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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggaagaagttgaatgcattacctgactacatgtttgctgattttagtcacctaggaccaggatcccaattaaatttgactggttaaatactgtgcttcagGTGACTCATGTAGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAGAAAGAAGGGGTGCCAGAAGGACTTTACATGTGAAAACACTGCTACATAT

Basic information

species Vitis vinifera
transcript Vv07s0005g05160.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os07g49150.1 (Oryza sativa), 3'ss of exon 4
ggaagaagttgaatgcattacctgactacatgtttgctgattttagtcacctaggaccaggatcccaattaaatttgactggttaaatactgtgctt---cagGTGACTCATGTAGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAGAAAGAAGGGGTGCCAGAAGGACTTTACATGTGAAAACACTGCTACATAT
     |   ||    |  |   ||| ||  |  | |  ||    | |  | | |  |     |||  |||      |    ||    |  | || ||   |||||||| ||||  ||||||||||||||||||||||||||||||||||||||||| ||||| ||||| || || ||||||||||||        ||      
--tttataatgtgctcgctcattgattatgt-ctggaagaaacaatttgcatggtcctcacttccacattcttaccgtggtgtgctgttttatgatttcacagGTGACACATGCTGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAGAAGGAAGGTGTGCCGGAGGGTCTTTACATGTGATGTGCTCACTGGTCGC

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 3'ss of exon 5
---------------------------------------------------------------------ggaagaagt-tgaatgcatt---acctgactacatgtt-tgct--gattttagtcacctaggaccaggatcccaattaaatttgactggttaaa--tactg---------tgcttcagGTGACTCATGTAGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAGAAAGAAGGGGTGCCAGAAGGACTTTACATGTGAAAACACTGCTACATAT
                                                                       |  ||||   ||| | ||   | |||| |    | |  |||  ||   || |  | | | |      ||    ||  | ||  ||  ||| |  | |||         ||||| ||||||| ||||  || ||||||||||| || |||||||| |||||||||||||| ||||| || || ||||| ||||| |||||| |   |  | ||  ||
gtaactcagctttgttttctcaaccagactccttgctctctagtactgttaatgttaaaactttcgagcatactaagtgccaatcctttcagatctgagtttgagctgcgctcagaacatatttgcatggaatgcaagtctttgttgcacttctctttttacatttgctgttcttctgttgctttagGTGACACATGCCGATTTCAAGAAGGCCAAAGAGAAGGTCATGTTCAAGAAGAAGGAAGGTGTACCGGAAGGGCTTTATATGTGAGACATCCACCACTCAT

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G095593_T02 (Zea mays), 3'ss of exon 1
ggaagaagttgaatgcattacctgactacatgtttgctgattttagtcacctaggaccaggatcccaattaaatttgactggttaaatactgtgcttcagGTGACTCATGTAGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAGAAAGAAGGGGTGCCAGAAGGACTTTACATGTGAAAACACTGCTACATAT------------------------------------
                                | |     ||  |      ||||  | |        | |  |||   |  ||   |||       |||||||| |||| ||| |||||||||||||||||||||||||||| ||||||||| ||||| || || || || || |||||||    |  ||  |    ||                                    
-------------------------------atatagcacttcgatctgattaggttctgagatttgctgatgtttttgtt-ttgggtaca----cccaggtgacccatgcagatttcaagaaggcaaaggagaagGTGATGTACAAGAAGAAGGAAGGTGTTCCGGATGGTCTCTACATGTAGCCAATCTATTCATCATGCCGAACAAGTTACCCGATTGTGTGTGTACTAGCAC

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G095593_T01 (Zea mays), 3'ss of exon 4
ggaagaagttgaatgcattacctgacta-catgtttgct--gattttagtcacctag----gaccaggatcccaattaaatttgactggttaaatactgtgc-ttcagGTGACTCATGTAGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAGAAAGAAGGGGTGCCAGAAGGACTTTACATGTGAAAACACTGCTACATAT
             |||||  | | |||  | ||| | ||  || | ||| ||| | |    ||  ||| ||  |  |    |    |  ||   |   || |   |||||||| |||| ||| |||||||||||||||||||||||||||| ||||||||| ||||| || || || || || |||||||    |  ||  |    ||
-------tccatttgcatagcataactgtcttgtctacttggaatatag-cacttcgatctgattaggttctgagatttgctgatgtttttgttttgggtacacccagGTGACCCATGCAGATTTCAAGAAGGCAAAGGAGAAGGTGATGTACAAGAAGAAGGAAGGTGTTCCGGATGGTCTCTACATGTAGCCAATCTATTCATCAT

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G056569_T01 (Zea mays), 3'ss of exon 4
ggaagaagttgaatgcattacctgactacatgtttgctgattttagtcacctaggacc--aggatcccaattaaatttg--actggttaaatactgtgcttcagGTGACTCATGTAGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAGAAAGAAGGGGTGCCAGAAGGACTTTACATGTGA-AAACA-CTGCTACATAT
         ||  || ||||||  | |     ||  ||   | |   ||  ||| ||   | | | ||| || |  |||    || ||   |   |     |||||||| |||| ||| |||||||| ||||||||||||||||||| ||||||||| ||||| || || || || || |||||||   | ||  || || | |  
---ttttagtgtgtgtattacccaatt-tgctttaactatgtctgagcatatagtactttatggttccatttgacattgctgatgttttgttttggatacccagGTGACCCATGCAGATTTCAAGAAAGCAAAGGAGAAGGTGATGTACAAGAAGAAGGAAGGTGTTCCGGATGGTCTCTACATGTAGTAGACGTCTCCTGCCT--

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 5
---ggaagaagttgaatgcattacctgactacatgtttgctgattttagtcacctaggaccaggatcccaattaaatttgactggttaaatactgt-gcttcagGTGACTCATGTAGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAGAAAGAAGGGGTGCCAGAAGGACTTTACATGTGAAAAC--ACTGCTACATAT
         |||| |   | ||   | |   | ||     ||| |  |    |  || |        |  || || |   | |  |||  | |||| || | |||| || |||| ||||||||||||||| || || ||||| |||||||||||||||||||| ||||| || || || || |||||| |     | ||  |    
attcaccagagttaa---ccttttgtaatagcctgcaacttgaatacaaggtcacagaaaatatccactcatgaactgctattt-ttattttctgttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAGAAAGAAGGCGTGCCGGAGGGCCTATATATGTGAGACTCATCAGCAGCGC--

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA19G35510.1 (Glycine max), 3'ss of exon 5
ggaagaagttgaatgcattacctgactacatgtttgctgattttagtcacctaggaccaggatcccaattaaa--tttgactggttaaatactgtgcttcagGTGACTCATGTAGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAGAAAGAAGGGGTGCCAGAAGGACTTTACATGTGAAAACACTGCTACATAT
  |   |    | |   ||  ||  ||   | |     | | |  |||   |      |   ||   |  |||  |||   |  | ||||  ||  ||||||||||| ||||  |||||||||||||||||||| ||||| ||||| ||||||||||||||||||||||||||||| || |||||||    || |  ||| |
-aagtgatcctattttgttttctacctttttttggaggggtgtgtgtcttttcct-ttactctcatgaccaaatgttttttttttaaaatcttgctcttcagGTGACGCATGCCGACTTCAAGAAGGCAAAGGATAAGGTTATGTTTAAGAAGAAAGAAGGGGTGCCAGAAGGACTGTATATGTGAAGCATCTTCATCATTT

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA13G19280.1 (Glycine max), 3'ss of exon 5
ggaagaagttgaatgcattacctgactacatgtttgctgattttagtcacctaggaccaggatcccaattaaatttgactggtta--aatactgtgct--tcagGTGACTCATGTAGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAGAAAGAAGGGGTGCCAGAAGGACTTTACATGTGAAAACACTGCTACATAT-
     | ||| |     |     |  |  ||  ||  | || | | |                ||||||| |   |  ||  |||  | |||| |  |  ||||||||||||||  ||||| |||||||| ||||| || |||||||| |||||||||||||||||||| ||||| || || ||||||||| |||      ||| 
---taatgtttatcttctctttggcttgtattgtttataatataatttgaa-gtttttttctccccaatttatgatatcttcttactattactattttggtcagGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAGAAAGAAGGGGTGCCTGAAGGGCTGTATATGTGAAAA-ACTATCCTCTATT

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA10G04920.1 (Glycine max), 3'ss of exon 5
ggaagaagttgaatgcattacctg-actacatgtttgctgatttta-gtcacctaggaccaggatcccaattaaatttgactggttaaatactgtgcttcagGTGACTCATGTAGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAGAAAGAAGGGGTGCCAGAAGGACTTTACATGTGAAAACACTGCTACATAT-
 |   ||  || ||   |    || | |  || |    | |||| | ||    |    ||   ||    || | || |   |  |   |   | |  |||||||||||||||  ||||| |||||||| ||||| || |||||||| |||||||||||||||||||| ||||| || || ||||||||  |||      ||| 
tgtttaatgtgtatctttggtttgtattgtatataatataatttgaagttttttttctccccaattt--atgatatcttcttactattacttttttgttcagGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAGAAAGAAGGGGTGCCTGAAGGGCTGTATATGTGAAA-TACTATCCTCTATC

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 5
ggaagaagttgaatgcattacctgacta--catgtttgctgattttagtcacctaggaccaggatcccaattaaatttgactggttaaatactgtgcttcagGTGACTCATGTAGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAGAAAGAAGGGGTGCCAGAAGGACTTTACATGTGAAAACACTGCTACATAT
     |  || |||    |   |   |     |||||      |||  | |     |   |   ||   |  ||||     |  ||  ||  ||  ||||||||||| ||||  ||||| |||||||||||||| || || ||||| |||||||||||||| ||||| |||||||| || |||||||    || |  ||  |
--tttatattcaattttctctgtattttattttgttttgcaccttttttgagtggtgtgtaccctcgtgaccaaatgcttttttttttatcttgctcttcagGTGACGCATGCCGACTTTAAGAAGGCAAAGGATAAAGTTATGTTTAAGAAGAAAGAAGGAGTGCCCGAAGGACTGTATATGTGAAGCATCTTCATCAATT

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 5
ggaagaagttgaatgcattacctgactacatg-tttgctgattttagtcacctaggaccaggatcccaattaaatttgactggttaaatactgtgcttcagGTGACTCATGTAGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAGAAAGAAGGGGTGCCAGAAGGACTTTACATGTGAAAACACTGCTACATAT
 | |    ||   ||  ||  || || || || ||    ||    | ||    |  |     |    ||     ||||  ||||    || ||   || ||||||| ||||| |||||||||||||| ||||||||||| |||||||||||||||||||| || || ||||| |||||||||||||       | ||   |
-gtaaggattctctggctt--ctcaccacttgattcatcgaacgcaatctttgaataattttactttaacc---tttgtttggtcttctattgg--tttagGTGACGCATGTGGACTTCAAGAAGGCGAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGAGTTCCTGAAGGTCTTTACATGTGAATGATGCACAACGACT

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 5
--ggaagaagttgaatgcattacctgactacatgtttgctgattt-tagtcac--ctaggaccaggatc--ccaattaaatttgactggttaaatactgtgc-ttcagGTGACTCATGTAGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAGAAAGAAGGGGTGCCAGAAGGACTTTACATGTGAAAACACTGCTACATAT
   ||     || |     |      |  ||||     |  |     |  |||  || || | |  |    ||| | |   |    || ||||||    |   |||||||||| |||   || |||||||| |||||||||||||| |||||||||||||||||||| || || ||||| || ||||||| |||  |     | ||  
gtagagactcttaaccatttagttcaagcacatacaaacacacacacacacaccacttgggcaattactagccactgacgctaatgtgtttaaattggatttgttcagGTGACACATCCTGATTTCAAGAAAGCAAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGCGTCCCTGAAGGCCTCTACATGTAAAATTATAATCATATCG

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S12_207V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------------------------ggaagaagttgaatgcattacctgac-tacatgtttgctgattttagtcacctaggaccaggatccc---aattaaatttgactggtt-aaatactgtgctt-cagGTGACTCATGTAGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAGAAAGAAGGGGTGCCAGAAGGACTTTACATGTGAAAACACTGCTACATAT
                                  | | | ||   |||  |  | ||||  |  ||    | || ||||  |||   | |||| || | |    ||| |  | | | || ||   ||  ||  ||| ||||||||||| || || ||||||||||| || |||||||| ||||  |||||||| ||||| || || || ||| | |||||||  |        | ||  |
gtaagattgtcgtcttttgtactttgcagttcgtgaatggaggctaattgaccagctgaaatgaataaaagttgcttttgatcaa--aagacctggtttcttgtaatgagttgttattgttttggatggtgatcttgcagGTGACTCAAGTTGATTTCAAGAAGGCCAAAGAGAAGGTAATGTATAAGAAGAAGGAAGGTGTACCTGAGGGATTATACATGTAGATTATTCAGTGCAGGT

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S4_277V6.1 (Physcomitrella patens), 3'ss of exon 5
---------------------------------------------------ggaagaagttgaatgc-----attacc----tgactacatgtttgctgatttt-agtcacctaggaccaggatcccaattaaat-ttgactggttaaatactgtgcttcagGTGACTCATGTAGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAGAAAGAAGGGGTGCCAGAAGGACTTTACATGTGAAA-ACACTGCTACATAT
                                                   |  ||| |||  |         || ||    || ||  ||  |||| |  ||| | |   || |             | ||| | |||||||   |       |||  ||||||||||| |  |||||||||||||| ||||| || ||||||| ||||||||| ||||| || || || ||  | || ||||  || || | |  |  |  
gtgagcttgccatttctttgtattcttttatatgtatttttaatgcgtctcgtcagaggttacacttttttagttgccctcatggctgtataattgcaggctttgaattggcttgttttgattctgtgactaagtattgactgtggattcttaatgccacagGTGACTCAAGCGGACTTCAAGAAGGCTAAGGACAAAGTGATGTACAAGAAGAAGGAAGGTGTACCCGAGGGGTTATATATGTAGAATACTCAGTCAAGTG-

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ20767 (Selaginella moellendorffii), 3'ss of exon 5
ggaagaagttgaatgcattacctgactacatgtttgctgattttagtcacctaggaccaggatcccaattaaatttgactggttaaatactgtgcttcagGTGACTCATGTAGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAGAAAGAAGGGGTGCCAGAAGGACTTTACATGTGAAAACACTGCTACATAT-
                                           ||||  |      |     || ||| |   ||  |  | ||   |  | | || ||||| ||||| |  || ||||||||||| || |||||||| |||| ||||||||||||||| || || || || || ||||||| || |  | |   ||  | 
------------------------------------------gtagtttctcgatgcttt--tcacaactttcttgtaacgattt--tcttcttctccagGTAACTCAAGCTGATTTCAAGAAGGCGAAAGAGAAGGTCATGTACAAGAAGAAAGAAGGCGTCCCGGAGGGCCTGTACATGTAAATA-GCCGTCCCAGCTT

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ32659 (Selaginella moellendorffii), 3'ss of exon 5
ggaagaagttgaatgcattacctgactacatgtttgctgattttagtcacctaggaccaggatcccaattaaatttgactggttaaatactgtgcttcagGTGACTCATGTAGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAGAAAGAAGGGGTGCCAGAAGGACTTTACATGTGAAAACACTGCTACATAT-
                                           ||||  |  |   |     || ||| |   ||  |  | ||   |  | | || ||||| ||||| |  || ||||||||||| || |||||||| |||| ||||||||||||||| || || || || || ||||||| || |  |     ||  | 
------------------------------------------gtagtttctcaatgcttt--tcacaactttcttgtaacgattt--tcttcttctccagGTAACTCAAGCTGATTTCAAGAAGGCGAAAGAGAAGGTCATGTACAAGAAGAAAGAAGGCGTCCCGGAGGGCCTGTACATGTAAATA-GCCATCCCAGCTT

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|229418620|gb|GO652857.1|GO652857
EST:     CAATATGCACTGAAGCTGGTTTGCTTGCTTTAAGAGAACGGCGTATGAAG                         GTGACTCATGTAGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAG
genomic: CAATATGCACTGAAGCTGGTTTGCTTGCTTTAAGAGAACGGCGTATGAAGgtgaggcttg ... tgtgcttcagGTGACTCATGTAGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAG
EST: gi|110703456|gb|EE080320.1|EE080320
EST:     CAATATGCACTGAAGCTGGTTTGCTTGCTTTAAGAGAACGGCGTATGAAG                         GTGACACATGTAGACTTCAAGAAAGCAAAGGAGAAAGTGATGTTCAAGAAG
genomic: CAATATGCACTGAAGCTGGTTTGCTTGCTTTAAGAGAACGGCGTATGAAGgtgaggcttg ... tgtgcttcagGTGACTCATGTAGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAG
EST: gi|110392599|gb|EC958132.1|EC958132
EST:     CAATATGCACTGAAGCTGGTTTGCTTGCTTTAAGAGAACGGCGTATGAAG                         GTGACTCATGTAGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAG
genomic: CAATATGCACTGAAGCTGGTTTGCTTGCTTTAAGAGAACGGCGTATGAAGgtgaggcttg ... tgtgcttcagGTGACTCATGTAGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAG
EST: gi|71881961|gb|DT031016.1|DT031016
EST:     CAATATGCACTGAAGCTGGTTTGCTTGCTTTAAGAGAACGGCGTATGAAG                         GTGACTCATGTAGACTTCAAGAA
genomic: CAATATGCACTGAAGCTGGTTTGCTTGCTTTAAGAGAACGGCGTATGAAGgtgaggcttg ... tgtgcttcagGTGACTCATGTAGACTTCAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcacctaggaccaggatcccaattaaatttgactggttaaatactgtgcttcagGTGACTCATGTAGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAGAAAGAAGGGGTGCCAGAAGGACTTTACATGTGAAAACACTGCTACATAT
                           atttgac  putative branch site (score: 4)
                     aattaaatttgact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggaagaagttgaatgcattacctgactacatgtttgctgattttagtcacctaggaccaggatcccaattaaatttgactggttaaatactgtgcttcagGTGACTCATGTAGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAGAAAGAAGGGGTGCCAGAAGGACTTTACATGTGAAAACACTGCTACATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
ggaagaa
- - - - - gaatgca
- - - - - - - - - - - - -ctacatg
- - - - - - - - - - - - - - - - - tgctgat
- - - - - - - - - - - - - - - - - - - - - - agtcacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aattaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgactgg