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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctccaccactccttacaaaatatttagcttctggaatttaagctcaggtgtttagtttgtgcgtcatttaacttataccttttcttgaatttatgatcagGCTACAATTGGTATTGATTTCCTATCAAAGACCATGTATCTTGAAGATCGAACCGTTCGTCTGCAGTTGTG

Basic information

species Vitis vinifera
transcript Vv02s0012g00710.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0012g00710.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os07g31370.1 (Oryza sativa), 3'ss of exon 1
ctccaccactccttacaaaatatttagcttctggaatttaagctcaggtgtttagtttgtgcg-tcatttaacttataccttttcttgaattt-atgatcagGCTACAATTGGTATTGATTTCCTATCAAAGACCATGTATCTTGAAGATCGAACCGTTCGTCTGCAGTTGTG
   ||    | |      |||| ||| |||      ||| || |    |  |||  || |  | || ||    |   |   ||| ||  ||||   || ||||||||||| |||||||| ||||| |||||||| ||||| ||||||||| | || ||  | |||||  | ||
--gcaatgtttcagttttaatacttatcttaaaatgtttcagttttaatacttatcttatctggtcgttatgttctcatgatttattctattttgcgaacagGCTACAATCGGTATTGACTTCCTGTCAAAGACAATGTACCTTGAAGATAGGACTGTCAGACTGCAACTTTG

upper sequence: Vv02s0012g00710.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G075719_T01 (Zea mays), 3'ss of exon 1
-------ctccaccactccttacaaaatatttagcttctggaatttaagctcaggtgtttagtttgtgcgtcatttaacttataccttttcttgaatttatgatcagGCTACAATTGGTATTGATTTCCTATCAAAGACCATGTATCTTGAAGATCGAACCGTTCGTCTGCAGTTGTG
        |          |||   ||| ||| |||| | | |    ||    | || ||||| | | |     ||  || | |  | || |      ||||  |||||||||||||||||||||||||| |||||||| ||||| ||||||||| |||| ||  | || ||  | ||
agtattattttgagttaatttatgtaatttttggcttgttgtac---agtaatgctggttagtctattca--ggtttgctcaaagttgttttctctggtatg--cagGCTACAATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG

upper sequence: Vv02s0012g00710.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G169694_T01 (Zea mays), 3'ss of exon 1
-ctccaccactccttacaaaatatttagcttctgg---aatttaagctcaggtgtttagtttgtgcgtcatttaacttataccttttcttgaatttatgatcagGCTACAATTGGTATTGATTTCCTATCAAAGACCATGTATCTTGAAGATCGAACCGTTCGTCTGCAGTTGTG
  |    ||    ||   | |  | ||  || |||   |   ||   || | || ||| | | | |     ||  || | |  | || |       |||  |||||||| ||||||||||||||||| |||||||| ||||| ||||||||| |||| ||  | || ||  | ||
cgtaggtcaagtttttttatacctgtattttttggcttatcatacagtctgctggttattctattca--ggtttgctcaaagttgttttctctcgaatg--cagGCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG

upper sequence: Vv02s0012g00710.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S39_147V6.2 (Physcomitrella patens), 3'ss of exon 2
------------------------------------------------------------------------------ctccaccactcc------ttacaaaatatttagcttctggaatttaagctcagg-tgtttagtttgtgcgtcatttaacttataccttttc--ttgaatttatgatcagGCTACAATTGGTATTGATTTCCTATCAAAGACCATGTATCTTGAAGATCGAACCGTTCGTCTGCAGTTGTG
                                                                              |||||  ||||       || ||   | |||   || |  | |   | |      ||    |||   |  |  |   | | ||   |||||  ||||     |   ||||| || |||||||||||||| || || ||||||||||||||||| ||||| || ||| | || ||| | ||
gttagcttctttccctcctagtcttcttgcataaaaattgtgtgctgctgacatttctggtttgccgtacatcaataactccat-actctggatggtttcattctttttgttttttctagtaagaacctgtcctggcaggttcaaggttggtgctattgatgagttttcccttgataactttggcagGCAACTATTGGTATTGATTTTCTCTCCAAGACCATGTATCTTGAGGATCGCACTGTTAGACTACAGCTCTG

upper sequence: Vv02s0012g00710.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ22994 (Selaginella moellendorffii), 3'ss of exon 1
ctccaccactccttacaaaatatttagcttctggaatttaagctcaggtgtttagtttgtgcgtcatttaacttataccttttcttgaatttatgatcagGCTACAATTGGTATTGATTTCCTATCAAAGACCATGTATCTTGAAGATCGAACCGTTCGTCTGCAGTTGTG
                                    | | || | | | ||||  | | |      |||  |  ||        | |||||| | |  ||||||| ||||| || |||||| |||| |||||||||||||| |||||||| || || ||  ||||| | ||
-----------------------------------gtatgagattacgagtttcttctct---cactttggcaaat--------tggaatttttca--agGCTACGATTGGGATCGATTTCTTATCCAAGACCATGTATCTGGAAGATCGCACAGTCCGCTTGCAGCTCTG

upper sequence: Vv02s0012g00710.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ30542 (Selaginella moellendorffii), 3'ss of exon 1
ctccaccactccttacaaaatatttagcttctggaatttaagctcaggtgtttagtttgtgcgtcatttaacttataccttttcttgaatttatgatcagGCTACAATTGGTATTGATTTCCTATCAAAGACCATGTATCTTGAAGATCGAACCGTTCGTCTGCAGTTGTG
                                    | | || | | | ||||   || |   ||| ||     |         | ||| || | |  ||||||| ||||| || |||||| |||| |||||||||||||| |||||||| || || ||  ||||| | ||
-----------------------------------gtatgagattacgagttt--cttctctctcactttggcaaa-------ttggaaattttca--agGCTACGATTGGGATCGATTTCTTATCCAAGACCATGTATCTGGAAGATCGCACAGTCCGCTTGCAGCTCTG

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|351046568|gb|FQ453184.1|FQ453184
EST:     CCAGCATCATCACTCGATTCATGTACGACAAATTCGATAATACCTATCAG                         GCTACAATTGGTATTGATTTCCTATCAAAGACCATGTATCTTGAAGATCGA
genomic: CCAGCATCATCACTCGATTCATGTACGACAAATTCGATAATACCTATCAGgtaattcaat ... ttatgatcagGCTACAATTGGTATTGATTTCCTATCAAAGACCATGTATCTTGAAGATCGA
EST: gi|294966167|gb|GW839390.1|GW839390
EST:     CCAGCATCATCACTCGATTCATGTACGACAAATTCGATAATACCTATCAG                         GCTACAATTGGTATTGATTTCCTATCAAAGACCATGTATCTTGAAGATCGA
genomic: CCAGCATCATCACTCGATTCATGTACGACAAATTCGATAATACCTATCAGgtaattcaat ... ttatgatcagGCTACAATTGGTATTGATTTCCTATCAAAGACCATGTATCTTGAAGATCGA
EST: gi|351042357|gb|FQ442824.1|FQ442824
EST:     CCAGCATCATCACTCGATTCATGTACGACAAATTCGATAATACCTATCAG                         GCTACAATTGGTATTGATTTCCTATCAAAGACCATGTATCTTGAAGATCGA
genomic: CCAGCATCATCACTCGATTCATGTACGACAAATTCGATAATACCTATCAGgtaattcaat ... ttatgatcagGCTACAATTGGTATTGATTTCCTATCAAAGACCATGTATCTTGAAGATCGA
EST: gi|110686975|gb|EE063981.1|EE063981
EST:     CCAGCATCATCACTCGATTCATGTACGACAAATTCGATAATACCTATCAG                         GCTACAATTGGTATTGATTTCCTATCAAAGACCATGTATCTTGAAGATCGA
genomic: CCAGCATCATCACTCGATTCATGTACGACAAATTCGATAATACCTATCAGgtaattcaat ... ttatgatcagGCTACAATTGGTATTGATTTCCTATCAAAGACCATGTATCTTGAAGATCGA
EST: gi|110723851|gb|EE099164.1|EE099164
EST:     CCAGCATCATCACTCGATTCATGTACGACAAATTCGATAATACCTATCAG                         GCTACAATTGGTATTGATTTCCTATCAAAGACCATGTATCTTGAAGATCGA
genomic: CCAGCATCATCACTCGATTCATGTACGACAAATTCGATAATACCTATCAGgtaattcaat ... ttatgatcagGCTACAATTGGTATTGATTTCCTATCAAAGACCATGTATCTTGAAGATCGA
EST: gi|351032522|gb|FQ458887.1|FQ458887
EST:     CCAGCATCATCACTCGATTCATGTACGACAAATTCGATAATACCTATCAG                         GCTACAATTGGTATTGATTTCCTATCAAAGACCATGTATCTCGAAGATCGA
genomic: CCAGCATCATCACTCGATTCATGTACGACAAATTCGATAATACCTATCAGgtaattcaat ... ttatgatcagGCTACAATTGGTATTGATTTCCTATCAAAGACCATGTATCTTGAAGATCGA
EST: gi|351056494|gb|FQ455146.1|FQ455146
EST:     CCAGCATCATCACTCGATTCATGTACGACAAATTCGATAATACCTATCAG                         GCTACAATTGGTATTGATTTCCTATCAAAGACCATGTATCTCGAAGATCGA
genomic: CCAGCATCATCACTCGATTCATGTACGACAAATTCGATAATACCTATCAGgtaattcaat ... ttatgatcagGCTACAATTGGTATTGATTTCCTATCAAAGACCATGTATCTTGAAGATCGA
EST: gi|351015547|gb|FQ447376.1|FQ447376
EST:     CCAGCATCATCACTCGATTCATGTACGACAAATTCGATAATACCTATCAG                         GCTACAATTGGTATTGATTTCCTATCAAAGACCATGTATCTTGAAGATCGA
genomic: CCAGCATCATCACTCGATTCATGTACGACAAATTCGATAATACCTATCAGgtaattcaat ... ttatgatcagGCTACAATTGGTATTGATTTCCTATCAAAGACCATGTATCTTGAAGATCGA
EST: gi|110731534|gb|EE106031.1|EE106031
EST:     CCAGCATCATCACTCGATTCATGTACGACAAATTCGATAATACCTATCAG                         GCTACAATTGGTATTGATTTCCTATCAAAGACCATGTATCTTGAAGATCGA
genomic: CCAGCATCATCACTCGATTCATGTACGACAAATTCGATAATACCTATCAGgtaattcaat ... ttatgatcagGCTACAATTGGTATTGATTTCCTATCAAAGACCATGTATCTTGAAGATCGA
EST: gi|351053354|gb|FQ455690.1|FQ455690
EST:     CCAGCATCATCACTCGATTCATGTACGACAAATTCGATAATACCTATCAG                         GCTACAATTGGTATTGATTTCCTATCAAAGACCATGTATCTTGAAGATCGA
genomic: CCAGCATCATCACTCGATTCATGTACGACAAATTCGATAATACCTATCAGgtaattcaat ... ttatgatcagGCTACAATTGGTATTGATTTCCTATCAAAGACCATGTATCTTGAAGATCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggtgtttagtttgtgcgtcatttaacttataccttttcttgaatttatgatcagGCTACAATTGGTATTGATTTCCTATCAAAGACCATGTATCTTGAAGATCGAACCGTTCGTCTGCAGTTGTG
                    atttaac  putative branch site (score: 3)
                                  ttttcttgaatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctccaccactccttacaaaatatttagcttctggaatttaagctcaggtgtttagtttgtgcgtcatttaacttataccttttcttgaatttatgatcagGCTACAATTGGTATTGATTTCCTATCAAAGACCATGTATCTTGAAGATCGAACCGTTCGTCTGCAGTTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
-tccacca
- - - - - - - -caaaata
- - - - - - - - - - - - - -cttctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tttgtgc