||  | | | |         |||| ||   ||| || || || ||||||||||| || |||||||||||||||| |||||| || || || ||| || ||||||| |  || ||||||| ||
atcgatc--catttgatcatg--tcatcgtttgcaaattatttctgccatgcttataata-gtgctataagtctatagcttacatgcttttttttttgt-----ctgtagGATATCCATGCTGAAGCGGTAAAGAAGAGGCGCCGCGCCACCAAGAAGCCATACTCCAGGTCAATTGTGGGTGCTTCCTTGGAAGTAATCCAGAAGAAGA

upper sequence: Vv13s0074g00140.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT3G53020.1 (Arabidopsis thaliana), 3'ss of exon 3
gtggaatgtcttttaatgatacttcattcattgaaa---agtttgctatatgcagct-gtatcatgtggttggacattacaaattttcttctttcatctatatgcaactcacagGACATAGCTGCGGAGGCTGTGAAGAAGAGGCGTCGTGCCACCAAGAAGCCATTCTCCAGATCCATAGTTGGTACTACCTTGGAGGCGATACAGAAGAGGA
           |  ||  | |  ||| | |||   |     |||| | | || |  | || |  | |  |||  | | |    ||  | |  |  | || | |     | | ||||   |||    |||||||||||||  ||| | ||||||||||||||||||| ||| || ||||| |||||| |||||||||| |  || ||||||| ||
----------gtaaaaaaaaaactcagtaatttggatctgttttgttgtttgtactttgttttttttcattgatcctgatttgttaacattctaaaactctgtttcttttatagGATGCAGCACAAGAGGCTGTGAAGAGAAGGAGACGTGCCACCAAGAAGCCATACTCAAGGTCCATTGTTGGTGCTACCTTGGAAGTAATTCAGAAGAAGA

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|37188150|gb|CF607501.1|CF607501
EST:     AGCCTTCAAAGCTTACCTGGACGGCTATGTATAGAAAGCAACATAAGAAG                         GACATAGCTGCGGAGGCTGTGAAGAAGAGGCGTCGTGCCACCAAGAAGCCA
genomic: AGCCTTCAAAGCTTACCTGGACGGCTATGTATAGAAAGCAACATAAGAAGgtggaatgtc ... caactcacagGACATAGCTGCGGAGGCTGTGAAGAAGAGGCGTCGTGCCACCAAGAAGCCA
EST: gi|22011818|gb|BQ796852.1|BQ796852
EST:     AGCCTTCAAAGCTTACCTGGACGGCTATGTATAGAAAGCAACATAAGAAG                         GACATAGCTGCGGAGGCTGTGAAGAAGAGGCGTCGTGCCACCAAGAAGCCA
genomic: AGCCTTCAAAGCTTACCTGGACGGCTATGTATAGAAAGCAACATAAGAAGgtggaatgtc ... caactcacagGACATAGCTGCGGAGGCTGTGAAGAAGAGGCGTCGTGCCACCAAGAAGCCA
EST: gi|71868597|gb|DT017652.1|DT017652
EST:     AGCCTTCAAAGCTTACCTGGACGGCTATGTATAGAAAGCAACATAAGAAG                         GACATAGCTGCGGAGGCTGTGAAGAAGAGGCGTCGTGCCACCAAGAAGCCA
genomic: AGCCTTCAAAGCTTACCTGGACGGCTATGTATAGAAAGCAACATAAGAAGgtggaatgtc ... caactcacagGACATAGCTGCGGAGGCTGTGAAGAAGAGGCGTCGTGCCACCAAGAAGCCA
EST: gi|77581842|gb|DV219879.1|DV219879
EST:     AGCCTTCAAAGCTTACCTGGACGGCTATGTATAGAAAGCAACATAAGAAG                         GACATAGCTGCGGAGGCTGTGAAGAAGAGGCGTCGTGCCACCAAGAAGCCA
genomic: AGCCTTCAAAGCTTACCTGGACGGCTATGTATAGAAAGCAACATAAGAAGgtggaatgtc ... caactcacagGACATAGCTGCGGAGGCTGTGAAGAAGAGGCGTCGTGCCACCAAGAAGCCA
EST: gi|71873024|gb|DT022079.1|DT022079
EST:     AGCCTTCAAAGCTTACCTGGACGGCTATGTATAGAAAGCAACATAAGAAG                         GACATAGCTGCGGAGGCTGTGAAGAAGAGGCGTCGTGCCACCAAGAAGCCA
genomic: AGCCTTCAAAGCTTACCTGGACGGCTATGTATAGAAAGCAACATAAGAAGgtggaatgtc ... caactcacagGACATAGCTGCGGAGGCTGTGAAGAAGAGGCGTCGTGCCACCAAGAAGCCA
EST: gi|110384865|gb|EC949331.1|EC949331
EST:     AGCCTTCAAAGCTTACCTGGACGGCTATGTATAGAAAGCAACATAAGAAG                         GACATAGCTGCGGAGGCTGTGAAGAAGAGGCGTCGTGCCACCAAGAAGCCA
genomic: AGCCTTCAAAGCTTACCTGGACGGCTATGTATAGAAAGCAACATAAGAAGgtggaatgtc ... caactcacagGACATAGCTGCGGAGGCTGTGAAGAAGAGGCGTCGTGCCACCAAGAAGCCA
EST: gi|110413307|gb|EC979086.1|EC979086
EST:     AGCCTTCAAAGCTTACCTGGACGGCTATGTATAGAAAGCAACATAAGAAG                         GACATAGCTGCGGAGGCTGTGAAGAAGAGGCGTCGTGCCACCAAGAAGCCA
genomic: AGCCTTCAAAGCTTACCTGGACGGCTATGTATAGAAAGCAACATAAGAAGgtggaatgtc ... caactcacagGACATAGCTGCGGAGGCTGTGAAGAAGAGGCGTCGTGCCACCAAGAAGCCA
EST: gi|71866495|gb|DT015550.1|DT015550
EST:     AGCCTTCAAAGCTTACCTGGACGGCTATGTATAGAAAGCAACATAAGAAG                         GACATAGCTGCGGAGGCTGTGAAGAAGAGGCGTCGTGCCACCAAGAAGCCA
genomic: AGCCTTCAAAGCTTACCTGGACGGCTATGTATAGAAAGCAACATAAGAAGgtggaatgtc ... caactcacagGACATAGCTGCGGAGGCTGTGAAGAAGAGGCGTCGTGCCACCAAGAAGCCA
EST: gi|30136747|gb|CB922085.1|CB922085
EST:     AGCCTTCAAAGCTTACCTGGACGGCTATGTATAGAAAGCAACATAAGAAG                         GACATAGCTGCGGAGGCTGTGAAGAAGAGGCGTCGTGCCACCAAGAAGCCA
genomic: AGCCTTCAAAGCTTACCTGGACGGCTATGTATAGAAAGCAACATAAGAAGgtggaatgtc ... caactcacagGACATAGCTGCGGAGGCTGTGAAGAAGAGGCGTCGTGCCACCAAGAAGCCA
EST: gi|110359284|gb|EC920528.1|EC920528
EST:     AGCCTTCAAAGCTTACCTGGACGGCTATGTATAGAAAGCAACATAAGAAG                         GACATAGCTGCGGAGGCTGTGAAGAAGAGGCGTCGTGCCACCAAGAAGCCA
genomic: AGCCTTCAAAGCTTACCTGGACGGCTATGTATAGAAAGCAACATAAGAAGgtggaatgtc ... caactcacagGACATAGCTGCGGAGGCTGTGAAGAAGAGGCGTCGTGCCACCAAGAAGCCA
EST: gi|110363994|gb|EC927631.1|EC927631
EST:     AGCCTTCAAAGCTTACCTGGACGGCTATGTATAGAAAGCAACATAAGAAG                         GACATAGCTGCGGAGGCTGTGAAGAAGAGGCGTCGTGCCACCAAGAAGCCA
genomic: AGCCTTCAAAGCTTACCTGGACGGCTATGTATAGAAAGCAACATAAGAAGgtggaatgtc ... caactcacagGACATAGCTGCGGAGGCTGTGAAGAAGAGGCGTCGTGCCACCAAGAAGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcatgtggttggacattacaaattttcttctttcatctatatgcaactcacagGACATAGCTGCGGAGGCTGTGAAGAAGAGGCGTCGTGCCACCAAGAAGCCATTCTCCAGATCCATAGTTGGTACTACCTTGGAGGCGATACAGAAGAGGA
                attacaaattttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggaatgtcttttaatgatacttcattcattgaaaagtttgctatatgcagctgtatcatgtggttggacattacaaattttcttctttcatctatatgcaactcacagGACATAGCTGCGGAGGCTGTGAAGAAGAGGCGTCGTGCCACCAAGAAGCCATTCTCCAGATCCATAGTTGGTACTACCTTGGAGGCGATACAGAAGAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA