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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgtgtattttcaaaattcacctgtaaactattcttcatgctgctgacctcgccttttattttaccatgaattatgaatgaatgactttgggaattcagGTGGGATAAACCAATACTAGTTGCATGGGGAATATCAGACAAGTATCTGCCTCAATCAGTGGCAGAAGAGTTTCAAAAGGGAAACCCTGATTATATAAAA

Basic information

species Vitis vinifera
transcript Vv09s0002g07500.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g07500.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G117531_T04 (Zea mays), 3'ss of exon 9
tttgtgtattttcaaaatt--cacctgtaaactattcttcatgctgctgacctcgccttttatt-ttaccatgaattatgaatgaatgactttgggaattcagGTGGGATAAACCAATACTAGTTGCATGGGGAATATCAGACAAGTATCTGCCTCAATCAGTGGCAGAAGAGTTTCAAAAGGGAAACCCTGATTATATAAAA
   ||  ||| | || |    ||  ||  |  || |  |||||  |    | | ||    ||||  |    |||  ||  ||  |||||   |   | | ||| ||||| |||||||||||  |||||||||||||||| ||||||||  | || |  ||  | || || || ||  |  | |  || ||||    | |||||
aaagttcattctgaatacaagcaattgatatatactagtcatgtgggcc-cttggcaacgtattgctgttctga--tacaaaaaaatgatcatcttattgcagTTGGGAAAAACCAATACTGCTTGCATGGGGAATATCTGACAAGTACTTACCGCTCTCGATAGCTGAGGAATTCAAGCAAGCTAATCCTGGCGTTGTAAAA

upper sequence: Vv09s0002g07500.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA07G03260.1 (Glycine max), 3'ss of exon 9
tttgtgtattttcaaaattcacctgta--aactattcttcatgctgctgacctcgccttttattttaccatga-attatgaatgaatgactttgggaattcagGTGGGATAAACCAATACTAGTTGCATGGGGAATATCAGACAAGTATCTGCCTCAATCAGTGGCAGAAGAGTTTCAAAAGGGAAACCCTGATTATATAAAA
 |   ||   |  ||     |  |||   ||       | |        | |   || |  |  | |   ||| |  || | |     | ||||  | | ||| |||||||||||||||||| |||| |||||| |||||||||||||  |||| || || ||||||||  ||||||| || ||||| || |   | ||  | 
-tcaggtgcatgtaattccaatttgtgggaaggggatgtaaaatcaaaaatcctaccctgaacct-atagtgataacataagttttgtaatttgt-attacagATGGGATAAACCAATACTACTTGCTTGGGGATTATCAGACAAGTACTTGCCCCAGTCTGTGGCAGAGCAGTTTCAGAAAGGAAATCCAGCACAAATCCAG

upper sequence: Vv09s0002g07500.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA08G22840.1 (Glycine max), 3'ss of exon 9
-tttgtgtattttcaaaattcacctgtaaactattcttcatgctgctgacctcgccttttattttaccatgaattatgaatgaatgactttgggaattcagGTGGGATAAACCAATACTAGTTGCATGGGGAATATCAGACAAGTATCTGCCTCAATCAGTGGCAGAAGAGTTTCAAAAGGGAAACCCTGATTATATAAAA
     |  |  | |||     |  |||          |       |  |   |  |  | |   ||    || | |  ||    ||   || | |   ||| |||||||||||||||||| |||| |||||| |||||||||||||  |||| || || || |||||  ||||||| || ||||| || |   | ||  | 
gcaattccaactccaattccaatttgtgggaaggagatgtaaaatcaaaatcctaccatgaacctatagcga-taacaaagttttgtaatttgtatcacagATGGGATAAACCAATACTACTTGCTTGGGGATTATCAGACAAGTACTTGCCCCAGTCTGTAGCAGAGCAGTTTCAGAAAGGAAATCCAGCACAAATCCAG

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|32250010|gb|CD715829.1|CD715829
EST:     AACTTCAAAGATATAGCAAGCCAAGTAGCTGCTGGATTTGCATCTGGAAG                         GTGGGATAAACCAATACTAGTTGCATGGGGAATATCAGACAAGTATCTGCC
genomic: AACTTCAAAGATATAGCAAGCCAAGTAGCTGCTGGATTTGCATCTGGAAGgtatatcatt ... gggaattcagGTGGGATAAACCAATACTAGTTGCATGGGGAATATCAGACAAGTATCTGCC
EST: gi|30320877|gb|CD004139.1|CD004139
EST:     TATAGCAAGCCAAGTAGCTGCTGGATTTGCATCTGGAAG                         GTGGGATAAACCAATACTAGTCGCATGGGGAATATCAGACAAGTATCTGCC
genomic: TATAGCAAGCCAAGTAGCTGCTGGATTTGCATCTGGAAGgtatatcatt ... gggaattcagGTGGGATAAACCAATACTAGTTGCATGGGGAATATCAGACAAGTATCTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgacctcgccttttattttaccatgaattatgaatgaatgactttgggaattcagGTGGGATAAACCAATACTAGTTGCATGGGGAATATCAGACAAGTATCTGCCTCAATCAGTGGCAGAAGAGTTTCAAAAGGGAAACCCTGATTATATAAAA
 tgctgac  putative branch site (score: 2)
          ttttattttaccatga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgtgtattttcaaaattcacctgtaaactattcttcatgctgctgacctcgccttttattttaccatgaattatgaatgaatgactttgggaattcagGTGGGATAAACCAATACTAGTTGCATGGGGAATATCAGACAAGTATCTGCCTCAATCAGTGGCAGAAGAGTTTCAAAAGGGAAACCCTGATTATATAAAA

- - - - - -tcaaaat
- - - - - - - - - -cacctgt
- - - - - - - - - - - - - - - - - - tcatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaatgaat