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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagagaatcacagaaaattcatatttgctgttatggttcctataactttggacatctcatgagccacaaaatttatcctttttggttttctttatgcagATATTAGATACAAACCCCCAACTATTTTTCCATCTCCAACAGCAAAGGTTGATAGAACTGATTCGGAATGGAAAAGTAGATGAGGCTCTGGAGTTTGCTC

Basic information

species Vitis vinifera
transcript Vv10s0116g00670.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0116g00670.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA13G31720.1 (Glycine max), 3'ss of exon 3
-----ttagagaatcacagaaaattcatatttgctgttatggttcctataactttggacatctcatgagccacaaaatttatcct-ttttggttttctttatgcagATATTAGATACAAACCCCCAACTATTTTTCCATCTCCAACAGCAAAGGTTGATAGAACTGATTCGGAATGGAAAAGTAGATGAGGCTCTGGAGTTTGCTC
      |   | |||  |  |||| ||||     | || |    |  | | || |  || | | ||   |      ||  ||  | |||||   | || | |||||||| | || ||||| |||||| ||||||||||||| ||||||||| | ||||||||||| || ||||||||||||||||| || ||||| |||||||| |
aactagtctggcatccaatcaaatacataacaatt-ttgtacacctcagagctatc-acttgttattgtctt----atccattttgttttgaaatactgtctgcagATACTGGACACAAATCCCCAATTATTTTTCCATCTTCAACAGCAACGATTGATAGAACTCATCCGGAATGGAAAAGTAGAAGAAGCTCTAGAGTTTGCCC

upper sequence: Vv10s0116g00670.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA15G07570.3 (Glycine max), 3'ss of exon 4
-----ttagagaatcacagaaaattcatatttgctgttatggttcctataactttggacatctcatgagccacaaaatttatcctttttggttttctttatgcagATATTAGATACAAACCCCCAACTATTTTTCCATCTCCAACAGCAAAGGTTGATAGAACTGATTCGGAATGGAAAAGTAGATGAGGCTCTGGAGTTTGCTC
      |   | |||  |  |||| ||||     | || |    |  | | || |       |  ||    || || ||| |    ||||   |||| | |||||||| | || ||||| |||||| ||||||||||||| ||||||||| | ||||||||||| || ||||||||||||||||| || || || |||||||| |
aactagtctggtatccaatcaaatacataacaatt-ttgtacacctcagagctatcacttgttattgtcttaccaattttgt----tttgtaattctgtctgcagATACTGGACACAAATCCCCAATTATTTTTCCATCTTCAACAGCAACGATTGATAGAACTCATCCGGAATGGAAAAGTAGAAGAAGCGCTAGAGTTTGCCC
















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|27579957|gb|CB002652.1|CB002652
EST:     GTGGGAATGTTGAGGATGCAATTGAGAAAGTAAATGATTTGAATCCTGAG                         ATATTAGATACAAACCCCCAACTATTTTTCCATCTCCAACAGCAAAGGTTG
genomic: GTGGGAATGTTGAGGATGCAATTGAGAAAGTAAATGATTTGAATCCTGAGgtatgttgct ... ctttatgcagATATTAGATACAAACCCCCAACTATTTTTCCATCTCCAACAGCAAAGGTTG
EST: gi|34546271|gb|CF514503.1|CF514503
EST:     GTGGGAATGTTGAGGATGCAATTGAGAAAGTAAATGATTTGAATCCTGAG                         ATATTAGATACAAACCCCCAACTATTTTTCCATCTCCAACAGCAAAGGTTG
genomic: GTGGGAATGTTGAGGATGCAATTGAGAAAGTAAATGATTTGAATCCTGAGgtatgttgct ... ctttatgcagATATTAGATACAAACCCCCAACTATTTTTCCATCTCCAACAGCAAAGGTTG
EST: gi|110702440|gb|EE081156.1|EE081156
EST:     GTGGGAATGTTGAGGATGCAATTGAGAAAGTAAATGATTTGAATCCTGAG                         ATATTAGATACAAACCCCCAACTATTTTTCCATCTCCAACAGCAAAGGTTG
genomic: GTGGGAATGTTGAGGATGCAATTGAGAAAGTAAATGATTTGAATCCTGAGgtatgttgct ... ctttatgcagATATTAGATACAAACCCCCAACTATTTTTCCATCTCCAACAGCAAAGGTTG
EST: gi|34544716|gb|CF512948.1|CF512948
EST:     AAAGTAAATGATTTTGAATCCTGAG                         ATATTAGATACAAACCCCCAACTATTTTTCCATCTCCAACAGCAAAGGTTG
genomic: AAAGTAAATGA-TTTGAATCCTGAGgtatgttgct ... ctttatgcagATATTAGATACAAACCCCCAACTATTTTTCCATCTCCAACAGCAAAGGTTG
EST: gi|110415950|gb|EC981891.1|EC981891
EST:     GTGGGAATGTTGAGGATGCAATTGAGAAAGTAAATGATTTGAATCCTGAG                         ATATTAGATACAAACCCCCAACTATTTTTCCATCTCCAACAGCAAAGGTTG
genomic: GTGGGAATGTTGAGGATGCAATTGAGAAAGTAAATGATTTGAATCCTGAGgtatgttgct ... ctttatgcagATATTAGATACAAACCCCCAACTATTTTTCCATCTCCAACAGCAAAGGTTG
EST: gi|30323272|gb|CD006534.1|CD006534
EST:     GTGGGAATGTTGAGGATGCAATTGAGAAAGTAAATGATTTGAATCCTGAG                         ATATTAGATACAAACCCCCAACTATTTTTCCATCTCCAACAGCAAAGGTTG
genomic: GTGGGAATGTTGAGGATGCAATTGAGAAAGTAAATGATTTGAATCCTGAGgtatgttgct ... ctttatgcagATATTAGATACAAACCCCCAACTATTTTTCCATCTCCAACAGCAAAGGTTG
EST: gi|27578911|gb|CB001606.1|CB001606
EST:     GTGGGAATGTTGAGGATGCAATTGAGAAAGTAAATGATTTGAATCCTGAG                         ATATTAGATACAAACCCCCAACTATTTTTCCATCTCCAACAGCAAAGGTTG
genomic: GTGGGAATGTTGAGGATGCAATTGAGAAAGTAAATGATTTGAATCCTGAGgtatgttgct ... ctttatgcagATATTAGATACAAACCCCCAACTATTTTTCCATCTCCAACAGCAAAGGTTG
EST: gi|110408401|gb|EC974037.1|EC974037
EST:     GTGGGAATGTTGAGGATGCAATTGAGAAAGTAAATGATTTGAATCCTGAG                         ATATTAGATACAAACCCCCAACTATTTTTCCATCTCCAACAGCAAAGGTTG
genomic: GTGGGAATGTTGAGGATGCAATTGAGAAAGTAAATGATTTGAATCCTGAGgtatgttgct ... ctttatgcagATATTAGATACAAACCCCCAACTATTTTTCCATCTCCAACAGCAAAGGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actttggacatctcatgagccacaaaatttatcctttttggttttctttatgcagATATTAGATACAAACCCCCAACTATTTTTCCATCTCCAACAGCAAAGGTTGATAGAACTGATTCGGAATGGAAAAGTAGATGAGGCTCTGGAGTTTGCTC
 ctataac  putative branch site (score: 3)
                           tttatcctttttggtt  putative PPT
                       aaaatttatccttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttagagaatcacagaaaattcatatttgctgttatggttcctataactttggacatctcatgagccacaaaatttatcctttttggttttctttatgcagATATTAGATACAAACCCCCAACTATTTTTCCATCTCCAACAGCAAAGGTTGATAGAACTGATTCGGAATGGAAAAGTAGATGAGGCTCTGGAGTTTGCTC

- - agaatca
- - - - - - agaaaat
- - - - - - - - - - - - - tgctgtt
- - - - - - - - - - - - - - - - - tggttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccacaaa