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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagatgccactctggtattttccaactgtcctaatttctaaatgtaccagatgccattttggttaataattgcttgagtctggaatttgcatttctcagGAATATAATCTGTACCAATTAATGGGAGAACAGAAAAGACCCCTTTCAGAGGAAGAGATACGGAGCTTTATGTCTCAAGTGCTGCAAGGACTTGCACACA

Basic information

species Vitis vinifera
transcript Vv07s0151g00350.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0151g00350.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA16G10820.2 (Glycine max), 3'ss of exon 6
ttagatgccactctggtattttcca--actgtcctaatttctaaatgtaccagatgccattttggttaataattgcttgagtctggaatttgcatttct-cagGAATATAATCTGTACCAATTAATGGGAGAACAGAAAAGACCCCTTTCAGAGGAAGAGATACGGAGCTTTATGTCTCAAGTGCTGCAAGGACTTGCACACA
  |||   | || | ||||     |  |  ||   |  ||||  ||  |||   |||  | |  | || |  |||   | | |   |  || ||| ||| ||||| | |||||| || ||||||||    ||     |||  ||| |||||||||||||||||||| ||||||||   |||||||| |||||||||   ||||
ccagaa--ctctttagtatccataattaaggttgaatgttctgtattgaccct-tgctttatcagatattgcttgacagtgacactagatttcatctcttcagGATTGTAATCTTTATCAATTAATAAAGGAGAGAGAAAAGCCCTTTTCAGAGGAAGAGATACGGTGCTTTATGAGGCAAGTGCTACAAGGACTTAGTCACA

upper sequence: Vv07s0151g00350.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA03G21610.2 (Glycine max), 3'ss of exon 5
ttagatgccactctggtattttcca--actgtcctaatttctaaatgtaccagatgccattttggttaataattgcttgagtctggaatttgcatttct-cagGAATATAATCTGTACCAATTAATGGGAGAACAGAAAAGACCCCTTTCAGAGGAAGAGATACGGAGCTTTATGTCTCAAGTGCTGCAAGGACTTGCACACA
  | |  |  ||   ||||     |  |  ||   |  ||||  ||  |||   |||  | |  | || |  |||   | | |   |  || ||| ||| ||||| | |||||| || ||||||||    ||     |||  ||| |||||||||||||||||||| ||||||||   |||||||| |||||||||   ||||
-caaaaact-cttcagtatccataattaaggttgaatgttctgtattgaccct-tgctttatcagatattccttgacagtgacactagatttcatctcttcagGATTGTAATCTTTATCAATTAATAAAGGAGAGAGAAAAGCCCTTTTCAGAGGAAGAGATACGGTGCTTTATGAGGCAAGTGCTACAAGGACTTAGTCACA
















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|351053929|gb|FQ441695.1|FQ441695
EST:     AGGAGATTGTCAGGGAAAACAATGAGCTGTTTTTCATATTTGAACACATG                         GAATATAATCTGTACCAAATAATGGGAGAACAGAAAAGACCCCTTTCAGAG
genomic: AGGAGATTGTCAGGGAAAACAATGAGCTGTTTTTCATATTTGAACACATGgtgaatattt ... catttctcagGAATATAATCTGTACCAATTAATGGGAGAACAGAAAAGACCCCTTTCAGAG
EST: gi|352794086|gb|FQ479328.1|FQ479328
EST:     AGGAGATTGTCAGGGAAAACAATGAGCTGTTTTTCATATTTGAACACATG                         GAATATAATCTGTACCAAATAATGGGAGAACAGAAAAGACCCCTTTCAGAG
genomic: AGGAGATTGTCAGGGAAAACAATGAGCTGTTTTTCATATTTGAACACATGgtgaatattt ... catttctcagGAATATAATCTGTACCAATTAATGGGAGAACAGAAAAGACCCCTTTCAGAG
EST: gi|351036041|gb|FQ463886.1|FQ463886
EST:     AGGAGATTGTCAGGGAAAACAATGAGCTGTTTTTCATATTTGAACACATG                         GAATATAATCTGTACCAAATAATGGGAGAACAGAAAAGACCCCTTTCAGAG
genomic: AGGAGATTGTCAGGGAAAACAATGAGCTGTTTTTCATATTTGAACACATGgtgaatattt ... catttctcagGAATATAATCTGTACCAATTAATGGGAGAACAGAAAAGACCCCTTTCAGAG
EST: gi|352794210|gb|FQ479452.1|FQ479452
EST:     AGGAGATTGTCAGGGAAAACAATGAGCTGTTTTTCATATTTGAACACATG                         GAATATAATCTGTACCAAATAATGGGAGAACAGAAAAGACCCCTTTCAGAG
genomic: AGGAGATTGTCAGGGAAAACAATGAGCTGTTTTTCATATTTGAACACATGgtgaatattt ... catttctcagGAATATAATCTGTACCAATTAATGGGAGAACAGAAAAGACCCCTTTCAGAG
EST: gi|351046353|gb|FQ452969.1|FQ452969
EST:     AGGAGATTGTCAGGGAAAACAATGAGCTGTTTTTCATATTTGAACACATG                         GAATATAATCTGTACCAAATAATGGGAGAACAGAAAAGACCCCTTTCAGAG
genomic: AGGAGATTGTCAGGGAAAACAATGAGCTGTTTTTCATATTTGAACACATGgtgaatattt ... catttctcagGAATATAATCTGTACCAATTAATGGGAGAACAGAAAAGACCCCTTTCAGAG
EST: gi|352794331|gb|FQ481562.1|FQ481562
EST:     AGGAGATTGTCAGGGAAAACAATGAGCTGTTTTTCATATTTGAACACATG                         GAATATAATCTGTACCAAATAATGGGAGAACAGAAAAGACCCCTTTCAGAG
genomic: AGGAGATTGTCAGGGAAAACAATGAGCTGTTTTTCATATTTGAACACATGgtgaatattt ... catttctcagGAATATAATCTGTACCAATTAATGGGAGAACAGAAAAGACCCCTTTCAGAG
EST: gi|352794414|gb|FQ481645.1|FQ481645
EST:     AGGAGATTGTCAGGGAAAACAATGAGCTGTTTTTCATATTTGAACACATG                         GAATATAATCTGTACCAAATAATGGGAGAACAGAAAAGACCCCTTTCAGAG
genomic: AGGAGATTGTCAGGGAAAACAATGAGCTGTTTTTCATATTTGAACACATGgtgaatattt ... catttctcagGAATATAATCTGTACCAATTAATGGGAGAACAGAAAAGACCCCTTTCAGAG
EST: gi|351047787|gb|FQ459007.1|FQ459007
EST:     AGGAGATTGTCACGGAAAACAATGAGCTGTTTTTCATATTTGAACACATG                         GAATATAATCTGTACCAAATAATGGGAGAACAGAAAAGACCCCTTTCAGAG
genomic: AGGAGATTGTCAGGGAAAACAATGAGCTGTTTTTCATATTTGAACACATGgtgaatattt ... catttctcagGAATATAATCTGTACCAATTAATGGGAGAACAGAAAAGACCCCTTTCAGAG
EST: gi|37190302|gb|CF609651.1|CF609651
EST:     AGGAGATTGTCAGGGAAAACAATGAGCTGTTTTTCATATTTGAACACATG                         GAATATAATCTGTACCAAATAATGGGAGAACAGAAAAGACCCCTTTCAGAG
genomic: AGGAGATTGTCAGGGAAAACAATGAGCTGTTTTTCATATTTGAACACATGgtgaatattt ... catttctcagGAATATAATCTGTACCAATTAATGGGAGAACAGAAAAGACCCCTTTCAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccagatgccattttggttaataattgcttgagtctggaatttgcatttctcagGAATATAATCTGTACCAATTAATGGGAGAACAGAAAAGACCCCTTTCAGAGGAAGAGATACGGAGCTTTATGTCTCAAGTGCTGCAAGGACTTGCACACA
                ggttaat  putative branch site (score: 4)
                                             catttctc  putative PPT
           attttggttaataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttagatgccactctggtattttccaactgtcctaatttctaaatgtaccagatgccattttggttaataattgcttgagtctggaatttgcatttctcagGAATATAATCTGTACCAATTAATGGGAGAACAGAAAAGACCCCTTTCAGAGGAAGAGATACGGAGCTTTATGTCTCAAGTGCTGCAAGGACTTGCACACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - gccactc
- - - - - - - - - - -tccaact
- - - - - - - - - - - - - - - - - - - - - - - -ccagatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttga