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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattaggttatctcctcatttttacatttcattcttattcctaaattaccatatatgaataatttgaatgctttttcatattcttgatttatgtttacagGAAGGTGCTGGCTTGTGTGGTTTGTGGGCGTCTAAAAAGTGCCTTCCAGATTGCCTCTCGAAGTGGAAGTGTGGCTGATGTTCAATATGTAGCGCATCAG

Basic information

species Vitis vinifera
transcript Vv04s0008g04520.t01
intron # 37
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g04520.t01 (Vitis vinifera), 3'ss of exon 37
lower sequence: LOC_Os01g40990.2 (Oryza sativa), 3'ss of exon 36
aattaggttatctcctcatttttacatttcattcttattcctaaattaccatatatgaataatttgaatgctttttcatattcttgatttatgtttacagGAAGGTGCTGGCTTGTGTGGTTTGTGGGCGTCTAAAAAGTGCCTTCCAGATTGCCTCTCGAAGTGGAAGTGTGGCTGATGTTCAATATGTAGCGCATCAG
  | |||  |    |   ||| |  ||  |  | | | |   |  | | | |  | | |    ||     |  ||||  |        | |  | | |||||| || || || ||||| || ||||| |||||||||||||| |||||||| ||||| |||||||||||||| ||||||||||||||||| || ||||||
gttcaggaaacaatcatgtttattaatgactctatgagtttaaggtgaactttgaagcacctcttttccaccctttctaacctgcttctgaactattcagGAAAGTACTTGCCTGTGTTGTGTGTGGCCGTCTAAAAAGTGCATTCCAGATAGCCTCCCGAAGTGGAAGTGTTGCTGATGTTCAATATGTTGCTCATCAG

upper sequence: Vv04s0008g04520.t01 (Vitis vinifera), 3'ss of exon 37
lower sequence: GLYMA06G07850.2 (Glycine max), 3'ss of exon 36
aattaggttatctcctcatttttacatttcattcttattcctaaattaccatatatgaataatttgaatgc-tttttcatattcttgatttatgtttacagGAAGGTGCTGGCTTGTGTGGTTTGTGGGCGTCTAAAAAGTGCCTTCCAGATTGCCTCTCGAAGTGGAAGTGTGGCTGATGTTCAATATGTAGCGCATCAG
  | |    ||     ||| |      | |||  || || |      || ||  |  ||  |||  ||    ||| |  |||| |||| ||  |  | ||||||||| || |||||||| |||||||| ||| |||||||||| ||||| ||||| || || ||||||||||| ||||||||||||||||| || ||||||
-ctcaatacatgatgccatgtgccttctccatagttttttccctgcaactattcagcaaccattgtaacatgtttattttatttttgaattgggcatgcagGAAGGTTCTTGCTTGTGTAGTTTGTGGTCGTTTAAAAAGTGCATTCCAAATTGCTTCACGGAGTGGAAGTGTTGCTGATGTTCAATATGTTGCTCATCAG

upper sequence: Vv04s0008g04520.t01 (Vitis vinifera), 3'ss of exon 37
lower sequence: GLYMA04G07760.1 (Glycine max), 3'ss of exon 8
aattaggttatctcctcatttttacatttcattcttattcctaaattaccatatatgaataatttgaatgctttttcatattcttgatttatgtttacagGAAGGTGCTGGCTTGTGTGGTTTGTGGGCGTCTAAAAAGTGCCTTCCAGATTGCCTCTCGAAGTGGAAGTGTGGCTGATGTTCAATATGTAGCGCATCAG
                                                                                                                                          || | || || ||||| ||    ||||||||||||||||||||||| ||||| || ||||||
------------------------------------------------------------------------------------------------------------------------------------------gtacatttcaaattgcatcatagagtggaagTGTGGCTGATGTTCAGTATGTTGCTCATCAG

upper sequence: Vv04s0008g04520.t01 (Vitis vinifera), 3'ss of exon 37
lower sequence: AT2G25730.2 (Arabidopsis thaliana), 3'ss of exon 34
--aattaggttatctcctcatttttacatttcattcttattcctaaattaccatatatgaataatttgaatgctttttcatat-tcttgatttatgtttacagGAAGGTGCTGGCTTGTGTGGTTTGTGGGCGTCTAAAAAGTGCCTTCCAGATTGCCTCTCGAAGTGGAAGTGTGGCTGATGTTCAATATGTAGCGCATCAG
  |  |  |  || | ||||| | |  | |  |||   | ||  |   ||| || ||||    ||    | |||  | ||  | |  |  |  | |  | ||| |||||||||||||||||||| ||||| || || ||||| || ||||||||||| |||  ||| ||||| ||||||||||||||||||||||| ||||| 
ctatgtcagagatgtgctcatgtatgtaataaattg--aatcgcactgtacaat-tatgcgggatcattaggctgatacacgtctgattgtaaacgagtgcagAAAGGTGCTGGCTTGTGTGGTATGTGGCCGCCTGAAAAGCGCATTCCAGATTGCATCTAAAAGCGGAAGCGTGGCTGATGTTCAATATGTAGCTCATCAA

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|110371695|gb|EC935817.1|EC935817
EST:     CACAAAGAACGCCCTGATCGGCTCATAGACATGCTGACAAGTAGCCACAG                         GAAGGTGCTGGCTTGTGTGGTTTGTGGGCGTCTAAAAAGTGCCTTCCAGAT
genomic: CACAAAGAACGCCCTGATCGGCTCATAGACATGCTGACAAGTAGCCACAGgtaatgctcc ... atgtttacagGAAGGTGCTGGCTTGTGTGGTTTGTGGGCGTCTAAAAAGTGCCTTCCAGAT
EST: gi|349809889|gb|FQ398514.1|FQ398514
EST:     CACAAAGAACGCCCTGATCGGCTCATAGACATGCTGACAAGTAGCCACAG                         GAAGGTGCTGGCTTGTGTGGTTTGTGGGCGTCTAAAAAGTGCCTTCCAGAT
genomic: CACAAAGAACGCCCTGATCGGCTCATAGACATGCTGACAAGTAGCCACAGgtaatgctcc ... atgtttacagGAAGGTGCTGGCTTGTGTGGTTTGTGGGCGTCTAAAAAGTGCCTTCCAGAT
EST: gi|349807218|gb|FQ401210.1|FQ401210
EST:     CACAAAGAACGCCCTGATCGGCTCATAGACATGCTGACAAGTAGCCACAG                         GAAGGTGCTGGCTTGTGTGGTTTGTGGGCGTCTAAAA-GTGCCTTCCAGAT
genomic: CACAAAGAACGCCCTGATCGGCTCATAGACATGCTGACAAGTAGCCACAGgtaatgctcc ... atgtttacagGAAGGTGCTGGCTTGTGTGGTTTGTGGGCGTCTAAAAAGTGCCTTCCAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaccatatatgaataatttgaatgctttttcatattcttgatttatgtttacagGAAGGTGCTGGCTTGTGTGGTTTGTGGGCGTCTAAAAAGTGCCTTCCAGATTGCCTCTCGAAGTGGAAGTGTGGCTGATGTTCAATATGTAGCGCATCAG
                                    tcttgat  putative branch site (score: 4)
                          tttttcatattcttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattaggttatctcctcatttttacatttcattcttattcctaaattaccatatatgaataatttgaatgctttttcatattcttgatttatgtttacagGAAGGTGCTGGCTTGTGTGGTTTGTGGGCGTCTAAAAAGTGCCTTCCAGATTGCCTCTCGAAGTGGAAGTGTGGCTGATGTTCAATATGTAGCGCATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - tctcctc
- - - - - - - - - - - - - - - - - - - - - - - - ccatata