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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTTGTTCCCAACAGCTGATTCTGCCCGGCCATTTTCCATGCTTGGACTTGGTGACATTGTAATCCCTGgtaaggtgtttgaaattcaattttaaaaatatcttcattgggttgtccattgttttctgtttgcagatatattagagaagacatttttgaagttgggagt...

Basic information

species Vitis vinifera
transcript Vv06s0009g03520.t01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: LOC_Os05g36070.1 (Oryza sativa), 5'ss of exon 10
CTTTTGTTCCCAACAGCTGATTCTGCCCGGCCATTTTCCATGCTTGGACTTGGTGACATTGTAATCCCTGgtaaggtgtttgaaattcaattttaaaaatatcttcattgggttgtccattgttttctgtttg--cagatatattagagaagaca--tttttgaagttgggagt
||| | || || |||| |||| |||| || || || || |||||||| ||||||||||||||||| |||||| || |  |  ||  |  |  |||   || ||  | ||   ||| ||  || |||||| |||   ||    |||   |  | ||  |   | |  ||| |   
CTTCTATTTCCTACAGGTGATGCTGCACGCCCGTTCTCTATGCTTGGCCTTGGTGACATTGTAATACCTGgttag-taataaaatctttagattatttatttcaacttttatttggcctgtgatttctggttgaatagggtcattcaggctgtcagctgcattagattgag---

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GRMZM2G044348_T01 (Zea mays), 5'ss of exon 9
CTTTTGTTCCCAACAGCTGATTCTGCCCGGCCATTTTCCATGCTTGGACTTGGTGACATTGTAATCCCTGgtaaggtgtttgaaattcaattttaaaa--atatcttcattgggttgtccattgttttctgtttgcagatatattagagaagacatttttgaagttgggagt
||| |||| ||||| || ||  |||  |||||||| ||||||||||| ||||||||||||||||| |||||| ||   |   || |||  |  ||     || | |  |||  | | | || || |     |||     | ||||  | |                      
CTTCTGTTTCCAACTGCAGACGCTGAACGGCCATTCTCCATGCTTGGCCTTGGTGACATTGTAATACCTGgttagtaatgaaaatttctttcctagtgctatgtttatattctgctttgcagtgatgcagatttttctctttattgaacag---------------------

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GRMZM2G150251_T01 (Zea mays), 5'ss of exon 9
CTTTTGTTCCCAACAGCTGATTCTGCCCGGCCATTTTCCATGCTTGGACTTGGTGACATTGTAATCCCTGgtaaggtgtttgaaattcaattt-taaaaatatctt-cattgggttgtccattgttttctgtttgcagatatattagagaa-gacatttttgaagttgggagt
||| |||| || || || |||  ||| |||||||| ||||||||||| ||||||||||||||||| |||||| || |  |  ||||| | ||  |     ||| || ||||  | | | || || | |   |||         |||  ||| |  | | |        | || 
CTTCTGTTTCCTACTGCGGATGATGCACGGCCATTCTCCATGCTTGGCCTTGGTGACATTGTAATACCTGgttag-taataaaaatttatttccttgtgctatgttacattctgctttgcagtgatgtagattt-tgccccccttattgaacggtaatatcagcccctgtag-

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GRMZM2G044348_T03 (Zea mays), 5'ss of exon 8
CTTTTGTTCCCAACAGCTGATTCTGCCCGGCCATTTTCCATGCTTGGACTTGGTGACATTGTAATCCCTGgtaaggtgtttgaaattcaattttaaaaatatcttcat--tgggttgtccattgttttctgtttgcagatatattagagaagacatttttgaagttgggagt
||| |||| ||||| || ||  |||  |||||||| ||||||||||| ||||||||||||||||| |||||| ||   |   || |||  |  ||    ||| || ||  |  | | | || || |     |||     | ||||  | |  | || |  |    ||   | 
CTTCTGTTTCCAACTGCAGACGCTGAACGGCCATTCTCCATGCTTGGCCTTGGTGACATTGTAATACCTGgttagtaatgaaaatttctttcctagtgctatgtttatattctgctttgcagtgatgcagatttttctctttattgaacagta-atatcagcctctgtagg-

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA14G21190.1 (Glycine max), 5'ss of exon 4
CTTTTGTTCCCAACAGCTGATTCTGCCCGGCCATTTTCCATGCTTGGACTTGGTGACATTGTAATCCCTGgtaaggtgtttgaaattcaattttaaaaatatcttcattgggttgtccattgtt-ttctgtttgcagatatattagagaagacatttttgaagttgggagt----
||||||||||| || || ||||||||  |||||||||| ||||||||||||||||||||||| |||||||||| |    |||||  |    | |  |  ||| ||| |    | ||  |  |   || |||  |  |  ||||||  |   |   ||||     | ||  |    
CTTTTGTTCCCCACCGCAGATTCTGCAAGGCCATTTTCAATGCTTGGACTTGGTGACATTGTTATCCCTGgtagg----ttgaatcttttatattgatgtattttcctctaat-gttgacagcccttttgtgagttgtaatattaatgtttagtattttactacttggtatacat

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA04G08510.1 (Glycine max), 5'ss of exon 9
CTTTTGTTCCCAACAGCTGATTCTGCCCGGCCATTTTCCATGCTTGGACTTGGTGACATTGTAATCCCTGgtaaggtg--tttgaaattcaattttaaaaatatcttcattgggttgtccattgttttctgtttgcagatatattagagaagacatttttgaagttgggagt-------
||||||||||| ||||| ||||| ||  |||||||||| |||||||| |||||||| ||||| |||||||||| | ||    | ||| || |||          |||||   | || |  | |    | |    | |||  ||||         |  ||   | ||    |        
CTTTTGTTCCCCACAGCAGATTCAGCAAGGCCATTTTCAATGCTTGGCCTTGGTGATATTGTTATCCCTGgtaggatgaccctcaaactctattcc-------ccttcacaagtttttgaactcccatttaa--ggagacttattcctttttctaccttcttacttcaatgcatgaata

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|71877015|gb|DT026070.1|DT026070
EST:     TTCTGCCCGGCCATTTTCCATGCTTGGACTTGGTGACATTGTAATCCCTG                         GCATTTTTGTAGCATTGGCATTGCGATTTGATGTGTCCAGAGGGAAAGGGA
genomic: TTCTGCCCGGCCATTTTCCATGCTTGGACTTGGTGACATTGTAATCCCTGgtaaggtgtt ... ctttctttagGCATTTTTGTAGCATTGGCATTGCGATTTGATGTGTCCAGAGGGAAAGGGA
EST: gi|27579299|gb|CB001994.1|CB001994
EST:     TTCTGCCCGGCCATTTTCCATGCTTGGACTTGGTGACATTGTAATCCCTG                         GCATTTTTGTAGCATTGGCATTGCGATTTGATGTGTCCAGAGGGAAAGGGA
genomic: TTCTGCCCGGCCATTTTCCATGCTTGGACTTGGTGACATTGTAATCCCTGgtaaggtgtt ... ctttctttagGCATTTTTGTAGCATTGGCATTGCGATTTGATGTGTCCAGAGGGAAAGGGA
EST: gi|110391760|gb|EC956760.1|EC956760
EST:     TTCTGCCCGGCCATTTTCCATGCTTGGACTTGGTGACATTGTAATCCCTG                         GCATTTTTGTAGCATTGGCATTGCGATTTGATGTGTCCAGAGGGAAAGGGA
genomic: TTCTGCCCGGCCATTTTCCATGCTTGGACTTGGTGACATTGTAATCCCTGgtaaggtgtt ... ctttctttagGCATTTTTGTAGCATTGGCATTGCGATTTGATGTGTCCAGAGGGAAAGGGA
EST: gi|32246622|gb|CD712441.1|CD712441
EST:     ACATTGTAATCCCTG                         GCATTTTTGTAGCATTGGCATTGCGATTTGATGTGTCCAGAGGGAAAGGGA
genomic: ACATTGTAATCCCTGgtaaggtgtt ... ctttctttagGCATTTTTGTAGCATTGGCATTGCGATTTGATGTGTCCAGAGGGAAAGGGA
EST: gi|34364249|gb|CF405834.1|CF405834
EST:     TTCTGCCCGGNCATTTTCCATGCTTGGACTTGGTGACATTGTAATCCCTG                         GCATTTTTGTAGCATTGGCATTGCGATTTGATGTGTCCAGAGGGAAAGGGA
genomic: TTCTGCCCGGCCATTTTCCATGCTTGGACTTGGTGACATTGTAATCCCTGgtaaggtgtt ... ctttctttagGCATTTTTGTAGCATTGGCATTGCGATTTGATGTGTCCAGAGGGAAAGGGA
EST: gi|110691134|gb|EE068892.1|EE068892
EST:     TTCTGCCCGGCCATTTTCCATGCTTGGACTTGGTGACATTGTAATCCCTG                         GCATTTTTGTAGCATTGGCATTGCGATTTGATGTGTCCAGAGGGAAAGGGA
genomic: TTCTGCCCGGCCATTTTCCATGCTTGGACTTGGTGACATTGTAATCCCTGgtaaggtgtt ... ctttctttagGCATTTTTGTAGCATTGGCATTGCGATTTGATGTGTCCAGAGGGAAAGGGA
EST: gi|110361505|gb|EC924984.1|EC924984
EST:     TTCTGCCCGGCCATTTTCCATGCTTGGACTTGGTGACATTGTAATCCCTG                         GCATTTTTGTAGCATTGGCATTGCGATTTGATGTGTCCAGAGGGAAAGGGA
genomic: TTCTGCCCGGCCATTTTCCATGCTTGGACTTGGTGACATTGTAATCCCTGgtaaggtgtt ... ctttctttagGCATTTTTGTAGCATTGGCATTGCGATTTGATGTGTCCAGAGGGAAAGGGA
EST: gi|77579348|gb|DV218502.1|DV218502
EST:     TTCTGCCCGGCCATTTTCCATGCTTGGACTTGGTGACATTGTAATCCCTG                         GCATTTTTGTAGCATTGGCATTGCGATTTGATGTGTCCAGAGGGAAAGGGA
genomic: TTCTGCCCGGCCATTTTCCATGCTTGGACTTGGTGACATTGTAATCCCTGgtaaggtgtt ... ctttctttagGCATTTTTGTAGCATTGGCATTGCGATTTGATGTGTCCAGAGGGAAAGGGA
EST: gi|161717568|gb|FC066896.1|FC066896
EST:     TTCTGCCCGGCCATTTTCCATGCTTGGACTTGGTGACATTGTAATCCCTG                         GCATTTTTGTAGCATTGGCATTGCGATTTGATGTGTCCAGAGGGAAAGGGA
genomic: TTCTGCCCGGCCATTTTCCATGCTTGGACTTGGTGACATTGTAATCCCTGgtaaggtgtt ... ctttctttagGCATTTTTGTAGCATTGGCATTGCGATTTGATGTGTCCAGAGGGAAAGGGA
EST: gi|110376904|gb|EC941978.1|EC941978
EST:     TTCTGCCCGGCCATTTTCCATGCTTGGACTTGGTGACATTGTAATCCCTG                         GCATTTTTGTAGCATTGGCATTGCGATTTGATGTGTCCAGAGGGAAAGGGA
genomic: TTCTGCCCGGCCATTTTCCATGCTTGGACTTGGTGACATTGTAATCCCTGgtaaggtgtt ... ctttctttagGCATTTTTGTAGCATTGGCATTGCGATTTGATGTGTCCAGAGGGAAAGGGA
EST: gi|27582830|gb|CB005525.1|CB005525
EST:     ATTTTCCATGCTTGGACTTGGTGACATTGTAATCCCTG                         GCATTTTTGTAGCATTGGCATTGCGATTTGATGTGTCCAGAGGGAAAGGGA
genomic: ATTTTCCATGCTTGGACTTGGTGACATTGTAATCCCTGgtaaggtgtt ... ctttctttagGCATTTTTGTAGCATTGGCATTGCGATTTGATGTGTCCAGAGGGAAAGGGA
EST: gi|110730433|gb|EE107509.1|EE107509
EST:     TTCTGCCCGGCCATTTTCCATGCTTGGACTTGGTGACATTGTAATCCCTG                         GCATTTTTGTAGCATTGGCATTGCGATTTGATGTGTCCAGAGGGAAAGGGA
genomic: TTCTGCCCGGCCATTTTCCATGCTTGGACTTGGTGACATTGTAATCCCTGgtaaggtgtt ... ctttctttagGCATTTTTGTAGCATTGGCATTGCGATTTGATGTGTCCAGAGGGAAAGGGA
EST: gi|71874644|gb|DT023699.1|DT023699
EST:     TTCTGCCCGGCCATTTTCCATGCTTGGACTTGGTGACATTGTAATCCCTG                         GCATTTTTGTAGCATTGGCATTGCGATTTGATGTGTCCAGAGGGAAAGGGA
genomic: TTCTGCCCGGCCATTTTCCATGCTTGGACTTGGTGACATTGTAATCCCTGgtaaggtgtt ... ctttctttagGCATTTTTGTAGCATTGGCATTGCGATTTGATGTGTCCAGAGGGAAAGGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTTTGTTCCCAACAGCTGATTCTGCCCGGCCATTTTCCATGCTTGGACTTGGTGACATTGTAATCCCTGgtaaggtgtttgaaattcaattttaaaaatatcttcattgggttgtccattgttttctgtttgcagatatattagagaagacatttttgaagttgggagt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaattcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gagaaga