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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagttgtggatgctcattttcacctttgtgctggtgttttgtgcatgagttacggctggtaatttctttttccagtcgttttaccctgacctgatttagATACTGTTACCAAGATGACTGCACCAAAGAGGATCCTTTGTCACAGGACGGATTCCGGAAACTTGCCTTGCCATTACCCTACTCAAAGCAGCATCACTCG

Basic information

species Vitis vinifera
transcript Vv13s0067g03560.t01
intron # 5
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0067g03560.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G38660.1 (Glycine max), 3'ss of exon 5
-----ttagttgtggatgctcattttcacctttgtgctggtgttttgtgcatgagttacggctggtaatttctttttccagtcgttttaccctgacctgatttagATACTGTTACCAAGATGACTGCACCAAAGAGGATCCTTTGTCACAGGACGGATTCCGGAAACTTGCCTTGCCATTACCCTACTCAAAGCAGCATCACTCG
     ||| ||||  ||     |  |   | ||      |||||  |||||||  ||    | | |||   || | |  ||   | || || |||||||||  ||||| |||||| | ||||| ||||| |||||||| || || |||||||| |  ||||| | ||| ||| |||||||||| || ||||||||||||||||| 
cctctttacttgtaaatttgattggttctcattccaactgtgttc-gtgcatgcattgtcacagctaa---ctctattgagatatgtt-ccttgacctgataaagATATTGTTACGAGGATGATTGCACAAAAGAGGACCCCTTATCACAGGAGGCTTTCCGCACACTAGCCATGCCATTACCATATTCAAAGCAGCATCACTCT

upper sequence: Vv13s0067g03560.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA10G43910.1 (Glycine max), 3'ss of exon 5
ttagttgtggatgctcat---tttcacctttgtgctggtgttttgtgcatgagttacggctggtaatttctttttccagtcgttttaccctgacctgatttagATACTGTTACCAAGATGACTGCACCAAAGAGGATCCTTTGTCACAGGACGGATTCCGGAAACTTGCCTTGCCATTACCCTACTCAAAGCAGCATCACTCG
||   |||||||| |  |     |||   || |  |  |      |   |   ||   ||     ||  || | |  ||   | || || |||| ||||  ||||| |||||  | ||||| ||||| |||||||| || || |||||||| |  ||||| | ||| ||| |||||||||| || ||||||||||||||||| 
ttttctgtggatgattttaaagctcatacttataataataaaacctctttactttt--gccacagataactctattgagatatatt-ccttgacttgataaagATATTGTTATGAGGATGATTGCACAAAAGAGGACCCCTTATCACAGGAGGCTTTCCGCACACTAGCCATGCCATTACCATATTCAAAGCAGCATCACTCT
















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|294964279|gb|GW838082.1|GW838082
EST:     CCTTTGCTGAATATATATCTGCAAGCAGGCTTGTCTGCTCTAAAAACTCC                         AAACTGTTACCAAGATGACTGCATCAAAGAGGA-CCTTTGTCACAGGACAG
genomic: CCTTTGCTGAATATATATCTGCAAGCAGGCTTGTCTGCTCTAAAAACTCCgtatcctcat ... cctgatttagATACTGTTACCAAGATGACTGCACCAAAGAGGATCCTTTGTCACAGGACGG
EST: gi|110699533|gb|EE076616.1|EE076616
EST:     CCTTTGCTGAATATATATCTGCAAGCAGGCTTGTCTGCTCTANAA-CTCC                         ATACTGTTACCAAGATGACTGCACCAAAGAGGACCCTTTGTCACAGGACGG
genomic: CCTTTGCTGAATATATATCTGCAAGCAGGCTTGTCTGCTCTAAAAACTCCgtatcctcat ... cctgatttagATACTGTTACCAAGATGACTGCACCAAAGAGGATCCTTTGTCACAGGACGG
EST: gi|30132591|gb|CB917930.1|CB917930
EST:     CCTTTGCTGAATATATATCTGCAGGCAGGCTTGTCTGCTCTAAAAACTCC                         ATACTGTTACCAAGATGACTGCACCAAAGAGGACCCTTTGTCACAGGACAG
genomic: CCTTTGCTGAATATATATCTGCAAGCAGGCTTGTCTGCTCTAAAAACTCCgtatcctcat ... cctgatttagATACTGTTACCAAGATGACTGCACCAAAGAGGATCCTTTGTCACAGGACGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgagttacggctggtaatttctttttccagtcgttttaccctgacctgatttagATACTGTTACCAAGATGACTGCACCAAAGAGGATCCTTTGTCACAGGACGGATTCCGGAAACTTGCCTTGCCATTACCCTACTCAAAGCAGCATCACTCG
                                     taccctgac  putative branch site 
               taatttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttagttgtggatgctcattttcacctttgtgctggtgttttgtgcatgagttacggctggtaatttctttttccagtcgttttaccctgacctgatttagATACTGTTACCAAGATGACTGCACCAAAGAGGATCCTTTGTCACAGGACGGATTCCGGAAACTTGCCTTGCCATTACCCTACTCAAAGCAGCATCACTCG

- - - - ggatgct
- - - - - - - - - - - - - - gtgctgg
- - - - - - - - - - - - - - - - - - - - - - catgagt
- - - - - - - - - - - - - - - - - - - - - - - - - - -cggctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -accctga