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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttagaatttaatctgcatggctttctggttagattgtgttattccctgatcatttattaaatatttttcactgtgatttgctgtttactgcctcacagTTCTTCACAACCAAACCTTATGCTTGTGAGCCTTCCAGCCTTCCAAAATATCCTCCCAGCAAGGAGATGGATGCTAAATTACGGGATGAAGAAGCCAGAA

Basic information

species Vitis vinifera
transcript Vv05s0020g01890.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os03g22700.1 (Oryza sativa), 3'ss of exon 3
ttttagaatttaatctgcatggctttctggttagattgtgttattccctgatcatttattaaatatttttcactgtgatttgctgtttactgcct-cacagTTCTTCACAACCAAACCTTATGCTTGTGAGCCTTCCAGCCTTCCAAAATATCCTCCCAGCAAGGAGATGGATGCTAAATTACGGGATGAAGAAGCCAGAA
   ||   | | |  |  ||   ||| | || |  ||   | |     ||     || ||  | | ||||      || |||||  ||||   ||   |||||||| |||||  |||||||||| ||||| || || || || |||  ||||||||| ||||| || |||||||| |||  | | ||||||||||||||| 
-gataatgtgtgaagtagatctgtttattgtcatctttgttgaaattatgtagcattgttttacacttttactaaagaattgcttattacaatctatgcagTTCTTTACAACTGAACCTTATGCATGTGAACCATCAAGTCTCCCAGCATATCCTCCAAGCAAAGAAATGGATGCAAAACGAAGAGATGAAGAAGCCAGAC

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G084347_T01 (Zea mays), 3'ss of exon 4
ttttagaatttaatctgcatggctttctggttagattgtgttattccctgatcatttattaaatatttttcactgtgatttgctgtttactgcct-----cacagTTCTTCACAACCAAACCTTATGCTTGTGAGCCTTCCAGCCTTCCAAAATATCCTCCCAGCAAGGAGATGGATGCTAAATTACGGGATGAAGAAGCCAGAA
|| ||| |   |   | |    | | || || | |   | || ||     |   ||| ||   | || | || |      |  |||  |||  ||       |||||||| |||||| |||||| ||| || || || || || ||||||||||||||||| ||||| ||||| ||||  |||  | | || |||||||||||| 
ttatagtacccagattcc----catccttgtcacac-attttgtttttgtagtttttttttggttttgtgcattaatgccttatgtgaactttctatgcatgcagTTCTTTACAACCGAACCTTTTGCATGCGAACCGTCAAGTCTTCCAAAATATCCTCCAAGCAAAGAGATAGATGTGAAACGAAGAGACGAAGAAGCCAGAC

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G156251_T01 (Zea mays), 3'ss of exon 4
ttttagaatttaatctgcatggctttctggttagattgtgttattccctgatcatttattaaatatttttcactgtgatttgctgtttactgcctca-------cagTTCTTCACAACCAAACCTTATGCTTGTGAGCCTTCCAGCCTTCCAAAATATCCTCCCAGCAAGGAGATGGATGCTAAATTACGGGATGAAGAAGCCAGAA
          | ||     |    | || || |     | ||||||| | || | | |  |  || |  ||| |||| | |  | |||| |     |        |||| ||  ||||| | |||||||||||| | ||||| || || |||| |||||| || ||||||||||||||||| || ||| | || || || || ||||
-----tggccttatgcatttatgctgcttgtaatgaactattattccgtcataact-accagttactcatca-tgtgctcttttttttattaaaaaaatggacttagTTTTTTTCAACCGAGCCTTATGCTTGTAACCCTTCAAGTCTGCCAACATATCCACCAAGCAAGGAGATGGATGCCAAGTTAAGAGACGAGGAGGCTAGAA

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G052206_T02 (Zea mays), 3'ss of exon 4
ttttagaatttaatctgcatggctttctggttagattgtgttattccctgatcatttattaaatatttttcactgtgatttgctgtttactgcct-----cacagTTCTTCACAACCAAACCTTATGCTTGTGAGCCTTCCAGCCTTCCAAAATATCCTCCCAGCAAGGAGATGGATGCTAAATTACGGGATGAAGAAGCCAGAA
   ||| |   |   | |    |||| |    | |||  ||| ||     ||  ||| ||   |||| |  | |      | |||||||||  ||       |||||||| |||||  |||||| ||| ||||| || || || ||||||||||||||||| ||||| || || ||||  |||  | | || |||||||||||| 
---tagcacccagattcc-catctttgtcac-acatttggtttttgtagcatattttttttggtattgtgtattcatgccttctgtttactttctatggatgcagTTCTTTACAACTGAACCTTTTGCATGTGAACCATCGAGTCTTCCAAAATATCCTCCAAGCAAAGAAATAGATGTGAAAAGAAGAGACGAAGAAGCCAGAC

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G10470.1 (Glycine max), 3'ss of exon 4
ttttagaattta----atctgcatggctttctggttagattgtgttattccctgatcatttattaaatatttttcactgtgatttgctgtttactgcctcacagTTCTTCACAACCAAACCTTATGCTTGTGAGCCTTCCAGCCTTCCAAAATATCCTCCCAGCAAGGAGATGGATGCTAAATTACGGGATGAAGAAGCCAGAA
  ||| | || |    ||    || |   |     |   |   | | ||| || ||  |   |  |||  |    | |   |     |   | ||   |  |||||||||||||| ||||| |||||||||||||| || |||||||||||||||||||||||||||||||||||||| ||  |||||||||||||||| || |
--ttaaatttgagaggatgaagattgtacttgcaatccttaaagcttttcactaattgtacgt--aatggtccgaatttaaagccatttggttctcttttgcagTTCTTCACAACAAAACCATATGCTTGTGAGCCCTCTAGCCTTCCAAAATATCCTCCCAGCAAGGAGATGGATGCAAAGCTACGGGATGAAGAAGCTAGGA

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G28650.1 (Glycine max), 3'ss of exon 4
ttttagaatttaatctgcatggctttctggtta-gattgtgttattccctgatca--tttattaaatatttttcactgtgatttgctgtttactgcctcacagTTCTTCACAACCAAACCTTATGCTTGTGAGCCTTCCAGCCTTCCAAAATATCCTCCCAGCAAGGAGATGGATGCTAAATTACGGGATGAAGAAGCCAGAA
   |  ||||| |   |       || |  ||   ||  |   |     | |  |  |  ||  |||  || | | |   |  |  |   | ||   |  |||||||| ||||| ||||| |||||||||||||| || |||||||||||||||||||||||||||||||||||||| ||  |||||||||||||||| ||||
---ttaaatttgagaggatgaaaattgtacttgcaatccttaaagcttttcactaagtggatgtaatggttctaatttaaagctatttggttctcttttgcagTTCTTTACAACAAAACCATATGCTTGTGAGCCCTCTAGCCTTCCAAAATATCCTCCCAGCAAGGAGATGGATGCAAAGCTACGGGATGAAGAAGCTAGAA

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA07G38140.1 (Glycine max), 3'ss of exon 4
-ttttagaatttaatctgcatggctttctggttagattgtgttattccctgatcatttattaaatatttttcactgtgat-ttgctgtttactgcctcacagTTCTTCACAACCAAACCTTATGCTTGTGAGCCTTCCAGCCTTCCAAAATATCCTCCCAGCAAGGAGATGGATGCTAAATTACGGGATGAAGAAGCCAGAA
  |||||  || | | || |||  ||  || ||  | |   |  |   |  |  ||||| || ||   |   | | | || ||  |   | ||   |  |||||||| ||| | ||||||||||| ||||| || || |||||||||||||||||||||||||||||||||||| | ||  |||||||||||||||| ||||
tatttagttttaagtatg-atgaatta-tgcttgaactccttagtgttccaacaatttaatatatgaatccaagtttaatgttaattgcttctcttttgcagTTCTTTACATCAAAACCTTATGCCTGTGAACCCTCTAGCCTTCCAAAATATCCTCCCAGCAAGGAGATGGATACAAAGCTACGGGATGAAGAAGCTAGAA

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G02580.1 (Glycine max), 3'ss of exon 4
-ttttagaatttaatctgcatggctttctggttagattgtgttattccctgatcatttattaaatatttttcactgtgat-ttgctgtttactgcctcacagTTCTTCACAACCAAACCTTATGCTTGTGAGCCTTCCAGCCTTCCAAAATATCCTCCCAGCAAGGAGATGGATGCTAAATTACGGGATGAAGAAGCCAGAA
  |||||  || | | || |||  ||  || ||  | |   |  |   |  |  ||||| || |    |   | | | || ||  |   | ||   |  |||||||| ||| | ||||||||||| ||||| || || |||||||||||||||||||||||||||||||||||| | ||  |||||||||||||||| ||||
tatttagttttaagtatg-atgaatta-tgcttgaactccttagtgttccaacaatttaatataagaatccaagtttaatgttaattgcttctcttttgcagTTCTTTACATCAAAACCTTATGCCTGTGAACCCTCTAGCCTTCCAAAATATCCTCCCAGCAAGGAGATGGATACAAAGCTACGGGATGAAGAAGCTAGAA

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|71873708|gb|DT022763.1|DT022763
EST:     CAATTGATCCAGCTGAACGTCAAACTGCCACTGCTGCATTGAGGAGTGAA                         TTCTTCACAACCAAACCTTATGCTTGTGAGCCTTCCAGCCTTCCAAAATAT
genomic: CAATTGATCCAGCTGAACGTCAAACTGCCACTGCTGCATTGAGGAGTGAAgtgagctttt ... tgcctcacagTTCTTCACAACCAAACCTTATGCTTGTGAGCCTTCCAGCCTTCCAAAATAT
EST: gi|110726282|gb|EE101925.1|EE101925
EST:     CAATTGATCCAGCTGAACGTCAAACTGCCACTGCTGCATTGAGGAGTGAA                         TTCTTCACAACCAAACCTTATGCTTGTGAGCCTTCCAGCCTTCCAAAATAT
genomic: CAATTGATCCAGCTGAACGTCAAACTGCCACTGCTGCATTGAGGAGTGAAgtgagctttt ... tgcctcacagTTCTTCACAACCAAACCTTATGCTTGTGAGCCTTCCAGCCTTCCAAAATAT
EST: gi|34544526|gb|CF512758.1|CF512758
EST:     CAATTGATCCAGCTGAACGTCAAACTGCCACTGCTGCATTGAGGAGTGAA                         TTCTTCACAACCAAACCTTATGCTTGTGAGCCTTCCAGCCTTCCAAAATAT
genomic: CAATTGATCCAGCTGAACGTCAAACTGCCACTGCTGCATTGAGGAGTGAAgtgagctttt ... tgcctcacagTTCTTCACAACCAAACCTTATGCTTGTGAGCCTTCCAGCCTTCCAAAATAT
EST: gi|71871637|gb|DT020692.1|DT020692
EST:     CAATTGATCCAGCTGAACGTCAAACTGCCACTGCTGCATTGAGGAGTGAA                         TTCTTCACAACCAAACCTTATGCTTGTGAGCCTTCCAGC
genomic: CAATTGATCCAGCTGAACGTCAAACTGCCACTGCTGCATTGAGGAGTGAAgtgagctttt ... tgcctcacagTTCTTCACAACCAAACCTTATGCTTGTGAGCCTTCCAGC
EST: gi|77586479|gb|DV222360.1|DV222360
EST:     CAATTGATCCAGCTGAACGTCAAACTGCCACTGCTGCATTGAGGAGTGAA                         TTCTTCACAACCAAACCTTATGCTTGTGAGCCTTCCAGCCTTCCAAAATAT
genomic: CAATTGATCCAGCTGAACGTCAAACTGCCACTGCTGCATTGAGGAGTGAAgtgagctttt ... tgcctcacagTTCTTCACAACCAAACCTTATGCTTGTGAGCCTTCCAGCCTTCCAAAATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccctgatcatttattaaatatttttcactgtgatttgctgtttactgcctcacagTTCTTCACAACCAAACCTTATGCTTGTGAGCCTTCCAGCCTTCCAAAATATCCTCCCAGCAAGGAGATGGATGCTAAATTACGGGATGAAGAAGCCAGAA
 ccctgat  putative branch site (score: 4)
                                            ctgcctc  putative PPT
        atttattaaatatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttagaatttaatctgcatggctttctggttagattgtgttattccctgatcatttattaaatatttttcactgtgatttgctgtttactgcctcacagTTCTTCACAACCAAACCTTATGCTTGTGAGCCTTCCAGCCTTCCAAAATATCCTCCCAGCAAGGAGATGGATGCTAAATTACGGGATGAAGAAGCCAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - gcatggc
- - - - - - - - - - - -tttctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgtt