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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTACAGTGTCTCATGATCGATACTTCATAAAGCAAATAGTTAATAGAGTAATTGAAGTTAAGGATGGGAATTTACAAGACTATGCAGGAGATTACAATgtaagtgtgacctcactccaatttaaacttcttgcatcattttatcacccttttattatttttgtttttaagaaaattggcatgttaggctttagctaat...

Basic information

species Vitis vinifera
transcript Vv07s0031g01640.t01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0031g01640.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: LOC_Os11g39020.1 (Oryza sativa), 5'ss of exon 7
TGTTACAGTGTCTCATGATCGATACTTCATAAAGCAAATAGTTAATAGAGTAATTGAAGTTAAGGATGGGAATTTACAAGACTATGCAGGAGATTACAATgtaagtgtgacctcactccaatttaaacttcttg-catcattttatcaccctt--ttattatttttgtttttaagaaaattggcatgttaggctttagctaat--
| | ||||| |||||||| || || ||| |||||||||| ||||| ||||| |||||||| || |||  || | | || ||||||  ||||||||||||||| |||         ||   || |||  | ||    || | |||   |||  |  ||  | | || |  |  || |   ||  |   |   | ||    || |  
TATAACAGTTTCTCATGACCGGTATTTCGTAAAGCAAATTGTTAACAGAGTTATTGAAGTGAAAGATCAGACTATTCAGGACTATCAAGGAGATTACAATgtgagt-----tatcctgtgatataagttactcaatattactttgcaacctgtatttgctgtattcgagtgaaatatggttaactcttcttgattataatagttt

upper sequence: Vv07s0031g01640.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G105570_T01 (Zea mays), 5'ss of exon 7
TGTTACAGTGTCTCATGATCGATACTTCATAAAGCAAATAGTTAATAGAGTAATTGAAGTTAAGGATGGGAATTTACAAGACTATGCAGGAGATTACAATgtaagtgtgacctcactccaatttaaacttcttgcatcattttatcacccttttattatttttgtttttaagaaaattggcatgttaggctttagctaat-
  | ||||| |||||||| || ||||||||||| ||||| || || ||||| || ||||| || |||  || | | |||||||||  ||||||||||||||| ||     |  |  ||  ||     | ||    ||  ||||   | | | | |||    | |   | ||  |   ||   | || |  | || |   | 
CATAACAGTTTCTCATGACCGGTACTTCATAAAACAAATTGTCAACAGAGTCATCGAAGTGAAAGATCAGACTATCCAAGACTATCAAGGAGATTACAATgtgagctgtcctacggtcttatactttcctcagctatggttttcagatc-tctgattccaatgggaatgaaatatgctgaactctttgcatataacagttc

upper sequence: Vv07s0031g01640.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA06G15200.1 (Glycine max), 5'ss of exon 7
TGTTACAGTGTCTCATGATCGATACTTCATAAAGCAAATAGTTAATAGAGTAATTGAAGTTAAGGATGGGAATTTACAAGACTATGCAGGAGATTACAATgtaagtgtgacctcactccaatttaaacttcttgcatcattttatcacccttttattatttttgtttttaagaaaattggcatgttaggctttag--ctaat
| | ||||| |||||||| |||||||| ||||||||||||||||||||||| || ||| |||| ||||| | | |||| || |||||||| |||||| |||||||| | | |   | |    |      |||| |   |   | ||      | |||   | || |  ||   || ||    | |||   || ||  |||  
TATCACAGTATCTCATGACCGATACTTTATAAAGCAAATAGTTAATAGAGTGATAGAAATTAAAGATGGCACTATACAGGATTATGCAGGTGATTACGATgtaagt-taatcaatcccttggtctcttctcttaccctaccctttctgtgactcattgagtgtgatagtatacaatttattgttttatatttcaggactag-

upper sequence: Vv07s0031g01640.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA04G39670.1 (Glycine max), 5'ss of exon 7
TGTTACAGTGTCTCATGATCGATACTTCATAAAGCAAATAGTTAATAGAGTAATTGAAGTTAAGGATGGGAATTTACAAGACTATGCAGGAGATTACAATgtaagtgtgacctcactccaatttaaacttcttgcatcattttatcacccttttattatttttgtttttaagaaaattggcatgt---taggctttagctaat
| | ||||| |||||||| |||||||| ||||||||||||||||||||||| || ||| |||| ||||| |   |||| || |||||||| |||||| |||||||| | | |   | |    |      |||| |   |   | ||      | |||   | || |  ||   || ||    | |   ||   |||||   ||
TATCACAGTATCTCATGACCGATACTTTATAAAGCAAATAGTTAATAGAGTGATAGAAATTAAAGATGGCACCATACAGGATTATGCAGGTGATTACGATgtaagt-taatcgatcccttgatctcttctcttaccctaccctttctgtggctcattgagtgtgatagtatacaatttattttatttttatattttag--gat

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|37190151|gb|CF609500.1|CF609500
EST:     TAATTGAAGTTAAGGATGGGAATTTACAAGACTATGCAGGAGATTACAAT                         TATTATCTGGAGAAGAACCTCGATGCAAGAGCAAGAGAGCTTGAACGCGAG
genomic: TAATTGAAGTTAAGGATGGGAATTTACAAGACTATGCAGGAGATTACAATgtaagtgtga ... aatgtcacagTATTATCTGGAGAAGAACCTCGATGCAAGAGCAAGAGAGCTTGAACGCGAG
EST: gi|110391761|gb|EC956761.1|EC956761
EST:     TAATTGAAGTTAAGGATGGGAATTTACAAGACTATGCAGGAGATTACAAT                         TATTATCTGGAGAAGAACCTCGATGCAAGAGCAAGAGAGCTTGAACGCGAG
genomic: TAATTGAAGTTAAGGATGGGAATTTACAAGACTATGCAGGAGATTACAATgtaagtgtga ... aatgtcacagTATTATCTGGAGAAGAACCTCGATGCAAGAGCAAGAGAGCTTGAACGCGAG
EST: gi|56409612|gb|CX017864.1|CX017864
EST:     TAATTGAAGTTAAGGATGGGAATTTACAAGACTATGCAGGAGATTACAAT                         TATTATCTGGAGAAGAACCTCGATGCAAGAGCAAGAGAGCTTGAACGCGAG
genomic: TAATTGAAGTTAAGGATGGGAATTTACAAGACTATGCAGGAGATTACAATgtaagtgtga ... aatgtcacagTATTATCTGGAGAAGAACCTCGATGCAAGAGCAAGAGAGCTTGAACGCGAG
EST: gi|352772399|gb|FQ469924.1|FQ469924
EST:     TAATTGAAGTTAAGGATGGGAATTTACAAGACTATGCAGGAGATTACAAT                         TATTATCTGGAGAAGAACCTCGATGCAAGAGCAAGAGAGCTTGAACGCGAG
genomic: TAATTGAAGTTAAGGATGGGAATTTACAAGACTATGCAGGAGATTACAATgtaagtgtga ... aatgtcacagTATTATCTGGAGAAGAACCTCGATGCAAGAGCAAGAGAGCTTGAACGCGAG
EST: gi|26261553|gb|CA812616.1|CA812616
EST:     TAATTGAAGTTAAGGATGGGAATTTACAAGACTATGCAGGAGATTACAAT                         TATTATCTGGAGAAGAACCTCGATGCAAGAGCAAGAGAGCTTGAACACGAG
genomic: TAATTGAAGTTAAGGATGGGAATTTACAAGACTATGCAGGAGATTACAATgtaagtgtga ... aatgtcacagTATTATCTGGAGAAGAACCTCGATGCAAGAGCAAGAGAGCTTGAACGCGAG
EST: gi|27755077|gb|CB035832.1|CB035832
EST:     TAATTGAAGTTAAGGATGGGAATTTACAAGACTATGCAGGAGATTACAAT                         TATTATCTGGAGAAGAACCTCGATGCAAGAGCAAGAGAGCTTGAACGCGAG
genomic: TAATTGAAGTTAAGGATGGGAATTTACAAGACTATGCAGGAGATTACAATgtaagtgtga ... aatgtcacagTATTATCTGGAGAAGAACCTCGATGCAAGAGCAAGAGAGCTTGAACGCGAG
EST: gi|30301899|gb|CB978693.1|CB978693
EST:     TAATTGAAGTTAAGGATGGGAATTTACAAGACTATGCAGGAGATTACAAT                         TATTATCTGGAGAAGAACCTCGATGCAAGAGCAAGAGAGCTTGAACGCGAG
genomic: TAATTGAAGTTAAGGATGGGAATTTACAAGACTATGCAGGAGATTACAATgtaagtgtga ... aatgtcacagTATTATCTGGAGAAGAACCTCGATGCAAGAGCAAGAGAGCTTGAACGCGAG
EST: gi|32248178|gb|CD713997.1|CD713997
EST:     TAATTGAAGTTAAGGATGGGAATTTACAAGACTATGCAGGAGATTACAAT                         TATTATCTGGAGAAGAACCTCGATGCAAGAGCAAGAGAGCTTGAACGCGAG
genomic: TAATTGAAGTTAAGGATGGGAATTTACAAGACTATGCAGGAGATTACAATgtaagtgtga ... aatgtcacagTATTATCTGGAGAAGAACCTCGATGCAAGAGCAAGAGAGCTTGAACGCGAG
EST: gi|30135054|gb|CB920392.1|CB920392
EST:     TAATTGAAGTTAAGGATGGGAATTTACAAGACTATGCAGGAGATTACAAT                         TATTATCTGGAGAAGAACCTCGATGCAAGAGCAAGAGAGCTTGAACGCGAG
genomic: TAATTGAAGTTAAGGATGGGAATTTACAAGACTATGCAGGAGATTACAATgtaagtgtga ... aatgtcacagTATTATCTGGAGAAGAACCTCGATGCAAGAGCAAGAGAGCTTGAACGCGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTACAGTGTCTCATGATCGATACTTCATAAAGCAAATAGTTAATAGAGTAATTGAAGTTAAGGATGGGAATTTACAAGACTATGCAGGAGATTACAATgtaagtgtgacctcactccaatttaaacttcttgcatcattttatcacccttttattatttttgtttttaagaaaattggcatgttaggctttagctaat

- - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcactcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagaaaa