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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttttgtttgtgctggcttttttgtttcctttcttcttcttctgaagtatgttacttgtttccttgactcttctagacgtttatgtactcttttggttatgcgttttttgttggattccagGCAGGTCACCTTCATCTTGTGAAGCCATATATGGTTGCAGTTCAGAGTAACAATGTTTCTGCTGTGAATGAGGCTTTGAATGGGATTTATGTTGAGGAGG

Basic information

species Vitis vinifera
transcript Vv13s0067g01290.t01
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 25
gtttttgtttgtgctggcttttttgtttcctttcttcttcttctgaagtatgttacttgtttccttgactcttctagacgtttatgtactcttttggttatgcgttttttgttggattccagGCAGGTCACCTTCATCTTGTGAAGCCATATATGGTTGCAGTTCAGAGTAACAATGTTTCTGCTGTGAATGAGGCTTTGAATGGGATTTATGTTGAGGAGG
                              ||  ||||| |      |  |  || | || |  |    | | ||     |  |  |  |    || |||    || |||||       ||||| |||||  | ||||||||||| ||||| ||||||||||||||||| |||||||| |||||||||||||| |||||||||| | |||||||||| ||||
----------------------------gtttgtttcttatggcagggccttctattggtcta-tcagttttgctctgtttcaaaattttgaactgtttaattattatttgta------cagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAAGCTTTGAATGAGCTTTATGTTGAAGAGG

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 25
gtttttgtttgtgctggcttttttgtttcctttcttcttcttctgaagtatgttacttgtttccttgactcttctagacgtttatgtactcttttggttatgcgttttttgttggattccagGCAGGTCACCTTCATCTTGTGAAGCCATATATGGTTGCAGTTCAGAGTAACAATGTTTCTGCTGTGAATGAGGCTTTGAATGGGATTTATGTTGAGGAGG
                              ||  ||||| |      |  |  || | || |  |    | | ||   |||||    | | ||    |  | | || ||  ||| |   ||||| |||||  | ||||||||||| ||||| ||||||||||||||||| |||||||| ||||||||||||||  ||||||||| | |||||||||| ||||
----------------------------gtttgtttcttatggcagggccttctattggtcta-tcagttttgctc--cgttt-caaaattttgaactatttcattattctttgta---cagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAATCTTTGAATGAGCTTTATGTTGAAGAGG

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 2
gtttttgtttgtgctggcttttttgtttcctttcttcttcttctgaagtatgttacttgtttccttgactcttctagacgtttatgtactcttttggttatgcgttttttgttggattccagGCAGGTCACCTTCATCTTGTGAAGCCATATATGGTTGCAGTTCAGAGTAACAATGTTTCTGCTGTGAATGAGGCTTTGAATGGGATTTATGTTGAGGAGG
|||    | ||    |   |||   |||||||    |   ||    | ||     | ||||||    | || |    |  | |   |||| | |||        ||  |  |||||   ||||| |||||  | ||||||||||| |||||||||||||||||||||||||| ||||| |||||||||||||| || ||||||| | |||||||||| ||||
gttagcatctgaatggaaattt--atttccttagcgcacttt---gaatagaagccctgtttca--aattccttccaaaatct---tactgtcttg--------ttgctctttgga---cagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAATAATGTCTCTGCTGTGAATGAAGCCTTGAATGAGCTTTATGTTGAAGAGG

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 2
gtttttgtttgtgctggcttttttgtttcctttcttcttcttctgaagtatgttacttgtttccttgactcttctagacgtttatgtactcttttggttatgcgttttttgttggattccagGCAGGTCACCTTCATCTTGTGAAGCCATATATGGTTGCAGTTCAGAGTAACAATGTTTCTGCTGTGAATGAGGCTTTGAATGGGATTTATGTTGAGGAGG
   || |  | ||   |    ||| |||||||    |   ||      ||     | ||||| |      ||||         |    ||   |||  |    |||  |  |||||   ||||| |||||  | ||||||||||| |||||||||||||||||||||||||||||||| |||||||||||||| || ||||| |   |||||||||| ||||
--gttagcatctgaatgaaaatttatttccttagcgcacttt---ggatagaagccctgttttcaaattccttcc-----cccaaaatctgacttgtct---tgttgctctttgga---cagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCTGTGAATGAAGCCTTGAACGAACTTTATGTTGAAGAGG

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 24
gtttttgtttgtgctggcttttttgtttcctttcttcttcttctgaagtatgttacttgtttccttgactcttctagacgtttatgtactcttttggttatgcgttttttgttggattccagGCAGGTCACCTTCATCTTGTGAAGCCATATATGGTTGCAGTTCAGAGTAACAATGTTTCTGCTGTGAATGAGGCTTTGAATGGGATTTATGTTGAGGAGG
                | |    | |         |||  | ||| |||    |  |||  |    | |   | |  |         |    | || || |  |||  |  |||||   ||||| |||||  | ||||||||||| |||||||||||||||||||||||||||||||| ||||| |||||||| || ||||||| | ||||||| || ||||
----------------gttagcatctgattgaaaatctattcctgcagtgcact--ttgaatagaagccctgtttcaattccgtcccaaaaatctgattct-tgttgctctttgga---cagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTATCTGCCGTGAATGAAGCCTTGAATGAGCTTTATGTCGAAGAGG

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: GRMZM2G062042_T02 (Zea mays), 3'ss of exon 10
gtttttgtttgtgctggcttttttgtttcctttcttcttcttctgaagtatgttacttgtttccttgactcttctagacgtttatgtactcttttggttatgcgttttttgttggattccagGCAGGTCACCTTCATCTTGTGAAGCCATATATGGTTGCAGTTCAGAGTAACAATGTTTCTGCTGTGAATGAGGCTTTGAATGGGATTTATGTTGAGGAGG
      |||    |||          |  |  | || | |      | ||     | ||||||  |  |  | | | |  | |    | ||||          |||  |  |||||   ||||| |||||  | ||||||||||| |||||||||||||||||||||||||||||||| ||||| |||||||| || |||||||   ||||||| || || |
-----agttgaaactgatgaaagaaatagccctgttttgcactgtgaatagaagccctgtttcaatt-ccgtcccaaaaatctg---attctt----------gttgctctttgga---cagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: GRMZM2G091121_T01 (Zea mays), 3'ss of exon 5
gtttttgtttgtgctggcttttttgtttcctttcttcttcttctgaagtatgttacttgtttccttgactcttctagacgtttatgtactcttttggttatgcgttttttgttggattccagGCAGGTCACCTTCATCTTGTGAAGCCATATATGGTTGCAGTTCAGAGTAACAATGTTTCTGCTGTGAATGAGGCTTTGAATGGGATTTATGTTGAGGAGG
                                            | |||    |  |||  |    | |   | |  |         |    | || || |  |||  |  |||||   ||||| |||||  | ||||||||||| |||||||||||||||||||||||||||||||| ||||| |||||||| || |||||||   ||||||| || || |
--------------------------------------------gtagtgcact--ttgaatagaagccctatttcaattccatcccaaaaatctgattct-tgttgctctttgga---cagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: GRMZM2G115138_T01 (Zea mays), 3'ss of exon 9
gtttttgtttgtgctggcttttttgtttcctttcttcttcttctgaagtatgttacttgtttccttgactcttctagacgtttatgtactcttttggttatgcgttttttgttggattccagGCAGGTCACCTTCATCTTGTGAAGCCATATATGGTTGCAGTTCAGAGTAACAATGTTTCTGCTGTGAATGAGGCTTTGAATGGGATTTATGTTGAGGAGG
                                            | |||    |  |||  |    | |   | |  |         |    | || || |  |||  |  |||||   ||||| |||||  | ||||||||||| |||||||||||||||||||||||||||||||| |||||  ||||||| || |||||||   ||||||| || || |
--------------------------------------------gtagtgcact--ttgaatagaagccctatttcaattccatcccaaaaatctgattct-tgttgctctttgga---cagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCATGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: GRMZM2G395549_T01 (Zea mays), 3'ss of exon 10
gtttttgtttgtgctggcttttttgtttcctttcttcttcttctgaagtatgttacttgtttccttgactcttctagacgtttatgtactcttttggttatgcgttttttgttggattccagGCAGGTCACCTTCATCTTGTGAAGCCATATATGGTTGCAGTTCAGAGTAACAATGTTTCTGCTGTGAATGAGGCTTTGAATGGGATTTATGTTGAGGAGG-----------------------------------------------------------------------
   |  |  | || | |    | | ||||     | |   ||    | ||     | ||||||  |    || | | |  | |    | ||||          |||  |  |||||   ||||| |||||  | ||||||||||| ||||||||||||||| |||||||||||||||| |||||  ||||||  || ||||||| | |||||||    ||||                                                                       
--gtaagcatctgattgaaaatctatttctgcagtgcacttt---gaatagaagccctgtttcaat--tcctcccaaaaatctg---attctt----------gttgctctttgga---caggctggtcagttgcatcttgtgaaaccatatatggttgcaattcagagtaacaatgtctctgccatgaatggagccttgaatgagctttatgtctgagagGAGGACTATGAGAGACTCCGTGAATCAGTTGACACGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAG

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 25
gtttttgtttgtgctggcttttttgtttcctttcttcttcttctgaagtatgttacttgtttccttgactcttctagacgtttatgtactcttttggttatgcgttttttgttggattccagGCAGGTCACCTTCATCTTGTGAAGCCATATATGGTTGCAGTTCAGAGTAACAATGTTTCTGCTGTGAATGAGGCTTTGAATGGGATTTATGTTGAGGAGG
                              |    || |     | |  |  ||| ||   |  ||   | ||  |  |    ||  |||||  |||  |       |||  |    |  |||| |||||||| | ||||||||| |||||||||||||||||||| || ||||| || |||||||| ||||| || ||||||| ||| |||||||||||||
-----------------------------gtaggatcattagtggtaaaaatttaattagata-ttagttgttgcatgc---cata-actctaatgggaaacttcactttaatatgctatagGCTGGTCACCTCCGTCTTGTGAAACCATATATGGTTGCAGTTCAAAGCAACAACGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTTGAGGAGG

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 24
gtttttgtttgtgctggcttttttgtttcctttcttct-tcttctgaagtatgttacttgtttccttgactcttctagacgtttatgtactcttttggttatgcgttttttgttggattccagGCAGGTCACCTTCATCTTGTGAAGCCATATATGGTTGCAGTTCAGAGTAACAATGTTTCTGCTGTGAATGAGGCTTTGAATGGGATTTATGTTGAGGAGG
                        ||  | ||  | || ||  |      || ||| || || | ||    | | |     |  || |     | ||  |||      | || || |||  |||| ||||| || | |||||| |||||||| |||||||||||||||||||||||||| |||||||| ||||| ||  | ||||  || |||||||||||||
------------------------gtagcattaatactgtcaacaatttcatcttaatttttactttataacctgt---tttccatttcactctatgaatattttccctgtgatgtattatagGCTGGTCATCTCCGTCTTGTCAAGCCATACATGGTTGCAGTTCAGAGTAACAATGTGTCTGCTGTTAATGAAGCCCTTAATGAAATATATGTTGAGGAGG

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 24
gtttttgtttgtgctggcttttttgtttcctttcttcttcttctgaagtatgttacttgtttccttgactcttctagacgtttatgtactcttttggttatgcgttttttgttggattccagGCAGGTCACCTTCATCTTGTGAAGCCATATATGGTTGCAGTTCAGAGTAACAATGTTTCTGCTGTGAATGAGGCTTTGAATGGGATTTATGTTGAGGAGG
              | || ||  |  |  |     | |  || |  ||| | ||||||  |  | ||  | ||| |    |||     | ||  ||  |||      | || || |||  |||| ||||| || | |||||| ||||| || ||||||||||||||||||||||| || |||||||| ||||| ||  ||||||  || |||||||||||||
-------------gtagcattaatactgtcaacaatttcatttt--agttt-ttactttataacctg--ttttcca----ttt-----cactgatgaatattttccctgtgatgtattatagGCTGGTCATCTCCGTCTTGTCAAGCCTTACATGGTTGCAGTTCAGAGTAACAACGTGTCTGCTGTTAATGAAGCCCTGAATGAAATATATGTTGAGGAGG

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 25
gtttttgtttgtgctggcttttttgtttcctttcttcttcttctgaagtatgttacttgtttccttgactcttctagacgtttatgtactcttttggttatgcgttttttgttggattccagGCAGGTCACCTTCATCTTGTGAAGCCATATATGGTTGCAGTTCAGAGTAACAATGTTTCTGCTGTGAATGAGGCTTTGAATGGGATTTATGTTGAGGAGG
      ||| | |   |    ||  |||  | | ||||  |    ||   | | ||  ||      | ||    ||    | ||| |   ||  || ||||   || ||| |  |||  ||||| |||||| | |  ||| | |||||||||||||||||||||||||| || ||||| |||||||| ||||| ||| |||||| ||| ||||  || || |
------gttagaggctgaccattgatttaatattttctgtta--aaaacttatcaccagt------ggct----taacaatctatat---ctgatgattatttcttgtttct--gatctcagGCTGGTCACTTGCGCCTTATTAAGCCATATATGGTTGCAGTTCAGAGCAATAATGTATCTGCTGTAAATGAAGCTCTGAATGAGATATATGCAGAAGAAG

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 25
gtttttgtttgtgctggcttttttgtttcctttcttcttcttctgaagtatgttacttgtttccttgactcttctagacgtttatgtactcttttggttatgcgtt--ttttgttggattccagGCAGGTCACCTTCATCTTGTGAAGCCATATATGGTTGCAGTTCAGAGTAACAATGTTTCTGCTGTGAATGAGGCTTTGAATGGGATTTATGTTGAGGAGG
                                         |  ||||     |  |   ||  ||   |  | || |      ||  ||   ||  |||    ||  |||  |  |||  ||||| |||||| | | |||| | |||||||| ||| ||||||||||||| |||||||| |||||||| ||||||||| |||||| ||| || || || || |
----------------------------------------gttagaagctgactgatgactttgtttttttctataaaaacaactgagctacattacttaacaattggtttcttctgatctcagGCTGGTCACTTGCGTCTTATCAAGCCATACATGATTGCAGTTCAGAGCAACAATGTCTCTGCTGTTAATGAGGCTCTGAATGAGATATACGTGGAAGAAG

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|71858842|gb|DT007897.1|DT007897
EST:     TGCTTGCACTTCGAGTAGACCATACTCGTGTGGTTGACATAATGCGGAAG                         GCAGGTCACCTTCATCTTGTGAAGCCATATATGGTTGCAGTTCAGAGCAAC
genomic: TGCTTGCACTTCGAGTAGACCATACTCGTGTGGTTGACATAATGCGGAAGgtttttgttt ... tggattccagGCAGGTCACCTTCATCTTGTGAAGCCATATATGGTTGCAGTTCAGAGTAAC
EST: gi|71857909|gb|DT006964.1|DT006964
EST:     TGCTTGCACTTCGAGTAGACCATACTCGTGTGGTTGACATAATGCGGAAG                         GCAGGTCACCTTCATCTTGTGAAGCCATATATGGTTGCAGTTCAGAGCAAC
genomic: TGCTTGCACTTCGAGTAGACCATACTCGTGTGGTTGACATAATGCGGAAGgtttttgttt ... tggattccagGCAGGTCACCTTCATCTTGTGAAGCCATATATGGTTGCAGTTCAGAGTAAC
EST: gi|71888995|gb|DT038050.1|DT038050
EST:     TGCTTGCACTTCGAGTAGACCATACTCGTGTGGTTGACATAATGCGGAAG                         GCAGGTCACCTTCATCTTGTGAAGCCATATATGGTTGCAGTTCAGAGTAAC
genomic: TGCTTGCACTTCGAGTAGACCATACTCGTGTGGTTGACATAATGCGGAAGgtttttgttt ... tggattccagGCAGGTCACCTTCATCTTGTGAAGCCATATATGGTTGCAGTTCAGAGTAAC
EST: gi|33402568|gb|CF208195.1|CF208195
EST:     TGCTTGCACTTCGAGTAGACCATACTCGTGTGGTTGACATAATGCGGAAG                         GCAGGTCACCTTCATCTTGTGAAGCCATATATGGTTGCAGTTCAGAGTAAC
genomic: TGCTTGCACTTCGAGTAGACCATACTCGTGTGGTTGACATAATGCGGAAGgtttttgttt ... tggattccagGCAGGTCACCTTCATCTTGTGAAGCCATATATGGTTGCAGTTCAGAGTAAC
EST: gi|30132054|gb|CB917393.1|CB917393
EST:     TGCTTGCACTTCGAGTAGACCATACTCGTGTGGTTGACATAATGCGGAAG                         GCAGGTCACCTTCATCTTGTGAAGCCATATATGGTTGCAGTTCAGAGCAAC
genomic: TGCTTGCACTTCGAGTAGACCATACTCGTGTGGTTGACATAATGCGGAAGgtttttgttt ... tggattccagGCAGGTCACCTTCATCTTGTGAAGCCATATATGGTTGCAGTTCAGAGTAAC
EST: gi|30132996|gb|CB918335.1|CB918335
EST:     TGCTTGCACTTCGAGTAGACCATACTCGTGTGGTTGACATAATGCGGAAG                         GCAGGTCACCTTCATCTTGTGAAGCCATATATGGTTGCAGTTCAGAGCAAC
genomic: TGCTTGCACTTCGAGTAGACCATACTCGTGTGGTTGACATAATGCGGAAGgtttttgttt ... tggattccagGCAGGTCACCTTCATCTTGTGAAGCCATATATGGTTGCAGTTCAGAGTAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actcttctagacgtttatgtactcttttggttatgcgttttttgttggattccagGCAGGTCACCTTCATCTTGTGAAGCCATATATGGTTGCAGTTCAGAGTAACAATGTTTCTGCTGTGAATGAGGCTTTGAATGGGATTTATGTTGAGGAGG
 ccttgac  putative branch site (score: 4)
                                     ttttttgtt  putative PPT
                                     ttttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttttgtttgtgctggcttttttgtttcctttcttcttcttctgaagtatgttacttgtttccttgactcttctagacgtttatgtactcttttggttatgcgttttttgttggattccagGCAGGTCACCTTCATCTTGTGAAGCCATATATGGTTGCAGTTCAGAGTAACAATGTTTCTGCTGTGAATGAGGCTTTGAATGGGATTTATGTTGAGGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG