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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttaaatttcctttgttcatgttttagaattccttcatatttctagtatgaaaggttattaataatcctactatcactggctaaggtctcaaatccttgctgcagATTGATAATCTTGTGAAGGGAGCTTCTGGTCAAGCCTTGCAGAATCTTAATGTGATGATGGGATTGCCGGAGAATACAGGACTTCTCTACCAGCCATTGT

Basic information

species Vitis vinifera
transcript Vv03s0063g01110.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0063g01110.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os03g42110.1 (Oryza sativa), 3'ss of exon 13
gtatgtttaaatttcctttgtt--catgttttagaattccttcatatttctagtatgaaaggttattaata-atcctactatcactggctaaggtctcaaatccttgctgcagATTGATAATCTTGTGAAGGGAGCTTCTGGTCAAGCCTTGCAGAATCTTAATGTGATGATGGGATTGCCGGAGAATACAGGACTTCTCTACCAGCCATTGT
       ||| | || ||  |   |||||||   ||    ||   | | ||| | | | ||  |    ||  ||  | ||||  || | |      ||||        ||||||| |||||||||||||||||||| || ||||| ||  | ||||| |||||| ||||||||||  |||| ||||| || || || |  || || ||  | |
------gtaagtgtctttcatctacatgtttctcaagcatttagcaat-ctaatgtcatagacttcagatgcataatcctatttcttgtt-----ttcaa-----caatgcagATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAATCTGATGATGGGTCTGCCAGAGAACACTGGGCTGCAATATCAACCCCTAT

upper sequence: Vv03s0063g01110.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os10g35170.1 (Oryza sativa), 3'ss of exon 13
gtatgt---ttaaatttcctttgttcatgttttagaattccttcatatttctagtatgaaaggttattaataatcctactatcactggctaaggtctcaaatccttgctgcagATTGATAATCTTGTGAAGGGAGCTTCTGGTCAAGCCTTGCAGAATCTTAATGTGATGATGGGATTGCCGGAGAATACAGGACTTCTCTACCAGCCATTGT
|||||    || ||    |||| | |   || |  || |  ||    | |  ||  | |||| |    |||  || || | ||  | | |      |||| |||      ||||| |||||||||||||||||||| |||||||| ||  | ||||| || ||| ||||||||||  |||| ||||| | ||| || |  || |||||  | |
gtatgcgtcttcaaccatctttatgcccattgtcaaactagtt----tcttcagacttaaagatgcgaaat--tcttattttc--ttgtt----cttcaactcc-----acagATAGATAATCTTGTGAAGGGAGCGTCTGGTCAGGCTGTCCAGAACCTCAATCTGATGATGGGCCTGCCTGAGAACAGAGGGCTGCAATATCAGCCCCTAT

upper sequence: Vv03s0063g01110.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G038848_T02 (Zea mays), 3'ss of exon 13
gtatgtttaaatttcctttgttcatgttttagaattccttcatatttctagtatgaaaggttattaataatcctactatcactggctaaggtctcaaatccttgctgcagATTGATAATCTTGTGAAGGGAGCTTCTGGTCAAGCCTTGCAGAATCTTAATGTGATGATGGGATTGCCGGAGAATACAGGACTTCTCTACCAGCCATTGT
       ||| |  | |  ||  |  || |   |       ||   || |  || | |    || | |||       ||         | |       ||     ||||||| |||||||||||||||||||| |||||||| || ||||| ||||||||| ||||||||||| |||| |||||||  || || |  ||||||||  |||
------gtaagtgccttcagtcaactttatcccacataagtatgcatcaaaaataatatcacataattaagatgcacatagaccttacaagctatgtttcaacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAATCTGATGATGGGACTGCCTGAGAATATGGGGCTGCAATACCAGCCCCTGT

upper sequence: Vv03s0063g01110.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G477770_T01 (Zea mays), 3'ss of exon 2
gtatgtttaaatttcctttgttcatgttttagaattccttcatatttctagtatgaaaggttattaataatcctactatcactggctaaggtctcaaatccttgctgcagATTGATAATCTTGTGAAGGGAGCTTCTGGTCAAGCCTTGCAGAATCTTAATGTGATGATGGGATTGCCGGAGAATACAGGACTTCTCTACCAGCCATTGT
       ||| |  | |  ||  |  || |   |       ||   || |  || | |    ||   |||       ||         | |       ||     ||||||| |||||||||||||||||||| |||||||| || ||||| ||||||||| ||||||||||| |||| |||||||  || || |  ||||||||  |||
------gtaagtgccttcagtcaactttatcccacataagtatgcatcaaaaataatatcacatacttaagatgcacatagaccttacaagctatgtttcaacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAATCTGATGATGGGACTGCCTGAGAATATGGGGCTACAATACCAGCCCCTGT

upper sequence: Vv03s0063g01110.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G378931_T01 (Zea mays), 3'ss of exon 2
gtatgtttaaatttcctttgttcatgttttagaattccttcatatttctagtatgaaaggttattaataatcctactatcactggctaaggtctcaaatccttgctgcagATTGATAATCTTGTGAAGGGAGCTTCTGGTCAAGCCTTGCAGAATCTTAATGTGATGATGGGATTGCCGGAGAATACAGGACTTCTCTACCAGCCATTGT
       ||| |  | |  ||  |  || |   |       ||   || |  || | |    ||   |||       ||         | |       ||     ||||||| |||||||||||||||||||| |||||||| || ||||| ||||||||| ||||||||||| |||| |||||||  || || |  ||||||||  |||
------gtaagtgccttcagtcaactttatcccacataagtatgcatcaaaaataatatcacatacttaagatgcacatagaccttacaagctatgtttcaacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAATCTGATGATGGGACTGCCTGAGAATATGGGGCTGCAATACCAGCCCCTGT

upper sequence: Vv03s0063g01110.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G535396_T01 (Zea mays), 3'ss of exon 1
gtatgtttaaatttcctttgttcatgttttagaattccttcatatttctagtatgaaaggttattaataatcctactatcactggctaaggtctcaaatccttgctgcagATTGATAATCTTGTGAAGGGAGCTTCTGGTCAAGCCTTGCAGAATCTTAATGTGATGATGGGATTGCCGGAGAATACAGGACTTCTCTACCAGCCATTGT
       ||| |  | |  ||  |  || |   |       ||   || |  || | |    ||   |||       ||         | |       ||     ||||||| ||||||||||| |||||||| |||| ||| || ||||| ||||||||| ||||||||||| |||| |||||||  || || |  ||||||||  |||
------gtaagtgccttcagtcaactttatcccacataagtatgcatcaaaaataatatcacatacttaagatgcacatagaccttacaagctatgtttcaacattgcagATAGATAATCTTGTCAAGGGAGCATCTGATCAGGCTTTGCAAAATCTTAATCTGATGATGGGACTGCCTGAGAATATGGGGCTGCAATACCAGCCCCTGT

upper sequence: Vv03s0063g01110.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA07G29630.1 (Glycine max), 3'ss of exon 13
gtatgtttaaatttcctttgttcatgttttagaattccttcatatttctagtatgaaaggttattaataatcctactatcactggctaaggtctcaaatccttgctgcagATTGATAATCTTGTGAAGGGAGCTTCTGGTCAAGCCTTGCAGAATCTTAATGTGATGATGGGATTGCCGGAGAATACAGGACTTCTCTACCAGCCATTGT
||||||| |  |||  |||  || | | |    || |      | || | ||||  || | ||||| | || ||| | |      | |   | |  |    ||| |||||||||||||||| |||||||||||||| |||||||| || || || |||||| || | |||||||| || || |||   |||||||  |||| |||  | |
gtatgttaagtttttttttcctcctatat----atccagctgaaattgt-gtatttaatgatatta-tgatactattgttgacatc-actatgttgatgtgttgttgcagATTGATAATCTAGTGAAGGGAGCTTCAGGTCAAGCTTTACAAAACCTTAATTTGTTAATGGGATTTCCAGAAAATTTGGGACTTCATTACCTGCCTCTTT

upper sequence: Vv03s0063g01110.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA20G01220.1 (Glycine max), 3'ss of exon 12
gtatgtttaaatttcctttgttc-atgttttagaattccttcatatttctagtatgaaaggttattaataatcctactatcactggctaag-gtctcaaatccttgctgcagATTGATAATCTTGTGAAGGGAGCTTCTGGTCAAGCCTTGCAGAATCTTAATGTGATGATGGGATTGCCGGAGAATACAGGACTTCTCTACCAGCCATTGT
|||||||| |||||  ||| | | || | |     |    |  | | | ||  |||| |   |  || || |  |   || |||  |||||  | |  |    ||| |||||||||||||| | |||||||||||||| |||||||| || || || |||||| || | |||||||| || || |||   |||||||  |||| |||  | |
gtatgttttaattttttttctcctatatatccagctgaaattgtgtattta--atgatattatgatattattgttgacatgact--ctaagtatgttgatgtgttgttgcagATTGATAATTTAGTGAAGGGAGCTTCAGGTCAAGCTTTACAAAACCTTAATTTGTTAATGGGATTTCCAGAAAATTTGGGACTTCATTACCTGCCTCTTT

upper sequence: Vv03s0063g01110.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT2G19940.2 (Arabidopsis thaliana), 3'ss of exon 12
gtatgtttaaatttcctttgttcatgttttagaattccttcatatttctagtatgaaaggttattaataatcctactatcactggctaaggtctcaaatccttgctgcagATTGATAATCTTGTGAAGGGAGCTTCTGGTCAAGCCTTGCAGAATCTTAATGTGATGATGGGATTGCCGGAGAATACAGGACTTCTCTACCAGCCATTGT
         ||||     |   |||  | |   ||    |||| |||            | | |  | |||  | || |   |    || |           || |||||||||||||||||||||| |||||||| || ||||| ||||||||||||||  | ||| ||||||  || || |  || || || ||  |||||||  | |
-------gtaattaagcataaccatcctctgttataaactcatcttt-----------agctttcgacaatattgctttgtgtataaaaagctct---ctggtgttgcagATTGATAATCTTGTGAAAGGAGCTTCGGGACAAGCGTTGCAGAATCTTAACATAATGTTGGGATATCCCGAAACAACGGGGCTCCTACACCAGCCGCTTT

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|83276518|gb|DV940526.1|DV940526
EST:     TGAATGTCTTTCCTGATCGAATCCCTGGACGAGCAATTATAGTATCTGTT                         ATTGATAATCTTGTGAAGGGAGCTTCTGGTCAAGCCTTGCAGAATCTTAAT
genomic: TGAATGTCTTTCCTGATCGAATCCCTGGACGAGCAATTATAGTATCTGTTgtatgtttaa ... cttgctgcagATTGATAATCTTGTGAAGGGAGCTTCTGGTCAAGCCTTGCAGAATCTTAAT
EST: gi|110390116|gb|EC955007.1|EC955007
EST:     TGAATGTCTTTCCTGATCGAATCCCTGGACGAGCAATTATAGTATCTGTT                         ATTGATAATCTTGTGAAGGGAGCTTCTGGTCAAGCCTTGCAGAATCTTAAT
genomic: TGAATGTCTTTCCTGATCGAATCCCTGGACGAGCAATTATAGTATCTGTTgtatgtttaa ... cttgctgcagATTGATAATCTTGTGAAGGGAGCTTCTGGTCAAGCCTTGCAGAATCTTAAT
EST: gi|30330207|gb|CD013469.1|CD013469
EST:     TGAATGTCTTTCCTGATCGAATCCCTGGACGAGCAATTATAGTATCTGTT                         ATTGATAATCTTGTGAAGGGAGCTTCTGGTCAAGCCTTGCAGAATCTTAAT
genomic: TGAATGTCTTTCCTGATCGAATCCCTGGACGAGCAATTATAGTATCTGTTgtatgtttaa ... cttgctgcagATTGATAATCTTGTGAAGGGAGCTTCTGGTCAAGCCTTGCAGAATCTTAAT
EST: gi|30134557|gb|CB919895.1|CB919895
EST:     TGAATGTCTTTCCTGATCGAATCCCTGGACGAGCAATTATAGTATCTGTT                         ATTGATAATCTTGTGAAGGGAGCTTCTGGTCAAGCCTTGCAGAATCTTAAT
genomic: TGAATGTCTTTCCTGATCGAATCCCTGGACGAGCAATTATAGTATCTGTTgtatgtttaa ... cttgctgcagATTGATAATCTTGTGAAGGGAGCTTCTGGTCAAGCCTTGCAGAATCTTAAT
EST: gi|87584416|gb|DY473601.1|DY473601
EST:     TGAATGTCTTTCCTGATCGAATCCCTGGACGAGCAATTATAGTATCTGTT                         ATTGATAATCTTGTGAAGGGAGCTTCTGGTCAAGCCTTGCAGAATCTTAAT
genomic: TGAATGTCTTTCCTGATCGAATCCCTGGACGAGCAATTATAGTATCTGTTgtatgtttaa ... cttgctgcagATTGATAATCTTGTGAAGGGAGCTTCTGGTCAAGCCTTGCAGAATCTTAAT
EST: gi|30329402|gb|CD012664.1|CD012664
EST:     TGAATGTCTTTCCTGATCGAATCCCTGGACGAGCAATTATAGTATCTGTT                         ATTGATAATCTTGTGAAGGGAGCTTCTGGTCAAGCCTTGCAGAATCTTAAT
genomic: TGAATGTCTTTCCTGATCGAATCCCTGGACGAGCAATTATAGTATCTGTTgtatgtttaa ... cttgctgcagATTGATAATCTTGTGAAGGGAGCTTCTGGTCAAGCCTTGCAGAATCTTAAT
EST: gi|30320747|gb|CD004009.1|CD004009
EST:     TGAATGTCTTTCCTGATCGAATCCCTGGACGAGCAATTATAGTATCTGTT                         ATTGATAATCTTGTGAAGGGAGCTTCTGGTCAAGCCTTGCAGAATCTTAAT
genomic: TGAATGTCTTTCCTGATCGAATCCCTGGACGAGCAATTATAGTATCTGTTgtatgtttaa ... cttgctgcagATTGATAATCTTGTGAAGGGAGCTTCTGGTCAAGCCTTGCAGAATCTTAAT
EST: gi|27583381|gb|CB006076.1|CB006076
EST:     TGAATGTCTTTCCTGATCGAATCCCTGGACGAGCAATTATAGTATCTGTT                         ATTGATAATCTTGTGAAGGGAGCTTCTGGTCAAGCCTTGCAGAATCTTAAT
genomic: TGAATGTCTTTCCTGATCGAATCCCTGGACGAGCAATTATAGTATCTGTTgtatgtttaa ... cttgctgcagATTGATAATCTTGTGAAGGGAGCTTCTGGTCAAGCCTTGCAGAATCTTAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaggttattaataatcctactatcactggctaaggtctcaaatccttgctgcagATTGATAATCTTGTGAAGGGAGCTTCTGGTCAAGCCTTGCAGAATCTTAATGTGATGATGGGATTGCCGGAGAATACAGGACTTCTCTACCAGCCATTGT
      tattaat  putative branch site (score: 2)
                                           tccttgct  putative PPT
     ttattaataatccta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttaaatttcctttgttcatgttttagaattccttcatatttctagtatgaaaggttattaataatcctactatcactggctaaggtctcaaatccttgctgcagATTGATAATCTTGTGAAGGGAGCTTCTGGTCAAGCCTTGCAGAATCTTAATGTGATGATGGGATTGCCGGAGAATACAGGACTTCTCTACCAGCCATTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA