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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgaaacttatatttttaagaaatatttattttgaaccttaatccattcccttgaacctcagtccctactttgacatttttttttgttttttattttagCTTCTGATATCAGGTTCACTTGATGGCTTGGATGTTGATGACCTACGATCTAATACCAATTATGCTGGTGGCTATCATAGT

Basic information

species Vitis vinifera
transcript Vv05s0077g00470.t01
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0077g00470.t01 (Vitis vinifera), 3'ss of exon 22
lower sequence: GLYMA17G04180.1 (Glycine max), 3'ss of exon 21
attgaaacttatatttttaagaaatatttattttgaaccttaatccattcccttg---aacctcagtccctactttgacatttttttttgttttttattttagCTTCTGATATCAGGTTCACTTGATGGCTTGGATGTTGATGACCTACGATCTAATACCAATTATGCTGGTGGCTATCATAGT
 |||||     | | |   | ||| | |   ||   ||||  |   ||  | ||     |  |  |   ||   |  |  ||  ||    || |||  |  |||||||||||||||||||||||||  |||||||| ||||||| || ||     ||||||| ||||| || |||||||||| |
-ttgaagtagttttctcctaaaaagaatg--ttaacacctgcaattatgtctttatgtgatatgtgattctgtatccaacttgcttgacattgttttctacagCTTCTGATATCAGGTTCACTTGACAGCTTGGATATTGATGATCTGCGGCTGCATACCAACTATGCAGGAGGCTATCATAAT

upper sequence: Vv05s0077g00470.t01 (Vitis vinifera), 3'ss of exon 22
lower sequence: GLYMA07G36390.1 (Glycine max), 3'ss of exon 21
attgaaac--ttatatttttaagaaatatttattttgaaccttaatccattcccttgaacctcagtccctactttgacatttttttttgttttttattttagCTTCTGATATCAGGTTCACTTGATGGCTTGGATGTTGATGACCTACGATCTAATACCAATTATGCTGGTGGCTATCATAGT
 || ||    || | |  | || |||| || |         |||   | ||   |   |  | | ||  || |   || ||  ||    || |||     |||||||||||||||||||||||||  |||||||| ||||||| || ||     ||||||| ||||| || ||||||||| ||
cttcaagtagttttctcctaaaaaaatgttaacacctgcaattatgtctttatgtgatatgtgattctgta-tccaac-ttgcttgacattgttttccacagCTTCTGATATCAGGTTCACTTGACAGCTTGGATATTGATGATCTGCGGCTGCATACCAACTATGCAGGAGGCTATCATGGT

upper sequence: Vv05s0077g00470.t01 (Vitis vinifera), 3'ss of exon 22
lower sequence: GLYMA09G03680.1 (Glycine max), 3'ss of exon 9
--attgaaacttatatttttaagaaatatttattttgaacct-taatccattcccttgaacc-tcagtccctactttgacatttttttttgttttttattttagCTTCTGATATCAGGTTCACTTGATGGCTTGGATGTTGATGACCTACGATCTAATACCAATTATGCTGGTGGCTATCATAGT
  ||| || |||  | |        | |||| ||| ||| || || |   |  |    |    |  || |  |  |||        | |||||||       ||||||||| |||||||||||||||  ||||||||||||||    | ||      ||| || ||||| || ||||||||||||
ggattcaatcttcaactaggtcttca-atttttttagaatctgtagtttgtgtctcaaagtgatttgtactcaacttgcttaacactattgttttccgc---agCTTCTGACATCAGGTTCACTTGACAGCTTGGATGTTGAT---TTGCGGCAGCGTACAAACTATGCAGGAGGCTATCATAGT

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|161710134|gb|FC061032.1|FC061032
EST:     AACTTATACAAAGAGATTGGATTGAAATGTTTGATGAGCATGAACTTCAG                         CTTCTGATTTCAGGTTCACTTGATGGCTTGGATGTTGATGACCTACGATCT
genomic: AACTTATACAAAGAGATTGGATTGAAATGTTTGATGAGCATGAACTTCAGgtactgtgtt ... tttattttagCTTCTGATATCAGGTTCACTTGATGGCTTGGATGTTGATGACCTACGATCT
EST: gi|110417942|gb|EC984047.1|EC984047
EST:     AACTTATACAAAGAGATTGGATTGAAATGTTTGATGAGCATGAACTTCAG                         CTTCTGATATCAGGTTCACTTGATGGCTTGGATGTTGATGACCTACGATCT
genomic: AACTTATACAAAGAGATTGGATTGAAATGTTTGATGAGCATGAACTTCAGgtactgtgtt ... tttattttagCTTCTGATATCAGGTTCACTTGATGGCTTGGATGTTGATGACCTACGATCT
EST: gi|110370035|gb|EC934210.1|EC934210
EST:     AACTTATACAAAGAGATTGGATTGAAATGTTTGATGAGCATGAACTTCAG                         CTTCTGATATCAGGTTCACTTGATGGCTTGGATGTTGATGACCTACGATCT
genomic: AACTTATACAAAGAGATTGGATTGAAATGTTTGATGAGCATGAACTTCAGgtactgtgtt ... tttattttagCTTCTGATATCAGGTTCACTTGATGGCTTGGATGTTGATGACCTACGATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattcccttgaacctcagtccctactttgacatttttttttgttttttattttagCTTCTGATATCAGGTTCACTTGATGGCTTGGATGTTGATGACCTACGATCTAATACCAATTATGCTGGTGGCTATCATAGT
                        ctttgac  putative branch site (score: 4)
                              catttttttttgtttt  CT-rich tract
                      tactttgacatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgaaacttatatttttaagaaatatttattttgaaccttaatccattcccttgaacctcagtccctactttgacatttttttttgttttttattttagCTTCTGATATCAGGTTCACTTGATGGCTTGGATGTTGATGACCTACGATCTAATACCAATTATGCTGGTGGCTATCATAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - aagaaat
- - - - - - - - - - - - - - - - - - - - - - ccattcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -aacctca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tccctac