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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatctcaagaaatcatgtcattccttaattgtagaatattggctccacataccacactaattgaagtgctgtgtgattatatttatagGTCATGGGAAGGTCTTCTCCAAATGACAAGCTTCTTCTTGTGCAAGCATTGAAAAAGAAAGGGCATGTTGTTGCTGTAACTGGAGATGGAACTAATGATG

Basic information

species Vitis vinifera
transcript Vv11s0052g00320.t01
intron # 26
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 26
lower sequence: LOC_Os02g08010.1 (Oryza sativa), 3'ss of exon 7
gtatgatctcaag-----aaatcatgtcattccttaattgta--gaatattggctcca-cataccacactaattgaagtgctgtgtgattatat-ttatagGTCATGGGAAGGTCTTCTCCAAATGACAAGCTTCTTCTTGTGCAAGCATTGAAAAAGAAAGGGCATGTTGTTGCTGTAACTGGAGATGGAACTAATGATG
  ||  | || ||     | || |     |||  || |||||  |  | || |||| | ||| | |    ||   |  || |||   |  ||   || |||||||||||||| |||||||||| |||||| ||||| || ||  ||||| |||||||||||||  ||||||||||||| |||||||||||||| |||||||
acatactttcgagtttacacattaccatgttcagtacttgtactggctgttagctcgatcattctaggggaagcaacctgatgt-caacaatgcattgtagGTCATGGGAAGATCTTCTCCAAGTGACAAACTTCTCCTAGTAAAAGCACTGAAAAAGAAAGGCAATGTTGTTGCTGTTACTGGAGATGGAACGAATGATG

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 26
lower sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 24
-------gtatgatctcaagaaatcatgtcattccttaattgtagaatattggctccacataccacactaattgaa-gtgctgtgtgattatatttatagGTCATGGGAAGGTCTTCTCCAAATGACAAGCTTCTTCTTGTGCAAGCATTGAAAAAGAAAGGGCATGTTGTTGCTGTAACTGGAGATGGAACTAATGATG
          ||        | | || |||  |  ||  |      || ||| ||      ||| |   |||| ||  | |  | ||   ||  ||| |||| ||||| |||||||| ||||||||||||||| | |||||  ||||||| | ||| | ||| |||||||||||||| ||||||||||| || |||||||
tgcattcaagtgcctagtttataccaggtcggtttttgttcagtatatgttgtctatcttcacctcgacaattaaatataccctatgtaaatggttacagGTGATGGGGAGGTCTTCACCAAATGACAAGCTTTTACTTGTTAAAGCATTAAGAAAAAGAGGTCATGTTGTTGCTGTGACTGGAGATGGCACAAATGATG

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 26
lower sequence: GRMZM2G140328_T03 (Zea mays), 3'ss of exon 24
--------gtatga-tctcaagaaatcatgt-cattccttaattgtaga-atattggctccacataccacactaattgaagtgctgtgtgattatatttatagGTCATGGGAAGGTCTTCTCCAAATGACAAGCTTCTTCTTGTGCAAGCATTGAAAAAGAAAGGGCATGTTGTTGCTGTAACTGGAGATGGAACTAATGATG
         ||| | |||  |    |  | | |||| |  || || ||| ||| |  || |   || |       || |  |    | | |  ||   || |||| ||||| |||||||| |||||||| || ||| | |||||  | ||| |||     | ||| |||||||||||||| ||||||||||| || |||||||
aagttcttatataaatcttcatttgttttatgcattgc--aaatgcagatatactatctacttttatctt-tgggttaatttatgctctaacaatggctacagGTGATGGGGAGGTCTTCACCAAATGATAAACTTTTACTTGTTAAGGCACTGAGGGCAAGAGGTCATGTTGTTGCTGTTACTGGAGATGGCACAAATGATG

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 26
lower sequence: GLYMA13G00420.1 (Glycine max), 3'ss of exon 24
gtatgatctcaagaaatcatgtcattccttaattgtagaatattggctccacataccacactaattgaagtgctgtgtgattatatttatagGTCATGGGAAGGTCTTCTCCAAATGACAAGCTTCTTCTTGTGCAAGCATTGAAAAAGAAAGGGCATGTTGTTGCTGTAACTGGAGATGGAACTAATGATG
|||| ||| ||| |||| ||  ||  ||||| |  |  |||  ||  |   || |  | | ||| ||     || ||  ||     | |||||| |||||| |||| ||||| |||||||||||| | ||||||||||||||||  | ||| ||||||||||| |||||||||||||||||||| |||||||
gtataatc-caacaaat-ataacag-ccttagtgatgtaat--tgtttgggca-atgagattaagtgt----ctatgctatg----taatagGTTATGGGACGGTCATCTCCTAATGACAAGCTTTTGCTTGTGCAAGCATTGAGGAGGAAGGGGCATGTTGTGGCTGTAACTGGAGATGGAACAAATGATG

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 26
lower sequence: GLYMA17G06520.1 (Glycine max), 3'ss of exon 26
gtatgatctcaagaaatcatgtcattccttaattgtagaatattggctccacataccacactaattgaagtgctgtgtgattatatttatagGTCATGGGAAGGTCTTCTCCAAATGACAAGCTTCTTCTTGTGCAAGCATTGAAAAAGAAAGGGCATGTTGTTGCTGTAACTGGAGATGGAACTAATGATG
|||| |||      ||  ||   |  |||||    |  ||   ||  |  |||      ||||  | |||||   | ||  ||| |  |||||| |||||| |||| ||||| |||||||||||| | ||||||||||||||||  | ||| ||||||||||| |||||||||||||||||||| || ||||
gtataatcc-----aactata--aagccttagcgatgtaac--tgtttggaca------actagattaagtgtc-tatg-ctatgta-atagGTTATGGGACGGTCATCTCCTAATGACAAGCTTTTGCTTGTGCAAGCATTGAGGAGGAAGGGGCATGTTGTGGCTGTAACTGGAGATGGAACAAACGATG

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 26
lower sequence: GLYMA15G18180.1 (Glycine max), 3'ss of exon 23
-----gtatgat--ctcaagaaatcatgtcattccttaattgtag-aatattggctccacataccacactaattga-agtgctgtgtgattatatttatagGTCATGGGAAGGTCTTCTCCAAATGACAAGCTTCTTCTTGTGCAAGCATTGAAAAAGAAAGGGCATGTTGTTGCTGTAACTGGAGATGGAACTAATGATG
      |   ||  ||     |  | |||  ||      ||||||   |||   ||  ||| |  ||| | ||||  | | |||||| |        | ||||||||||| |||| ||||| |||||||| ||  | || || ||||||||||  | ||| || |||||||| ||||||||||| |||||||| |||||||
gtagaatccaattactatgacaggcttgtttttgtgctcttgtagtggtatgttctttacaaataacatttattgccaatactgtgttaa-------acagGTCATGGGACGGTCATCTCCCAATGACAAACTATTGCTAGTACAAGCATTGAGGAGGAAGGGTCATGTTGTGGCTGTAACTGGGGATGGAACAAATGATG

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 26
lower sequence: GLYMA09G06890.1 (Glycine max), 3'ss of exon 23
--------gtatgatctcaagaaatca--tgtcattccttaattgtagaatattggctccacataccacactaattga-agtgctgtgtgattatatttatagGTCATGGGAAGGTCTTCTCCAAATGACAAGCTTCTTCTTGTGCAAGCATTGAAAAAGAAAGGGCATGTTGTTGCTGTAACTGGAGATGGAACTAATGATG
          || |  |  | |       | |  | |  |  |  ||| || ||   |  | | |  ||| | ||||  | | |||||| |        | ||||||||||| |||| ||||| |||||||| ||  |  | || ||||||||||  | ||| || |||||||| ||||||||||| |||||||| |||||||
gtagaattcaattactttgacaggcttgtttttgtgctcttgtattagtatgttctttgtaaa-ataacatttattgccaatactgtgtaaa-------acagGTCATGGGACGGTCATCTCCCAATGACAAACTATTGTTAGTACAAGCATTGAGGAGGAAGGGTCATGTTGTGGCTGTAACTGGGGATGGAACAAATGATG

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|110712227|gb|EE089604.1|EE089604
EST:     TTCGTGCCTTACCTGAATTGCAAAGACAGGATATTGCTGATAAGATATCG                         GTCATGGGAAGGTCTTCTCCAAATGACAAGCTTCTTCTTGTGCAAGCATTG
genomic: TTCGTGCCTTACCTGAATTGCAAAGACAGGATATTGCTGATAAGATATCGgtatgatctc ... atatttatagGTCATGGGAAGGTCTTCTCCAAATGACAAGCTTCTTCTTGTGCAAGCATTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatattggctccacataccacactaattgaagtgctgtgtgattatatttatagGTCATGGGAAGGTCTTCTCCAAATGACAAGCTTCTTCTTGTGCAAGCATTGAAAAAGAAAGGGCATGTTGTTGCTGTAACTGGAGATGGAACTAATGATG
                     cactaat  putative branch site (score: 2)
                                      tgtgattatatttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatctcaagaaatcatgtcattccttaattgtagaatattggctccacataccacactaattgaagtgctgtgtgattatatttatagGTCATGGGAAGGTCTTCTCCAAATGACAAGCTTCTTCTTGTGCAAGCATTGAAAAAGAAAGGGCATGTTGTTGCTGTAACTGGAGATGGAACTAATGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA