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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgacatgtggaaaaaatgggaactcttttccatatttgatagtcatctttttcattatcttaatttttcttttgatggcagATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCCAGAAGAGGAGGGCCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTT

Basic information

species Vitis vinifera
transcript Vv11s0118g00670.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0118g00670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os02g40880.1 (Oryza sativa), 3'ss of exon 3
gtaatgacatgtggaaaaaatgggaactcttttccatatttgatagtcatctttttcatt--atcttaatttt--tcttttgatggcagATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCCAGAAGAGGAGGGCCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTT
    |   |||              | || | ||   | ||  |  |     |     |   |||| | |  |  |  ||  ||   ||||||||||||||||||||||||||| || |||||||  ||| | ||||||||||||||||| || || || ||||||||||| ||||||||| | |||||
--gttagtatgaatgttgtgctaccaatcctatcagcagttatttatttctgtccatgtctaatctgagtggtggttattctatttaagATGTTAAGAACAAGTGGGAGAATAGCTCATGGGGCAAGAAGCTAATTGTCCAGAAGAGGAGAGCGTCACTCAATGACTTTGACAGGTTCAAGGTTATGTT

upper sequence: Vv11s0118g00670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os04g43540.1 (Oryza sativa), 3'ss of exon 3
gtaatgacatgtggaaaaaatgggaactcttttccatatttgatagtcatctttttcattatcttaatttttcttttgatggcagATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCCAGAAGAGGAGGGCCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTT
|| ||||    |        |  ||||| |||| |     || ||       |||| |||      | |    |  ||||  ||||||| ||||||||||||||||| || || ||||| |  ||  ||||||||||||||||||| || || || || |||||||| ||||||||| | |||||
gtgatgaaccattcttcggctatgaactttttttcca--ctgttaagtgcagttttaattg-----aatgccatcctgattacagATGTGAAGAACAAGTGGGAGAACAGCTCATGGGGTAAGAAACTGATTGTCCAGAAGAGGAGAGCATCCCTCAACGACTTTGACAGGTTCAAGGTTATGTT

upper sequence: Vv11s0118g00670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G140116_T01 (Zea mays), 3'ss of exon 3
--------------------------------------gtaatgacatgtggaa-----aaaatgggaactcttttccatatttga-tagtcat-ctttttcattatcttaatttttcttttgatggcagATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCCAGAAGAGGAGGGCCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTT
                                      |  |     | |  ||     | | |    |   ||  |||||   || | || |  ||| ||   | ||||  | ||  ||||     ||||||| |||| |||||||||||| || || |||||||  ||| ||||||||||||||||||| || || || ||||||||||||||||||||  ||||| |
gtaactctagagcttatgttgtggacctctttagcaccgccacactttattcaacttctatattctagatgattgcccataagagaatggtgacacttatttgatctcttgctattctttttt----cagATGTGAAGACCAAGTGGGAGAACAGCTCATGGGGCAAGAAGCTGATTGTCCAGAAGAGGAGAGCATCGCTCAATGACTTTGATAGGTTCAAAGTCATGCT

upper sequence: Vv11s0118g00670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G028883_T01 (Zea mays), 3'ss of exon 3
gtaatgacatgtggaaaaaatgggaactcttttccatatttgatagtcatctttttcattatcttaatttttcttttgatggcagATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCCAGAAGAGGAGGGCCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTT
     |  || |        |||   |  | ||  ||| ||    |   ||| |  |   | || |  |  | |  |||  |||||||| || | ||||||||||||||| || |||||||  ||| ||||||| ||||||||||| || || || ||||||||||| ||||||||| |||||||
-----gtgatttactgtccctggactcattctttaatacttacctgatgtctatagc-ccacctca--tcctatcctgactgcagATGTGAAAAGCAAGTGGGAGAATAGCTCATGGGGCAAGAAGCTGATTGTTCAGAAGAGGAGAGCATCACTCAATGACTTTGACAGGTTCAAGGTCATGTT

upper sequence: Vv11s0118g00670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G168330_T02 (Zea mays), 3'ss of exon 3
--------------------gtaatgacatgtggaaaaaatgggaactcttt-tccatatt-----tgatagtcatctttttcattatct--taatttttcttttgatggcagATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCCAGAAGAGGAGGGCCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTT
                    ||       |   | |||  || |   | ||  || |||||     |||   | ||  |    ||||  |  |  ||| |  ||   |   |||||| ||||  |||||||| || || || |||||||  ||| ||||||||||||||||||||||  | || | ||||||||| ||||||||| ||||| |
gtaatgatgaacctcatatagtggacctcttcagcaaagttgtgctttattcatctatattctagatgaagataatagtgacaattaattgatgctttgttattcttttttagATGTGAAGACGAAGTGGGAAAACAGCTCATGGGGCAAGAAGCTGATTGTCCAGAAGAGGAGGGCTGCGCTCAGTGACTTTGACAGGTTCAAGGTCATGCT

upper sequence: Vv11s0118g00670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT2G20450.1 (Arabidopsis thaliana), 3'ss of exon 3
-----------gtaatgacatgtggaaaaaatgggaactctttt--ccatatttgatagtcatctt--tttcattatcttaatttttcttttgatggcagATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCCAGAAGAGGAGGGCCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTT
           |||      | | ||  |   |     | | ||  || | |||  | ||    |   ||   | ||||||  | |    ||    |||||||| ||||||||||||||||| ||||| ||||| || ||  | ||||| |||||||| || ||  | || ||||| ||||| |||||||||||||||||
gtgagtttgttgtagcatacttttgattattcgtaggttttattggcctttttttgttgttggttgggttgggtcatcttagctctaaagttatatgcagATGTGAAGAACAAGTGGGAGAAGAGTTCATGGGGTAGGAAACTTATTGTGCAGAAGAGAAGAGCTGCCCTCAATGATTTTGACAGGTTCAAGATCATGTT

upper sequence: Vv11s0118g00670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT4G27090.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaatgacatgtggaaaaaatgggaactcttttccatatttgatagtcatctttttcattatcttaatttttcttttga-----tggcagATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCCAGAAGAGGAGGGCCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTT
                     | ||   ||     || |   ||| |    ||||  | | | | ||| ||   |   |     | |||||||| ||||||||||||||||| || || ||||| || ||| | || || |||||  | |||||    ||||| ||||||||||||||||||||||||||
---------------------gtgagtgctgcgtaatgta-aatatttgaattttgaagtgtttcaatcttaactggaaaagtcttgcagATGTGAAGAACAAGTGGGAGAAAAGCTCATGGGGTAGGAAGCTTATCGTGCAGAAACGTAGGGCTAACCTTAACGACTTTGATAGGTTCAAGATCATGTT

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|30134455|gb|CB919793.1|CB919793
EST:     CAAAAGGGTGCCTAAGNNNNNNNCATTGATTGAAGCTATGAATGCCGCGG                         ATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
genomic: CAAAAGGGTGCCTAAGAAAAAAACATTGATTGAAGCTATGAATGCCGCGGgtaatgacat ... ttgatggcagATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
EST: gi|37187972|gb|CF607323.1|CF607323
EST:     CAAAAGGGTGCCTAAGNNNNNNNCATTGATTGAAGCTATGAATGCCGCGG                         ATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
genomic: CAAAAGGGTGCCTAAGAAAAAAACATTGATTGAAGCTATGAATGCCGCGGgtaatgacat ... ttgatggcagATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
EST: gi|77580814|gb|DV219318.1|DV219318
EST:     CAAAAGGGTGCCTAAGNNNNNNNCATTGATTGAAGCTATGAATGCCGCGG                         ATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
genomic: CAAAAGGGTGCCTAAGAAAAAAACATTGATTGAAGCTATGAATGCCGCGGgtaatgacat ... ttgatggcagATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
EST: gi|110429198|gb|EC995687.1|EC995687
EST:     CAAAAGGGTGCCTAAGNNNNNNNCATTGATTGAAGCTATGAATGCCGCGG                         ATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
genomic: CAAAAGGGTGCCTAAGAAAAAAACATTGATTGAAGCTATGAATGCCGCGGgtaatgacat ... ttgatggcagATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
EST: gi|71869827|gb|DT018882.1|DT018882
EST:     CAAAAGGGTGCCTAAGNNNNNNNCATTGATTGAAGCTATGAATGCCGCGG                         ATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
genomic: CAAAAGGGTGCCTAAGAAAAAAACATTGATTGAAGCTATGAATGCCGCGGgtaatgacat ... ttgatggcagATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
EST: gi|34319412|gb|CF372166.1|CF372166
EST:     CAAAAGGGTGCCTAAGNNNNNNNCATTGATTGAAGCTATGAATGCCGCGG                         ATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
genomic: CAAAAGGGTGCCTAAGAAAAAAACATTGATTGAAGCTATGAATGCCGCGGgtaatgacat ... ttgatggcagATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
EST: gi|27581709|gb|CB004404.1|CB004404
EST:     CAAAAGGGTGCCTAAGNNNNNNNCATTGATTGAAGCTATGAATGCCGCGG                         ATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
genomic: CAAAAGGGTGCCTAAGAAAAAAACATTGATTGAAGCTATGAATGCCGCGGgtaatgacat ... ttgatggcagATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
EST: gi|110706377|gb|EE081851.1|EE081851
EST:     CAAAAGGGTGCCTAAGNNNNNNNCATTGATTGAAGCTATGAATGCCGCGG                         ATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
genomic: CAAAAGGGTGCCTAAGAAAAAAACATTGATTGAAGCTATGAATGCCGCGGgtaatgacat ... ttgatggcagATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
EST: gi|71865933|gb|DT014988.1|DT014988
EST:     CAAAAGGGTGCCTAAGNNNNNNNCATTGATTGAAGCTATGAATGCCGCGG                         ATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
genomic: CAAAAGGGTGCCTAAGAAAAAAACATTGATTGAAGCTATGAATGCCGCGGgtaatgacat ... ttgatggcagATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
EST: gi|34543799|gb|CF512031.1|CF512031
EST:     CAAAAGGGTGCCTAAGNNNNNNNCATTGATTGAAGCTATGAATGCCGCGG                         ATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
genomic: CAAAAGGGTGCCTAAGAAAAAAACATTGATTGAAGCTATGAATGCCGCGGgtaatgacat ... ttgatggcagATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
EST: gi|71880453|gb|DT029508.1|DT029508
EST:     CAAAAGGGTGCCTAAGNNNNNNNCATTGATTGAAGCTATGAATGCCGCGG                         ATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
genomic: CAAAAGGGTGCCTAAGAAAAAAACATTGATTGAAGCTATGAATGCCGCGGgtaatgacat ... ttgatggcagATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
EST: gi|110361702|gb|EC925195.1|EC925195
EST:     CAAAAGGGTGCCTAAGNNNNNNNCATTGATTGAAGCTATGAATGCCGCGG                         ATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
genomic: CAAAAGGGTGCCTAAGAAAAAAACATTGATTGAAGCTATGAATGCCGCGGgtaatgacat ... ttgatggcagATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
EST: gi|77577814|gb|DV217659.1|DV217659
EST:     CAAAAGGGTGCCTAAGNNNNNNNCATTGATTGAAGCTATGAATGCCGCGG                         ATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
genomic: CAAAAGGGTGCCTAAGAAAAAAACATTGATTGAAGCTATGAATGCCGCGGgtaatgacat ... ttgatggcagATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
EST: gi|352795130|gb|FQ477240.1|FQ477240
EST:     CAAAAGGGTGCCTAAGNNNNNNNCATTGATTGAAGCTATGAATGCCGCGG                         ATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
genomic: CAAAAGGGTGCCTAAGAAAAAAACATTGATTGAAGCTATGAATGCCGCGGgtaatgacat ... ttgatggcagATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
EST: gi|32460994|gb|CD802168.1|CD802168
EST:     CAAAAGGGTGCCTAAGNNNNNNNCATTGATTGAAGCTATGAATGCCGCGG                         ATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
genomic: CAAAAGGGTGCCTAAGAAAAAAACATTGATTGAAGCTATGAATGCCGCGGgtaatgacat ... ttgatggcagATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
EST: gi|351017039|gb|FQ424466.1|FQ424466
EST:     AAAAGGGTGCCTAAGNNNNNNNNCATTGATTGAAGCTATGAATGCCGCGG                         ATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
genomic: AAAAGGGTGCCTAAG-AAAAAAACATTGATTGAAGCTATGAATGCCGCGGgtaatgacat ... ttgatggcagATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
EST: gi|110428543|gb|EC995018.1|EC995018
EST:     CAAAAGGGTGCCTAAGNNNNNNNCATTGATTGAAGCTATGAATGCCGCGG                         ATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
genomic: CAAAAGGGTGCCTAAGAAAAAAACATTGATTGAAGCTATGAATGCCGCGGgtaatgacat ... ttgatggcagATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
EST: gi|110420972|gb|EC987259.1|EC987259
EST:     CAAAAGGGTGCCTAAGNNNNNNNCATTGATTGAAGCTATGAATGCCGCGG                         ATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
genomic: CAAAAGGGTGCCTAAGAAAAAAACATTGATTGAAGCTATGAATGCCGCGGgtaatgacat ... ttgatggcagATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
EST: gi|110424520|gb|EC990883.1|EC990883
EST:     CAAAAGGGTGCCTAAGNNNNNNNCATTGATTGAAGCTATGAATGCCGCGG                         ATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
genomic: CAAAAGGGTGCCTAAGAAAAAAACATTGATTGAAGCTATGAATGCCGCGGgtaatgacat ... ttgatggcagATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
EST: gi|110714507|gb|EE091492.1|EE091492
EST:     CAAAAGGGTGCCTAAGNNNNNNNCATTGATTGAAGCTATGAATGCCGCGG                         ATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC
genomic: CAAAAGGGTGCCTAAGAAAAAAACATTGATTGAAGCTATGAATGCCGCGGgtaatgacat ... ttgatggcagATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttccatatttgatagtcatctttttcattatcttaatttttcttttgatggcagATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCCAGAAGAGGAGGGCCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTT
                   tctttttcattatctt  CT-rich tract
                  atctttttcattatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgacatgtggaaaaaatgggaactcttttccatatttgatagtcatctttttcattatcttaatttttcttttgatggcagATGTTAAGAACAAGTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCCAGAAGAGGAGGGCCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA