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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agggagtgattcttaaaggcaatttttgtcttccctaattaaaaatttgagctattacccataaatgtactgggcctaaacttatttctctctgtgacagTGACATGGAATGTTACATGCACGTATTCACAATTCCTGTCTCAGAAAACCCCCACTTGCTGTGTCTCGCTCTCATCTTTCTACAATGACACAATTGTACC

Basic information

species Vitis vinifera
transcript Vv14s0083g01160.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0083g01160.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os03g54750.1 (Oryza sativa), 3'ss of exon 3
agggagtgattcttaaaggcaatttttgtcttccctaattaaaaatttgagctattacccataaatgt------actgggcctaaacttatttctctctg-tgacagTGACATGGAATGTTACATGCACGTATTCACAATTCCTGTCTCAGAAAACCCCCACTTGCTGTGTCTCGCTCTCATCTTTCTACAATGACACAATTGTACC
       |  || | | |||  | |  |   |   ||| | |   ||| ||   |   ||| |||| |      | ||   || |||    |   ||||  |  |||||||||||||||| || ||||| || |||||||| ||  ||||||| || || || || ||||| || ||||| || || |||||||||||||||||   
----taagcatcgtgatggcgttatgagaagt---taaattatgttttaagtcttataccagaaatttctctttattgattcttaacaagataaactctacttgcagTGACATGGAATGTGACCTGCACATACTCACAATTTCTTGCTCAGAAGACTCCAACCTGTTGTGTATCTCTCTCGTCATTTTACAATGACACAATTGTGAA

upper sequence: Vv14s0083g01160.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 1
-agggagtgattcttaaaggcaatttttgtcttccctaattaaaaatttgagct--attacccataaatgtactgggcctaaacttatttctctctgtgacagTGACATGGAATGTTACATGCACGTATTCACAATTCCTGTCTCAGAAAACCCCCACTTGCTGTGTCTCGCTCTCATCTTTCTACAATGACACAATTGTACC
     ||||  ||   |  | | ||    |  ||   |  | | |   | |  |  |||     |   |||       | ||| | |  ||| | ||   |||||||||||||||| || ||||| || || ||||| ||  ||||||| || ||  | |||||||| || |||||||| || || ||||||||||||||   
atcatagtggctccatatagaagttaaatttgtcaaaatcttataccataaagttcatttttgttttttgtttcttaacaaaaataaaatctgtttg---cagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA

upper sequence: Vv14s0083g01160.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G071970_T01 (Zea mays), 3'ss of exon 3
----agggagtgattcttaaaggcaatttttgtcttccctaattaaaaatttgagctattacccataaatgtactgggcctaaacttatttctctctgtgacagTGACATGGAATGTTACATGCACGTATTCACAATTCCTGTCTCAGAAAACCCCCACTTGCTGTGTCTCGCTCTCATCTTTCTACAATGACACAATTGTACC
    |   |  |||  |   ||| || |||          || |   | |||   ||||     |||    |   ||  || |||  |  |   |      |||||||||||||||| || ||||| ||||| ||||| ||  ||||||| || ||  | |||||||| || |||||||| || || ||||||||||||||   
ttctaatcacagatagtcttaggaaaatttc----catacaagttgcagtttcgtctatattttatagcactgagggttcttaacagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA

upper sequence: Vv14s0083g01160.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G009154_T01 (Zea mays), 3'ss of exon 2
----agggagtgattcttaaaggcaatttttgtcttccctaattaaaaatttgagctattacccataaatgtactgggcctaaacttatttctctctgtgacagTGACATGGAATGTTACATGCACGTATTCACAATTCCTGTCTCAGAAAACCCCCACTTGCTGTGTCTCGCTCTCATCTTTCTACAATGACACAATTGTACC
    |   |  |||  |   ||| || |||   |    | | ||  |  ||||  ||||     |||    |    |  || | |  |  |   |      |||||||||||||||| || ||||| ||||| ||||| ||  ||||||| || |   | |||||||| || |||||||| || || ||||||||||||||   
ttctaatcacagatagtcttaggaaaattt---ccatacaagttgcagttttgt-ctatattttatagcattgagagttcttatcagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCTGTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA

upper sequence: Vv14s0083g01160.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM5G826714_T01 (Zea mays), 3'ss of exon 3
----agggagtgattcttaaaggcaatttttgtcttccctaattaaaaatttgagctattacccataaatgtactgggcctaaacttatttctctctgtgacagTGACATGGAATGTTACATGCACGTATTCACAATTCCTGTCTCAGAAAACCCCCACTTGCTGTGTCTCGCTCTCATCTTTCTACAATGACACAATTGTACC
      | ||  | || ||     ||||     |       | |      | ||  |  || |    |  || ||   |  | || | | | | ||||   |||||||||||||||| || ||||| ||||| ||||| ||  ||||||| || ||  | |||||||| || || ||||| || || ||||||||||||||   
ctaatcgcagatagtcctaggaagaattccatacaagttgcacttttgtctagattttatagcagagagggttcttaacagagacat-tctttatctg---cagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTATCATCGTTTTATAATGACACAATTGTGAA

upper sequence: Vv14s0083g01160.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G167520_T02 (Zea mays), 3'ss of exon 4
agggagtgattcttaaaggcaatttttgtcttccctaattaaaaatttgagctattacccataaatgtactgggcctaaacttatttc-tctctgtg-acagTGACATGGAATGTTACATGCACGTATTCACAATTCCTGTCTCAGAAAACCCCCACTTGCTGTGTCTCGCTCTCATCTTTCTACAATGACACAATTGTACC
                          |   |    | |||||    |  |||  |  |  ||  ||| | ||    |  |||| |||  | |||  |  ||||||| ||||| || || |||||||| || || |||||  | |||| | | || || ||||||||||||||||| || |||||||| ||||| |||||   
-------------------------gtacgtaagatgattaac--ctcaagcc-taccaaattcatgcattgacgatcgacttgtttaatttcttcgcgcagTGACCTGGAACGTGACGTGCACGTACTCCCAGTTCCTTGCCCAGAGATCTCCAACCTGCTGTGTCTCGCTCTCGTCGTTCTACAACGACACCATTGTTAG

upper sequence: Vv14s0083g01160.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA02G35400.1 (Glycine max), 3'ss of exon 3
-agggagtgattcttaaaggcaatttttgtcttccctaattaaaaatttgagctattacccataaatgta--ctgggcctaaacttatttctctctgtgacagTGACATGGAATGTTACATGCACGTATTCACAATTCCTGTCTCAGAAAACCCCCACTTGCTGTGTCTCGCTCTCATCTTTCTACAATGACACAATTGTACC
      | |||    | |  || || || |      | | |    | | |    |  | |||| ||  ||   ||  | |||  ||  |    | | |  |||||||||||||||| |||||||| ||||||||||| ||  |||||| ||| |||| |||||||||||||||||||||||||||  |  | ||| |||||||
ccatatgggatctaaataaacagttgttctgagtttttacttcctactag---caaaatccatcaacttagtttgaccttaacattgctctgatttattgcagTGACATGGAATGTGACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGTGTCTCGCTCTCATCTTTCTATGACAATACAGTTGTACC

upper sequence: Vv14s0083g01160.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA13G06660.1 (Glycine max), 3'ss of exon 3
-agggagtgattcttaaaggcaatttttgtcttccctaattaaaaatttgagctattacccataaatgta--ctgggcctaaacttatttctctctgtgacagTGACATGGAATGTTACATGCACGTATTCACAATTCCTGTCTCAGAAAACCCCCACTTGCTGTGTCTCGCTCTCATCTTTCTACAATGACACAATTGTACC
      | |||    | |  || || || |      | | |    | | |    |  | |||| ||  ||   ||  | |||  ||  |    | | |  |||||||||||||||| |||||||| ||||||||||| ||  |||||| ||| |||| ||||||||||||||||||||||||||| ||  | ||| |||||||
ccatacgggatctaaataaacagttgttctgagtttttacttcctactag---caaaatccatcaacttagtttgaccttaacattgctctgatttattgcagTGACATGGAATGTGACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGTGTCTCGCTCTCATCTTTCTATAACAATACAGTTGTACC

upper sequence: Vv14s0083g01160.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA18G50760.1 (Glycine max), 3'ss of exon 3
agggagtgattcttaaagg--caatttttgtcttccctaattaaaaatttgagctattacccataaa-tgtactgggcctaaacttatttctctctgtgacagTGACATGGAATGTTACATGCACGTATTCACAATTCCTGTCTCAGAAAACCCCCACTTGCTGTGTCTCGCTCTCATCTTTCTACAATGACACAATTGTACC
 | |  | | | | |||      |   ||    |   ||  |  || | | ||||| | |    ||  |||  |   | |||  | | || | | |    |||||||||||||||| |||||||| || |||||||| ||| |||||||||| ||| ||||||||||||| || ||||||||||| ||||| ||  |||| ||
-gtgcttaaatttaaaacaactgaaaattacagttggtacctgtaactatcagctaattctagcaatctgttatatccttaacatcacttgtttttt--gcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAGAAAACTCCCTCTTGCTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC

upper sequence: Vv14s0083g01160.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA17G08830.1 (Glycine max), 3'ss of exon 2
agggagtgattcttaaaggcaatttttgtct---tccctaattaaaaatttgagctattacccat-aaatgtactgggcctaaacttatttctctctgtgacagTGACATGGAATGTTACATGCACGTATTCACAATTCCTGTCTCAGAAAACCCCCACTTGCTGTGTCTCGCTCTCATCTTTCTACAATGACACAATTGTACC
    | | || ||| |   || | ||    |   |   || |   |||     | | |      | | || |  |    || ||  |   | | | | || ||||||| ||||||||||| ||||| ||||| ||||||||| ||||||| ||||| ||||||||||| || |||||||| ||||| ||  | ||| | |||  
---tatttatgctttata-cattgttcagataaattattagtatgaaaaccatgttttagtttttcagatttggtttagcttaatctgcatatatttttggcagTGACCTGGAATGTTACCTGCACATATTCTCAATTCCTGGCTCAGAAGACCCCAACTTGCTGTGTTTCTCTCTCATCCTTCTATAACAATACAGTAGTAAA

upper sequence: Vv14s0083g01160.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA19G04210.1 (Glycine max), 3'ss of exon 3
--agggagtgattcttaaaggcaatttttgtcttccctaattaaaaatttgagctattacccataaatgtactgggcctaaacttatttctctctgtgacagTGACATGGAATGTTACATGCACGTATTCACAATTCCTGTCTCAGAAAACCCCCACTTGCTGTGTCTCGCTCTCATCTTTCTACAATGACACAATTGTACC
  |       |   |  |||  ||   ||||  |   |  |||     |      |  | |||| ||  || |  | |  |  ||  |    | | || |||||||||||||||| |||||||| ||||||||||| ||  |||||| ||| |||| |||||| |||||||| ||||||||||| || || ||  |||||||
ttatccgaaaagggtccaagttaacagttgttctgagtttttagttcctactagcaagatccatcaacttagtttgaccca--ttgctctgatttatggcagTGACATGGAATGTAACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGCGTCTCGCTTTCATCTTTCTATAACGATACTGTTGTACC

upper sequence: Vv14s0083g01160.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G27560.1 (Glycine max), 3'ss of exon 3
agggagtgattcttaa--aggcaatttttgtcttccctaattaaaaatttgagctattacccataaatgtactgggcc--taaacttatttctctctgtgacagTGACATGGAATGTTACATGCACGTATTCACAATTCCTGTCTCAGAAAACCCCCACTTGCTGTGTCTCGCTCTCATCTTTCTACAATGACACAATTGTACC
   |  | | | | ||  |    |  |||    |   || |   || | | ||  | | |    || | ||||    |  |||  | | |  | | | |  |||||||||||||||| |||||||| || |||||||| ||| |||| ||||| ||| |||| |||||||| || ||||||||||| ||||| ||  |||| ||
---gcttaaatttaaaacaattgaagtttacagttggtattagtaactatcagaaaattctggcaatt-tactatatccataacatcactcttgtttattgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAAAAAACTCCCTCTTGTTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC

upper sequence: Vv14s0083g01160.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G00210.1 (Glycine max), 3'ss of exon 5
agggagtgattcttaaaggcaatttttgtcttccctaattaaaaatttgagctattacccataaatgtactgggcctaaacttatttctctctgtgacagTGACATGGAATGTTACATGCACGTATTCACAATTCCTGTCTCAGAAAACCCCCACTTGCTGTGTCTCGCTCTCATCTTTCTACAATGACACAATTGTACC----------------------------------------------
                                      |||  | | |||      |||||    |    |  || ||| ||    | | | | || ||||||| ||||||||||| ||||| ||||| ||||||||| ||||||| ||||| |||||| |||| ||  ||||||| ||||| ||  | ||||| |||                                                
--------------------------------------ttattagtatgaa-----acccaagttttggtttagcttaatct-gcatatatttttggcagtgacctggaatgttacctgcacatattctcaattcctggctcagAAGACCCCAACTTGCCGTGTTTC--TCTCATCCTTCTATAACAATACAATAGTAAACTGCCCTACCTGCACCTGTGGTTGCCAAAACAAAACAGAACCTGGC

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|30128146|gb|CB913485.1|CB913485
EST:     ACCTACTAGATTTGTGACACAAGATGGAAGGAGAGTCACTCAAGCTTTGA                         TGACATGGAATGTTACATGCACATATTCACAATTCCTGTCTCAGAAAACCC
genomic: ACCTACTAGATTTGTGACACAAGATGGAAGGAGAGTCACTCAAGCTTTGAgtaagtttct ... tctgtgacagTGACATGGAATGTTACATGCACGTATTCACAATTCCTGTCTCAGAAAACCC
EST: gi|110371120|gb|EC934895.1|EC934895
EST:     ACCTACTAGATTTGTGACACAAGATGGAAGGAGAGTCACTCAAGCTTTGA                         TGACATGGAATGTTACATGCACATATTCACAATTCCTGTCTCAGAAAACCC
genomic: ACCTACTAGATTTGTGACACAAGATGGAAGGAGAGTCACTCAAGCTTTGAgtaagtttct ... tctgtgacagTGACATGGAATGTTACATGCACGTATTCACAATTCCTGTCTCAGAAAACCC
EST: gi|110699176|gb|EE075944.1|EE075944
EST:     ACCTACTAGATTTGTGACACAAGATGGAAGGAGAGTCACTCAAGCTTTGA                         TGACATGGGATGTTACATGCACATATTCACAATTCCTGTCTCAGA
genomic: ACCTACTAGATTTGTGACACAAGATGGAAGGAGAGTCACTCAAGCTTTGAgtaagtttct ... tctgtgacagTGACATGGAATGTTACATGCACGTATTCACAATTCCTGTCTCAGA
EST: gi|30137657|gb|CB922995.1|CB922995
EST:     ACCTACTAGATTTGTGACACAAGATGGAAGGAGAGTCACTCAAGCTTTGA                         TGACATGGAATGTTACATGCACATATTCACAATTCCTGTCTCAGAAAACCC
genomic: ACCTACTAGATTTGTGACACAAGATGGAAGGAGAGTCACTCAAGCTTTGAgtaagtttct ... tctgtgacagTGACATGGAATGTTACATGCACGTATTCACAATTCCTGTCTCAGAAAACCC
EST: gi|110724325|gb|EE100052.1|EE100052
EST:     ACCTACTAGATTTGTGACACAAGATGGAAGGAGAGTCACTCAAGCTTTGA                         TGACATGGAATGTTACATGCACATATTCACAATTCCTGTCTCNNNNNNNCC
genomic: ACCTACTAGATTTGTGACACAAGATGGAAGGAGAGTCACTCAAGCTTTGAgtaagtttct ... tctgtgacagTGACATGGAATGTTACATGCACGTATTCACAATTCCTGTCTCAGAAAACCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgagctattacccataaatgtactgggcctaaacttatttctctctgtgacagTGACATGGAATGTTACATGCACGTATTCACAATTCCTGTCTCAGAAAACCCCCACTTGCTGTGTCTCGCTCTCATCTTTCTACAATGACACAATTGTACC
                            gcctaaa  putative branch site (score: 3)
                                   cttatttctctctgt  CT-rich tract
                               taaacttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agggagtgattcttaaaggcaatttttgtcttccctaattaaaaatttgagctattacccataaatgtactgggcctaaacttatttctctctgtgacagTGACATGGAATGTTACATGCACGTATTCACAATTCCTGTCTCAGAAAACCCCCACTTGCTGTGTCTCGCTCTCATCTTTCTACAATGACACAATTGTACC

-gggagtg
- - - - - - - aaaggca
- - - - - - - - - - - - - - tcttccc
- - - - - - - - - - - - - - - - - - aattaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccataa