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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggagagacacggcattattggctaagctgaaactttttctgctgcagatagttaatactttttgtcctagtttatattcatagattcccatgtattgcagGTGGTATGCAAAAAGGTTCTTGCATCCTGATGTTGTTGCTGCTTATGAATATATTTTTATATGGGATGAAGACCTAGATGTAAAGCACTTCAATGGAGAG

Basic information

species Vitis vinifera
transcript Vv06s0004g02700.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g02700.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os02g19510.2 (Oryza sativa), 3'ss of exon 7
ggagagacacggcattattggctaagctgaaactttttctgctgcagatagtt-aatactttttgtcctagtttatattcatagattcccat-gtattgc---agGTGGTATGCAAAAAGGTTCTTGCATCCTGATGTTGTTGCTGCTTATGAATATATTTTTATATGGGATGAAGACCTAGATGTAAAGCACTTCAATGGAGAG
| ||  | | |  ||| ||   ||     |   | | | ||||| |   | || |||  ||  |||      |||      ||  | |   | || || |   ||||||||||||||  |||| ||||||||||||||||||||    ||||| || || || || |||||||| ||||||| |||  |||| ||||||| ||||
gtaggtaaaggttattgtta-ttattaatatgttatctgtgctgaatccatttgaatttttgctgtgaagtcttaatactgtatgtacttgttgttttacctaagGTGGTATGCAAAGCGGTTTTTGCATCCTGATGTTGTTGCCCGATATGACTACATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAG

upper sequence: Vv06s0004g02700.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os05g01760.1 (Oryza sativa), 3'ss of exon 7
ggagagacacggcattattggctaagctgaaactttttctgctgcagatagttaatactttttgtcctagtttat--attcatagattcccatgtattgcagGTGGTATGCAAAAAGGTTCTTGCATCCTGATGTTGTTGCTGCTTATGAATATATTTTTATATGGGATGAAGACCTAGATGTAAAGCACTTCAATGGAGAG
          |  | | |  |||  | ||  | | |   |    ||| |  | |||  |    |   |  | ||   ||| ||  || | |||  || | ||||||||||| ||||| ||| ||||||||||| |||| || |||||||| || || || || |||||||| ||||| |  ||  |||| |||||||  |||
------gtctgctacttt--gctctgatgctattgtcattctctcaggtgctcaattttgaaggatatcttctaaagatttatttatgcacatacat-gtagGTGGTATGCCAAAAGATTCCTGCATCCTGATATTGTGGCAGCTTATGAGTACATATTCATCTGGGATGAGGACCTTGGGGTGGAGCATTTCAATGCGGAG

upper sequence: Vv06s0004g02700.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G119725_T04 (Zea mays), 3'ss of exon 7
ggagagacacggcattattggctaagctg---aaactttttctgctgcagatagttaata---ctttttgtcctagtttatattcata-gattcccatg--tattgcagGTGGTATGCAAAAAGGTTCTTGCATCCTGATGTTGTTGCTGCTTATGAATATATTTTTATATGGGATGAAGACCTAGATGTAAAGCACTTCAATGGAGAG
        | || | |||||    |  |    ||  | ||| |  |||   | || ||||     ||||| | |   || |||| ||  |||||   ||  |||   ||||||||||||||| | || |||||||| |||||||||||    ||||| || ||||| || |||||||| || |||| |||| |||| ||||| | ||||
------gtatggtagtattgctgtaattatacaatgtctttttattgccctt-gtcaatataatgttttgacttcaattttattgatgtgattcttgtgtttatacaagGTGGTATGCAAAACGATTTTTGCATCCCGATGTTGTTGCCAGATATGATTACATTTTCATCTGGGATGAGGATCTAGGTGTAGAGCATTTCAACGCAGAG

upper sequence: Vv06s0004g02700.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM5G846339_T01 (Zea mays), 3'ss of exon 7
ggagagacacggcattattggctaagctgaaactttttctgctgcagatagttaatactttttgtcctagtttatattcatagattcccatgta---ttgcagGTGGTATGCAAAAAGGTTCTTGCATCCTGATGTTGTTGCTGCTTATGAATATATTTTTATATGGGATGAAGACCTAGATGTAAAGCACTTCAATGGAGAG
   | ||     ||||  ||    ||     ||| ||     | ||  |  |||||      ||  |||||    |||  |   ||       |    |  ||||||||||| || || ||| ||||||||||| |||| || |||||||| || || || || |||||||| ||||| |  ||  | || || |||| ||||
---gtga-gtttcatttgtgctctagt--gtactgttcgcagttcaattgcttaatttgaaatgatctagtgctaatttttttgtttgtgcacacaactctagGTGGTATGCCAAGAGATTCCTGCATCCTGATATTGTGGCAGCTTATGAGTACATATTCATTTGGGATGAGGACCTTGGGGTTGAACATTTTAATGCAGAG

upper sequence: Vv06s0004g02700.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA13G39990.1 (Glycine max), 3'ss of exon 7
--------------------------------------------------------------------------------------ggagagacacggcattattggctaagctgaaactttttc----tgctg--cagatagttaatactttttgtcctagtttatattcatagattcccatgtattgcagGTGGTATGCAAAAAGGTTCTTGCATCCTGATGTTGTTGCTGCTTATGAATATATTTTTATATGGGATGAAGACCTAGATGTAAAGCACTTCAATGGAGAG
                                                                                          |     || ||| ||     | || |   || ||     || ||  |  || | ||      ||||   |  |  |  ||  | |    | ||||  |||||||||||||| ||||| || ||||| |||||| | ||  | |||||||||||||||||||| ||||||||||| || |  ||| | |||||||||| ||| 
gtatagttttctccaatcatttttttgcatttaacttatgaaagtcataggtattggacatgggaagcctatttttttgtgatcacatttaactttggaattcttaaaagaccttatcattcttaggagtgatgaccttattgctatactcctttgcttttatacaattttctcgtactcaatgttgtgcagGTGGTATGCTAAAAGATTTTTGCACCCTGATATAGTATCAGCTTATGAATATATTTTTATTTGGGATGAAGATCTTGGAGTAGAACACTTCAATGCAGAC

upper sequence: Vv06s0004g02700.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA12G29800.1 (Glycine max), 3'ss of exon 7
-----------------------------------------------------------------------------ggagag-acacggcattattggctaagctgaaactttttctgctgcagatagttaatacttt-ttgtcctagtttatattcatagattcccatgtattgcagGTGGTATGCAAAAAGGTTCTTGCATCCTGATGTTGTTGCTGCTTATGAATATATTTTTATATGGGATGAAGACCTAGATGTAAAGCACTTCAATGGAGAG
                                                                             || ||  |||    | | | |  |      ||    ||     |      ||| |  || || |||   |  |  |  ||| | |      ||||  |||||||||||||| ||||| || ||||| |||||| | ||  | |||||||||||||||||||| ||||||||||| || |  ||| | |||||||||| ||| 
gtatagttttctccaatcatttttttgcatttaacttatgaaagtcataggtattggacatgggaagcctattttttggtgatcacatttaactttggaattcttaaaagaccttatcattcttaggagtgatgaccttattgcttttatgcaatttcctcgtacttaatgttgtgcagGTGGTATGCTAAAAGATTTTTGCACCCTGATATAGTATCAGCTTATGAATATATTTTTATTTGGGATGAAGATCTTGGAGTAGAACACTTCAATGCAGAC

upper sequence: Vv06s0004g02700.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT1G08040.1 (Arabidopsis thaliana), 3'ss of exon 7
ggagagacacggcattattggctaagctgaaa----ctttttctgctgcagatagttaatactttttgtcctagtttatattcatagattcccatgtattgcagGTGGTATGCAAAAAGGTTCTTGCATCCTGATGTTGTTGCTGCTTATGAATATATTTTTATATGGGATGAAGACCTAGATGTAAAGCACTTCAATGGAGAG
| |   |  | | | | | ||  |    || |    ||  |||| ||     |  | || | || |   |  | |    |     || |    || | | |||||||||||||||| || || |||||||||||||||||  | |||||||| ||||| ||||||||||||||||| || |  ||  |||||||||||| ||| 
gtaagaaatctgaaatgtaggtcagcacgatatactctaattcttctaatagtcatgaaaatttatctacaaaatcctcaccttgagctgtttatctttggcagGTGGTATGCAAAGAGATTTTTGCATCCTGATGTTGTCTCAGCTTATGAGTATATATTTATATGGGATGAAGATCTTGGAGTCGAGCACTTCAATGCAGAT

upper sequence: Vv06s0004g02700.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT2G28310.1 (Arabidopsis thaliana), 3'ss of exon 7
ggagagacacggcattattggctaagctgaaactttttctgctgcagatagttaatactttttgtcctagtttatattcatagattcccatgtatt--gcagGTGGTATGCAAAAAGGTTCTTGCATCCTGATGTTGTTGCTGCTTATGAATATATTTTTATATGGGATGAAGACCTAGATGTAAAGCACTTCAATGGAGAG
                 || |  |  |||    |||  | | |    |  ||  ||  || | |     |||| |||  | |   ||   ||  ||  |||||||||| || || ||||| |||||||||||||||||  | |||||||| || || ||||||||||||||||| || |  ||  |||| |||||||  || 
----------------gttagtcat-ctggtcatttaccggttattaa--gt--atgtttgtcgagtatgtttttatcgaaattctctactggttttggcagGTGGTACGCGAAGAGGTTTTTGCATCCTGATGTTGTGTCAGCTTATGAGTACATATTTATATGGGATGAAGATCTTGGAGTGGAGCATTTCAATGCGGAT

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|110378258|gb|EC943381.1|EC943381
EST:     GAGTGGTCAAAAACTGCAATTCATGTTAGTGCAAGAAAACAAACAAAATG                         GTGGTATGCAAAAAGGTTCTTGCATCCTGATGTTGTTGCTGCTTATGAATA
genomic: GAGTGGTCAAAAACTGCAATTCATGTTAGTGCAAGAAAACAAACAAAATGgtaaggactc ... tgtattgcagGTGGTATGCAAAAAGGTTCTTGCATCCTGATGTTGTTGCTGCTTATGAATA
EST: gi|37184080|gb|CF603434.1|CF603434
EST:     GAGTGGTCAAAAACTGCAATTCATGTTAGTGCAAGAAAACAAACAAAATG                         GTGGTATGCAAAAAGGTTCTTGCATCCTGATGTTGTTGCTGCTTATGAATA
genomic: GAGTGGTCAAAAACTGCAATTCATGTTAGTGCAAGAAAACAAACAAAATGgtaaggactc ... tgtattgcagGTGGTATGCAAAAAGGTTCTTGCATCCTGATGTTGTTGCTGCTTATGAATA
EST: gi|110687082|gb|EE064179.1|EE064179
EST:     GAGTGGTCAAAAACTGCAATTCATGTTAGTGCAAGAAA-CAAACAAAATG                         GTGGTATGCAAAAAGGTTCTTG
genomic: GAGTGGTCAAAAACTGCAATTCATGTTAGTGCAAGAAAACAAACAAAATGgtaaggactc ... tgtattgcagGTGGTATGCAAAAAGGTTCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatagttaatactttttgtcctagtttatattcatagattcccatgtattgcagGTGGTATGCAAAAAGGTTCTTGCATCCTGATGTTGTTGCTGCTTATGAATATATTTTTATATGGGATGAAGACCTAGATGTAAAGCACTTCAATGGAGAG
    agttaat  putative branch site (score: 4)
                                       ttcccat  putative PPT
                         tttatattcatagatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggagagacacggcattattggctaagctgaaactttttctgctgcagatagttaatactttttgtcctagtttatattcatagattcccatgtattgcagGTGGTATGCAAAAAGGTTCTTGCATCCTGATGTTGTTGCTGCTTATGAATATATTTTTATATGGGATGAAGACCTAGATGTAAAGCACTTCAATGGAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- agagaca
- - - - - ggcatta
- - - - - - - - - - - - - ctgaaac
- - - - - - - - - - - - - - - - - - -tctgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -attccca