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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtatttgtgatgatgacatgatcttgtaattgcaagcttatgcaaatttttacgcttaaacagttagcagggaaagacataatgcatcttttggttgcagGAATTATATCATGAGTTGCATGCCTTGGACAGATTTGAACAAGATTATCGGCGCAAGCTTCAGGAAGAGGATAACTCGAATGCAGCTCAACGAG

Basic information

species Vitis vinifera
transcript Vv18s0076g00260.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0076g00260.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g65330.2 (Oryza sativa), 3'ss of exon 4
gtatttgtgatgatgacatgatcttgtaa--ttgcaagcttatgcaaatttttacgcttaaacagttagcagggaaagacataatgcatcttttggttgcagGAATTATATCATGAGTTGCATGCCTTGGACAGATTTGAACAAGATTATCGGCGCAAGCTTCAGGAAGAGGATAACTCGAATGCAGCTCAACGAG
 |||   || | |   |||  |  | | |   |||  || | |   | ||||     ||     ||      | ||  ||| | | ||  ||||  || |||||| |||| |||||  |||||||  |||| ||||||||||||||||||| |||||| |  ||||||||||||   || | || |   ||| |||
atatac-tgttaactgcatcttactatcaatctgctggcatttatcagttttcttcttttgcatgtcttgttgaaattacaaatttcaattttttttt-cagGAACTATACCATGAAATGCATGCACTGGATAGATTTGAACAAGATTATCAGCGCAAACAGCAGGAAGAGGATGGTTCAAGTGTACACCAAAGAG

upper sequence: Vv18s0076g00260.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os05g35530.1 (Oryza sativa), 3'ss of exon 5
------gtatttgtgatgatgacatgatcttgtaattgcaagcttatgcaaatttttacgcttaaacagttagcagggaaagacataatgcatcttttggttgcagGAATTATATCATGAGTTGCATGCCTTGGACAGATTTGAACAAGATTATCGGCGCAAGCTTCAGGAAGAGGATAACTCGAATGCAGCTCAACGAG
      || |   |  ||   ||    || ||| ||| |  |  |   |   || |     | | |    |  |  |        |  | | |  |||  |   |||||||||||||||| |||||| | ||||| |||||||||||||| | ||| || || |  || |||  ||||   | |  | ||          
agcaccgtttgccttctgtgcactgattcgtgttatttctggactt--ctggttatagatttcacatcactgactcgct----tctctttctttcttttctcctagGAATTATATCATGAATTGCATACTTTGGATAGATTTGAACAAGACTGTCGTCGTAAACAGCAAGAACTGGATGGTTTGGGTTCAAGAG------

upper sequence: Vv18s0076g00260.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G077621_T01 (Zea mays), 3'ss of exon 4
gtatttgtgatgatgacatgatcttgtaatt--gcaagcttatgcaaatttttacgcttaaac-agttagcagggaaagacataatgcatcttttggttgcagGAATTATATCATGAGTTGCATGCCTTGGACAGATTTGAACAAGATTATCGGCGCAAGCTTCAGGAAGAGGATAACTCGAATGCAGCTCAACGAG
  ||||||| |  |    | |||    ||||  ||   ||||| |   || |||   | | |  | |||           | |  | | | |||||    ||||||||||||||||| |||||||| ||||| ||||| ||||| |||||||| |  || |   | ||| |||||  || || |  |          
-aatttgtg-tatttttgtcatcggccaatttggccttcttattctggttattagcatcacattacttatttatttttttcttcctac-ttttttgcactcagGAATTATATCATGAATTGCATGCTTTGGATAGATTGGAACATGATTATCGCCTTAAACAGAAAGAACAGGATGGCTTGAGTTTAAGAG------

upper sequence: Vv18s0076g00260.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G320615_T01 (Zea mays), 3'ss of exon 4
--gtatttgtgatgatgacatgatcttgtaatt--gcaagcttatgcaaatttttacgcttaaacagttagcagggaaagacataatgcatcttttggttgcagGAATTATATCATGAGTTGCATGCCTTGGACAGATTTGAACAAGATTATCGGCGCAAGCTTCAGGAAGAGGATAACTCGAATGCAGCTCAACGAG
  | ||||||| |  |    | |||    ||||  ||   ||||| |   || |||   | | |    |   |        | |  | | | |||||     |||||||||||||||| |||||||| ||||| ||||| ||||| |||||||| |  || |   | ||| | |||   | || |  |          
atgaatttgtg-tatttttgtcatcggccaatttggccttcttattctgtttattagcgtcacattact--tattttttttcttcctac-ttttttgcacttagGAATTATATCATGAATTGCATGCTTTGGATAGATTGGAACATGATTATCGCCTTAAACAAAAAGAACATGATGGTTTGAGTTTAAGAG------

upper sequence: Vv18s0076g00260.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G097502_T01 (Zea mays), 3'ss of exon 4
gtatttgtgatgatgacatgatcttgtaatt--gcaagcttatgcaaatttttacgcttaaacagttagcagggaaagacataatgcatcttttggttgcagGAATTATATCATGAGTTGCATGCCTTGGACAGATTTGAACAAGATTATCGGCGCAAGCTTCAGGAAGAGGATAACTCGAATGCAGCTCAACGAG
| |||||| ||| |    | ||||   ||||  |    ||||| |   || |||   | | |    | |        |   |  | | | |||||    ||||||||||||||||| |||||||| ||||| |||||||| || |||| ||| |  || |   | ||| |||||  || || | ||          
gaatttgt-atgtttttgtcatctgccaatttggtcttcttattctggttattagtttcacattacttgtctattttgttttcctac-ttttttgcactcagGAATTATATCATGAATTGCATGCTTTGGATAGATTTGAGCATGATTGTCGTCTTAAACAGAAAGAACAGGATGGCTTGAGTTCAAGAG------

upper sequence: Vv18s0076g00260.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G31400.1 (Glycine max), 3'ss of exon 7
--gtatttgtgatgatgacatgatcttgtaattgcaagcttatgcaaatttttacgcttaaacagttagcagggaaagacataatgcatcttttggttgcagGAATTATATCATGAGTTGCATGCCTTGGACAGATTTGAACAAGATTATCGGCGCAAGCTTCAGGAAGAGGATAACTCGAATGCAGCTCAACGAG
  |   |  |||||   |  || |  | || ||       | | ||  |  ||      | ||  | |        ||    | |   |  ||||  ||||||||||||| ||||| ||||||||||| ||||||||||| ||||||||||||||||||||||| |||||||| || || |||||  | ||| |||
tagacatcctgatggaaagttggttct-tatttctttagctgtacagctgattttatcaagacc-tgatttcatttagtttgacttttttctttgcgtgcagGAATTATACCATGAATTGCATGCCTTAGACAGATTTGATCAAGATTATCGGCGCAAGCTTCAAGAAGAGGACAATTCAAATGCTACACAAAGAG

upper sequence: Vv18s0076g00260.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G36210.1 (Glycine max), 3'ss of exon 7
gtatttgtgatgatgacatgatcttgtaattgcaagcttatgcaaatttttacgc-ttaaacag------ttagcagggaaagacataatgcatctttt---ggttgcagGAATTATATCATGAGTTGCATGCCTTGGACAGATTTGAACAAGATTATCGGCGCAAGCTTCAGGAAGAGGATAACTCGAATGCAGCTCAACGAG
            |  ||  ||  |  | || | ||| | || |  |||| | |   || |||||      ||   | |     |  || |  |  ||||   |  ||||||||||||||||||| ||||||||||| || |||||||| |||||||||||||||||| |||| |||||||| || || |||||  | ||| |||
----------gcaaaactagacatcctgatggaaagttgattcttatttcttcatgttgaacagctgattttgttaagtcttaatttagtatactttttcctgagtgcagGAATTATATCATGAATTGCATGCCTTAGATAGATTTGATCAAGATTATCGGCGCAAGTTTCAAGAAGAGGACAATTCAAATGCCACACAAAGAG

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|352781806|gb|FQ469104.1|FQ469104
EST:     AAGCAGATACAGTGATGCAGCAATTGATGACTTTGGTTCAATATACAGCT                         GAATTATATCATGAGTTGCATGCCTTGGACAGATTTGAACAAGATTATCGG
genomic: AAGCAGATACAGTGATGCAGCAATTGATGACTTTGGTTCAATATACAGCTgtgagtattt ... ttggttgcagGAATTATATCATGAGTTGCATGCCTTGGACAGATTTGAACAAGATTATCGG
EST: gi|352778150|gb|FQ468812.1|FQ468812
EST:     AAGCAGATACAGTGATGCAGCAATTGATGACTTTGGTTCAATATACAGCT                         GAATTATATCATGAGTTGCATGCCTTGGACAGATTTGAACAAGATTATCGG
genomic: AAGCAGATACAGTGATGCAGCAATTGATGACTTTGGTTCAATATACAGCTgtgagtattt ... ttggttgcagGAATTATATCATGAGTTGCATGCCTTGGACAGATTTGAACAAGATTATCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttacgcttaaacagttagcagggaaagacataatgcatcttttggttgcagGAATTATATCATGAGTTGCATGCCTTGGACAGATTTGAACAAGATTATCGGCGCAAGCTTCAGGAAGAGGATAACTCGAATGCAGCTCAACGAG
                                       catctttt  CT-rich tract
          ttaaaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttgtgatgatgacatgatcttgtaattgcaagcttatgcaaatttttacgcttaaacagttagcagggaaagacataatgcatcttttggttgcagGAATTATATCATGAGTTGCATGCCTTGGACAGATTTGAACAAGATTATCGGCGCAAGCTTCAGGAAGAGGATAACTCGAATGCAGCTCAACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - catgatc
- - - - - - - - - - - - - - - - - - cttatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacagt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgcat