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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctgaagcttttagtggtcttgtctatcacctttgtgttaccttgttatggaaggtgctgagatgatgttctccaactaatatgattgtgggtttttcagGTATCACTATAGCTGAATACTTCAGAGATATGGGCTACAATGTTAGTATGATGGCAGATTCAACATCTCGATGGGCAGAGGCATTGCGAGAAATATCAGG

Basic information

species Vitis vinifera
transcript Vv09s0054g00890.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 11
--cctgaagcttttagtggtcttgtctatcacctttgtgttaccttgttatggaaggtgctgagatgatgttctccaactaatatgattgtgggtttttcagGTATCACTATAGCTGAATACTTCAGAGATATGGGCTACAATGTTAGTATGATGGCAGATTCAACATCTCGATGGGCAGAGGCATTGCGAGAAATATCAGG
   ||   |   || |   |  | | | |    | ||          | ||      || |   ||  |   |   | || |||||| | ||       |||| || || |||||||| || | | | || ||||| |||||||| || |||||||| ||||| || || |||||||| ||||||||||| ||||| || ||
ttgctttggtcatttggactgctatatgtattttatggaccttaagttcatcaccaatgatctcattgtaaacaaaatcttatatgactttg--ccccccagGAATTACGATAGCTGAGTATTACCGTGACATGGGTTACAATGTCAGCATGATGGCTGATTCCACCTCACGATGGGCTGAGGCATTGCGTGAAATTTCTGG

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 11
cctgaagcttttagtggtcttgtctatcacctttgtgttaccttgttatggaaggtgc-tgagatgatgttctccaactaatatgattgtgggtttttc--------agGTATCACTATAGCTGAATACTTCAGAGATATGGGCTACAATGTTAGTATGATGGCAGATTCAACATCTCGATGGGCAGAGGCATTGCGAGAAATATCAGG
     || || | || |     |  |     |     || | | ||||||     ||| |||  |  | ||   |||| || |  ||  |   ||||||        ||| || || || |||||||||||| | || |||||||| ||||| ||||||||||| ||||| || ||||| ||||| || || ||||| || || |||||
-----agtttcttgtagaacactaaaaggagtcc---ttgcttagttatgctttatgcctgatgttttctttatcaacaaa-acaatcatatttttttctgcccaccagGAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGG

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 8
cctgaagcttttagtggtcttgtctatcacctttgtgttaccttgttatggaaggtgctgagatgatgttctccaactaatatgattgtgggtttttc----agGTATCACTATAGCTGAATACTTCAGAGATATGGGCTACAATGTTAGTATGATGGCAGATTCAACATCTCGATGGGCAGAGGCATTGCGAGAAATATCAGG
    | | | |  |||    |||| |||       |||  |  || |       || | | |  ||  ||||   |  |||   |||||   ||||||    ||| || || || || || || ||  | |||||||||||||| |||||||||||||| || || || || |||||||| ||||| ||||| || || |||||
----atgatatgggtgcctctgtccatctgtcagttgtatctctgcttgtcgctgttcggtgtggagtttctgttaacaatcatattgtacctttttcccgcagGAATTACAATTGCCGAGTATTTTCGTGATATGGGCTACAACGTTAGTATGATGGCTGACTCCACCTCACGATGGGCTGAGGCTTTGCGTGAGATCTCAGG

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 11
cctgaagcttttagtggtctt-gtctatcacctttgtgttaccttgtta-tggaaggtgctgagatgatgttctccaactaatatgattgtgggtttttcagGTATCACTATAGCTGAATACTTCAGAGATATGGGCTACAATGTTAGTATGATGGCAGATTCAACATCTCGATGGGCAGAGGCATTGCGAGAAATATCAGG
  |||      |     | |  || | ||| || | | |   |||||   |     |||| ||| |  ||||  | | |   |   |   |   |   ||||| || || || ||||| || ||| | |||||||||||||| || ||||||||||| || || || || || ||||| ||||||||||| || || |||||
--tgatatgggtgcctctttcagtttgtcagctgtatttctgcttgtcgcttttcagtgcagagtttctgttaacaatcatgttgtaccttttttaactcagGAATTACAATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGATGGCTGACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGG

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 12
cctgaagcttttagtggtcttgtctatcacctttgtgttaccttgtta-tggaaggtgctgaga-tgatgttctccaactaatatgattgtgggtttttcagGTATCACTATAGCTGAATACTTCAGAGATATGGGCTACAATGTTAGTATGATGGCAGATTCAACATCTCGATGGGCAGAGGCATTGCGAGAAATATCAGG
  |  |  |     |    |  |  || |  | | ||      || |  | ||  ||  | | | |||| ||    |  || |    || |     || |||| |||||  ||||||| || |||||||||||||| || ||||| ||||||||||||||||| |||||| |||||||||| |||||||| ||||| || ||
--tatatttgcccttaaaatgattaatgaattgtttgaccgtgtgctgcttgagagttttaacactgattttgataatatatttcttttttttcaattgcagGAATCACATTAGCTGAGTATTTCAGAGATATGGGTTATAATGTCAGTATGATGGCAGATTCTACATCTAGATGGGCAGAAGCATTGCGTGAAATCTCTGG

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 12
cctgaagcttttagtggtcttgtctatcacctttgtgttacct-tgttatg-gaaggtgctgaga-tgatgttctccaactaatatgattgtgggtttttcagGTATCACTATAGCTGAATACTTCAGAGATATGGGCTACAATGTTAGTATGATGGCAGATTCAACATCTCGATGGGCAGAGGCATTGCGAGAAATATCAGG
  | |   |||   |  |  ||  ||  |  ||||| |  ||| || |    ||  ||  | | | |||| ||    |  ||||    || ||  ||   |||| |||||  ||||||| || || ||||||||||| || ||||| ||||||||||||||||| |||||| |||||||||| |||||||| ||||| || ||
-atcatattttcccttataatgattaataaatttgtttggcctgtgctgcatgagagttttaacactgattttgataatgtaattcttttttgaattg--cagGAATCACATTAGCTGAGTATTTTAGAGATATGGGTTATAATGTCAGTATGATGGCAGATTCTACATCTAGATGGGCAGAAGCATTGCGTGAAATCTCTGG

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 12
cctgaagcttttagtggtcttgtctatcacctttgtgttaccttgttatggaaggtgc-tgagatgatgttctccaactaatatgattgtgggtttttcagGTATCACTATAGCTGAATACTTCAGAGATATGGGCTACAATGTTAGTATGATGGCAGATTCAACATCTCGATGGGCAGAGGCATTGCGAGAAATATCAGG
           || || ||  |   |     ||  |  |   |  | |       ||| |  | | || || |     |  | | | ||||  ||   |||| ||||| || |||||||| || ||||||||||||||||||||||||||||||||||| ||||| || || |||||||| |||||  ||||||| |||||
----------gtaatgttcaggcacacagatttaatagttattgatgaatcccattgcctatgctcattttttttttttttttttaatgtgaattc--cagGAATCACAATCGCTGAATATTTTAGAGATATGGGCTACAATGTTAGTATGATGGCAGACTCAACTTCCCGTTGGGCAGAAGCATTAAGAGAAATTTCAGG

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: PP1S10_201V6.1 (Physcomitrella patens), 3'ss of exon 12
--------cctgaagcttttagtggtcttgtctatcacctttgtgttaccttgttatggaaggtgctgagatgatgttctccaactaatatgattgtgggtttttcagGTATCACTATAGCTGAATACTTCAGAGATATGGGCTACAATGTTAGTATGATGGCAGATTCAACATCTCGATGGGCAGAGGCATTGCGAGAAATATCAGG
        | |||    ||  |  |  |    | | | |    ||| |||||    |   |  |  ||| | ||| ||       | | ||  |  |   | || ||||||| ||  | || || |||||||| |||||||| || ||||| ||||||||||| || ||||||||||| |||||||||||  |  ||||||| || ||
gttcccatcttgagttattctgaagcttaacttttgatcgcaatgtgaccttaaagtttgaaatcttga-aggattttacgttcatcacattttgttatctgttgcagGTATTACCTTGGCGGAGTACTTCAGGGATATGGGGTATAATGTCAGTATGATGGCGGACTCAACATCTCGCTGGGCAGAGGCTCTTAGAGAAATTTCCGG

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: PP1S44_102V6.1 (Physcomitrella patens), 3'ss of exon 12
-------------------------------------------------------cctgaagcttttagtggtcttgtctatcacctttgtgttaccttgttatggaag---gtgctgagatgatgttctccaactaatatgattgtgggtttttcagGTATCACTATAGCTGAATACTTCAGAGATATGGGCTACAATGTTAGTATGATGGCAGATTCAACATCTCGATGGGCAGAGGCATTGCGAGAAATATCAGG
                                                        ||  |   |||      | | |  ||| | |   ||  |  ||   ||  ||    || ||      || | |||  |  | | || ||     | || |||| || ||| |||| || ||||||||||||||||| || ||||| ||||||||||| || || || ||||| |||||||||||  | |||||||| || ||
gtttcctcctttttattctctctaaagtttaagtgttcattgctgcggcacctcatctagataatttctcaaacgttttcatcgcttccttggaattttcgcatataattgcgtcctttctacatttgctctgaagattctgttttc---tgttgcagGCATTACTTTAGCAGAGTACTTCAGAGATATGGGGTATAATGTCAGTATGATGGCTGACTCTACGTCTCGCTGGGCAGAGGCCCTTCGAGAAATTTCTGG

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 12
---------------cctgaagct----tttagtggtcttgtctatcacctttgtgttacctt--gttatggaaggtgctga-------gatgatgttctccaac----taatatgattgtgggttttt----cagGTATCACTATAGCTGAATACTTCAGAGATATGGGCTACAATGTTAGTATGATGGCAGATTCAACATCTCGATGGGCAGAGGCATTGCGAGAAATATCAGG
                ||||  ||    |||   |||  ||| |   ||| ||   |   |||  | | |   |  ||||         |||    | || |  |    | ||   | ||  | ||  |    ||||||||||| | || ||||||||||| |||||||| |||||||| |||||||||||||| || |||||||| ||||| |||||  | || || || || ||
gttattttcttttcttctgagactctactttctaggtgctgtatgaaaccatttcatcctctttggatgtttgaaatgctatcctgtatgatcgcatacttccgcatcattatgcaaatgctgtttcctgttgcagGTATCACTTTGGCAGAATACTTCAGGGATATGGGTTACAATGTCAGTATGATGGCAGACTCTACATCTCGCTGGGCTGAGGCGCTTCGTGAGATTTCTGG

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|110720887|gb|EE097200.1|EE097200
EST:     CAACACTTCAAATATGCCTGTGGCTGCTCGTGAGGCTTCAATTTATACAG                         GTATCACTATAGCTGAATACTTCAGAGATATGGGCTACAATGTTAGTATGA
genomic: CAACACTTCAAATATGCCTGTGGCTGCTCGTGAGGCTTCAATTTATACAGgtaaatatat ... ggtttttcagGTATCACTATAGCTGAATACTTCAGAGATATGGGCTACAATGTTAGTATGA
EST: gi|110715176|gb|EE092929.1|EE092929
EST:     CAACACTTCAAATATGCCTGTGGCTGCTCGTGAGGCTTCAATTTATACAG                         GTATCACTATAGCTGAATACTTCAGAGATATGGGCTACAATGTTAGTATGA
genomic: CAACACTTCAAATATGCCTGTGGCTGCTCGTGAGGCTTCAATTTATACAGgtaaatatat ... ggtttttcagGTATCACTATAGCTGAATACTTCAGAGATATGGGCTACAATGTTAGTATGA
EST: gi|110707093|gb|EE083190.1|EE083190
EST:     CAACACTTCAAATATGCCTGTGGCTGCTCGTGAGGCTTCAATTTATACAG                         GTATCACTATAGCTGAATACTTCAGAGATATGGGCTACAATGTTAGTATGA
genomic: CAACACTTCAAATATGCCTGTGGCTGCTCGTGAGGCTTCAATTTATACAGgtaaatatat ... ggtttttcagGTATCACTATAGCTGAATACTTCAGAGATATGGGCTACAATGTTAGTATGA
EST: gi|110692053|gb|EE070859.1|EE070859
EST:     CAACACTTCAAATATGCCTGTGGCTGCTCGTGAGGCTTCAATTTATACAG                         GTATCACTATAGCTGAATACTTCAGAGATATGGGCTACAATGTTAGTATGA
genomic: CAACACTTCAAATATGCCTGTGGCTGCTCGTGAGGCTTCAATTTATACAGgtaaatatat ... ggtttttcagGTATCACTATAGCTGAATACTTCAGAGATATGGGCTACAATGTTAGTATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatggaaggtgctgagatgatgttctccaactaatatgattgtgggtttttcagGTATCACTATAGCTGAATACTTCAGAGATATGGGCTACAATGTTAGTATGATGGCAGATTCAACATCTCGATGGGCAGAGGCATTGCGAGAAATATCAGG
                             aactaat  putative branch site (score: 2)
                                               tttttc  putative PPT
                                taatatgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctgaagcttttagtggtcttgtctatcacctttgtgttaccttgttatggaaggtgctgagatgatgttctccaactaatatgattgtgggtttttcagGTATCACTATAGCTGAATACTTCAGAGATATGGGCTACAATGTTAGTATGATGGCAGATTCAACATCTCGATGGGCAGAGGCATTGCGAGAAATATCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- tgaagct
- - - - - - - - - - - - - - - - - - - taccttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - gtgctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aactaat