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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttaccttcttcagtagtgttataatttcttttgcattatgttattcatggggctgtcagtttggtgaaggtattgattacactggacaccgcattaagtctttcgtattgcaaatattggttttgcagCTAACTCAGGATATGGGAATTGAGCCTCCTATACCTATCAGTGCAAAGTTGGGAGATTTCAATACCATATTCCGTAGGATTATTGCTGCAGCTGAACATC

Basic information

species Vitis vinifera
transcript Vv14s0128g00400.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0128g00400.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA20G37730.1 (Glycine max), 3'ss of exon 12
gtatttaccttcttcagtagtgttataatttcttttgcattatgttattcatggggctgtcagtttggtgaaggtattgattacactggacaccgcattaagtctttcgtattgcaaatattggttttgcagCTAACTCAGGATATGGGAATTGAGCCTCCTATACCTATCAGTGCAAAGTTGGGAGATTTCAATACCATATTCCGTAGGATTATTGCTGCAGCTGAACATC
                              |   ||| |  | ||  |   ||  ||||  |  ||    |     |   |||   |||| |       | |||  | |   ||  ||| |  |||||| || | | ||| ||||||||| ||||| ||||||||||||||||||  || || ||||||||||| |   | |||||||  ||| |  | || ||||| ||||
-----------------------------atgaattgtaacaagt-gtggttgatgctgagaaattttcaagcaactaatttattatggataaattgcaatgtcacttggcatgtcaatgt--gttttgtagGTTAGTCAAGATATGGGAGTTGAGGCTCCTATACCTATCAGTGTGAAATTAGGAGATTTCAACAGTCTGTTCCGTAAAATTGTAACGGCTGCTGAGCATC
















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|110391490|gb|EC956469.1|EC956469
EST:     CGAAAGATGATCTGGATCCTTATCCGATGGCAATACACGATTCAACAAGG                         CTAACTCAGGATATGGGAATTGAGCCTCCTATACCTATCAGTGCAAAGTTG
genomic: CGAAAGATGATCTGGATCCTTATCCGATGGCAATACACGATTCAACAAGGgtatttacct ... ggttttgcagCTAACTCAGGATATGGGAATTGAGCCTCCTATACCTATCAGTGCAAAGTTG
EST: gi|161707836|gb|FC055236.1|FC055236
EST:     CGAAAGATGATCTGGATCCTTATCCGATGGCAATACACGATTCAACAAGG                         CTTACTCAGGATATGGGAATTGAGCCTCCTATACCTATCAGTGCAAAGTTG
genomic: CGAAAGATGATCTGGATCCTTATCCGATGGCAATACACGATTCAACAAGGgtatttacct ... ggttttgcagCTAACTCAGGATATGGGAATTGAGCCTCCTATACCTATCAGTGCAAAGTTG
EST: gi|33406468|gb|CF212095.1|CF212095
EST:     CGAAAGATGATCTGGATCCTTATCCGATGGCAATACACGATTCAACAAGG                         CTTACTCAGGATATGGGAATTGAGCCTCCTATACCTATCAGTGNAAAGTTG
genomic: CGAAAGATGATCTGGATCCTTATCCGATGGCAATACACGATTCAACAAGGgtatttacct ... ggttttgcagCTAACTCAGGATATGGGAATTGAGCCTCCTATACCTATCAGTGCAAAGTTG
EST: gi|33406387|gb|CF212014.1|CF212014
EST:     GATTCAACAAGG                         CTTACTCAGGATATGGGAATTGAGCCTCCTATACCTATCAGTGCAAAGTTG
genomic: GATTCAACAAGGgtatttacct ... ggttttgcagCTAACTCAGGATATGGGAATTGAGCCTCCTATACCTATCAGTGCAAAGTTG
EST: gi|110399392|gb|EC965896.1|EC965896
EST:     CGAAAGATGATCTGGATCCTTATCCGATGGCAATACACGATTCAACAAGG                         CTAACTCAGGATATGGGAATTGAGCCTCCTATACCTATCAGTGCAAAGTTG
genomic: CGAAAGATGATCTGGATCCTTATCCGATGGCAATACACGATTCAACAAGGgtatttacct ... ggttttgcagCTAACTCAGGATATGGGAATTGAGCCTCCTATACCTATCAGTGCAAAGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattacactggacaccgcattaagtctttcgtattgcaaatattggttttgcagCTAACTCAGGATATGGGAATTGAGCCTCCTATACCTATCAGTGCAAAGTTGGGAGATTTCAATACCATATTCCGTAGGATTATTGCTGCAGCTGAACATC
 tattgat  putative branch site (score: 3)
                                      aaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttaccttcttcagtagtgttataatttcttttgcattatgttattcatggggctgtcagtttggtgaaggtattgattacactggacaccgcattaagtctttcgtattgcaaatattggttttgcagCTAACTCAGGATATGGGAATTGAGCCTCCTATACCTATCAGTGCAAAGTTGGGAGATTTCAATACCATATTCCGTAGGATTATTGCTGCAGCTGAACATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA