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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGACAAGTCCATCAAAATTGCAGACTTTGGGGTTGCTCGAATAGAGGTGCAAACAGAAGGAATGACACCAGAGACAGGGACATACCGCTGGATGGCCCCgtaagccttttgattcttttcctgtctagatttgtctttagtttttcattactctcttttaaaattcactgggatgctttgcaatctcttgatttgtggt...

Basic information

species Vitis vinifera
transcript Vv11s0065g00140.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0065g00140.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os06g45300.1 (Oryza sativa), 5'ss of exon 2
CAGACAAGTCCATCAAAATTGCAGACTTTGGGGTTGCTCGAATAGAGGTGCAAACAGAAGGAATGACACCAGAGACAGGGACATACCGCTGGATGGCCCCgtaagccttt-tgattcttttcctgtc-tagatttgtctttagtttttcattactctcttttaaaattcactgggatgctttgcaatctcttgatttgtggt
||||||| |||||||| || || |||||||| ||||||||||| ||||| ||||| || |||||||| ||||||||||| || ||||| |||||||| ||||||| | |  | |  | ||  |  || | |  |  | ||||  |||| |  | ||||| | ||| |   ||    |   |||| |||              
CAGACAAATCCATCAAGATAGCTGACTTTGGAGTTGCTCGAATTGAGGTACAAACTGAGGGAATGACCCCAGAGACAGGAACCTACCGTTGGATGGCACCgtaagtcataatcacgcattcacgctcattgcctactgtttaccttttta--aatctctgtcaaa-tatgct----tatcttgccatcatgcag--------

upper sequence: Vv11s0065g00140.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os02g07790.1 (Oryza sativa), 5'ss of exon 2
CAGACAAGTCCATCAAAATTGCAGACTTTGGGGTTGCTCGAATAGAGGTGCAAACAGAAGGAATGACACCAGAGACAGGGACATACCGCTGGATGGCCCCgtaagccttttgattcttttcctgtctagatttgtctttagtttttcattactctcttttaaaattcactgggatgctttgcaatctcttgatttgtggt--
|||| || ||||| || ||||| |||||||| || ||||| || || ||  |||| || || ||||||||||||||||| || |||||||||||||| |||||||   | |  | |  |   | | |   | |  || |  | |||   ||  |    | |    |  ||   ||   ||||||   ||| | ||  |    
CAGATAAATCCATTAAGATTGCTGACTTTGGAGTGGCTCGCATCGAAGTAAAAACTGAGGGTATGACACCAGAGACAGGAACCTACCGCTGGATGGCACCgtaagttatatattcccctgtttatttttttctccctgtgttatttgtatatgccaactcatgtatagctt--atcacttgcaaggacttcactttagaatg

upper sequence: Vv11s0065g00140.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os08g12750.1 (Oryza sativa), 5'ss of exon 2
CAGACAAGTCCATCAAAATTGCAGACTTTGGGGTTGCTCGAATAGAGGTGCAAACAGAAGGAATGACACCAGAGACAGGGACATACCGCTGGATGGCCCCgtaagccttttgattcttttcctgtctagatttgtctttagtttttcattactctcttttaaaattca--ctgggatgctttgcaatctcttgatttgtggt-
 |||||| || ||||| ||||| |||||||| || ||| | || || ||| | || || ||||||||||| || ||||| || |||||||||||||| |||||||       |     |   | ||| | ||    |||| |   | ||||       ||   ||| |  |   | || |||    | |||| | | |   | 
GAGACAAATCTATCAAGATTGCTGACTTTGGAGTGGCTAGGATTGAAGTGAAGACTGAGGGAATGACACCTGAAACAGGAACTTACCGCTGGATGGCTCCgtaagttggcatacatgctctttatcttgctta--ttttaatcagtaattatctcaaattcgtattaagacaatgctgttttatt-tttcttcactcggcatt

upper sequence: Vv11s0065g00140.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA08G03010.2 (Glycine max), 5'ss of exon 3
CAGACAAGTCCATCAAAATTGCAGACTTTGGGGTTGCTCGAATAGAGGTGCAAACAGAAGGAATGACACCAGAGACAGGGACATACCGCTGGATGGCCCCgtaagccttttgattcttttcctgtctagatttgtctttagtttttcat-tactctcttttaaaattcactgggatgctttgcaatctcttgatttgtggt--
  |||||||| || |||||||| |||||||| |||||||| || ||||||||||| |||||||||||||| ||||| || |||||||| |||||||| |||||||    ||   | || || | | |   | |   | || ||||  ||  | |||   ||    ||      |||  || |  | ||  |   || ||||  
GTGACAAGTCAATTAAAATTGCTGACTTTGGAGTTGCTCGTATTGAGGTGCAAACTGAAGGAATGACACCTGAGACTGGAACATACCGTTGGATGGCTCCgtaagatcatttgctattctctttttt---tatacttataattttatatgcattctagcttcttttttggaatgatttttggagagcttctcgattatggtta

upper sequence: Vv11s0065g00140.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA05G36540.2 (Glycine max), 5'ss of exon 2
CAGACAAGTCCATCAAAATTGCAGACTTTGGGGTTGCTCGAATAGAGGTGCAAACAGAAGGAATGACACCAGAGACAGGGACATACCGCTGGATGGCCCCgtaag-ccttttgattcttttcctgtctagatttgtctttagtttttcat-tactctcttttaaaattcactgggatgctttgcaatctcttgatttgtggt
  |||||||| || |||||||| |||||||| ||||| || || ||||||||||| |||||||||||||| ||||| || |||||||| |||||||| |||||||  |||||| |  | |  || | || |||| | |  ||||||  ||  | |||   || |  ||      |||  || |  | ||  |   || ||||
GTGACAAGTCAATTAAAATTGCTGACTTTGGAGTTGCCCGTATTGAGGTGCAAACTGAAGGAATGACACCTGAGACTGGAACATACCGTTGGATGGCTCCgtaagatcttttgctgttctctctttttatatttatat--agttttatatgcattctagcttcatttttggaatgatttttggagagcttctctattatggt

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|110718294|gb|EE094959.1|EE094959
EST:     CAAACAGAAGGAATGACACCAGAGACAGGGACATACCGCTGGATGGCCCC                         GGAGATGATCCAGCACAGGCCTTACACACAGAGAGTCGACGTGTATAGCTT
genomic: CAAACAGAAGGAATGACACCAGAGACAGGGACATACCGCTGGATGGCCCCgtaagccttt ... caacctgcagGGAGATGATCCAGCACAGGCCTTACACACAGAAAGTCGACGTGTATAGCTT
EST: gi|351015785|gb|FQ431740.1|FQ431740
EST:     CAAACAGAAGGAATGACACCAGAGACAGGGACATACCGCTGGATGGCCCC                         GGAGATGATCCAGTACAGGCCTTACACACAGAAAGTCGACGTGTATAGCTT
genomic: CAAACAGAAGGAATGACACCAGAGACAGGGACATACCGCTGGATGGCCCCgtaagccttt ... caacctgcagGGAGATGATCCAGCACAGGCCTTACACACAGAAAGTCGACGTGTATAGCTT
EST: gi|34548487|gb|CF516719.1|CF516719
EST:     CAAACAGAAGGAATGACACCAGAGACAGGGACATACCGCTGGATGGCCCC                         GGAGATGATCCAGCACAGGCCTTACACACAGAAAGTCGACGTGTATAGCTT
genomic: CAAACAGAAGGAATGACACCAGAGACAGGGACATACCGCTGGATGGCCCCgtaagccttt ... caacctgcagGGAGATGATCCAGCACAGGCCTTACACACAGAAAGTCGACGTGTATAGCTT
EST: gi|110419425|gb|EC985649.1|EC985649
EST:     CAAACAGAAGGAATGACACCAGGGACAGGGACATACCGCTGGATGGCCCC                         GGAGATGATCCAGCACAGGCCTTACACACAGAAAGTCGACGTGTATAGCTT
genomic: CAAACAGAAGGAATGACACCAGAGACAGGGACATACCGCTGGATGGCCCCgtaagccttt ... caacctgcagGGAGATGATCCAGCACAGGCCTTACACACAGAAAGTCGACGTGTATAGCTT
EST: gi|110730189|gb|EE106985.1|EE106985
EST:     CAAACAGAAGGAATGACACCAGAGACAGGGACATACCGCTGGATGGCCCC                         GGAGATGATCCAGCACAGGCCTTACACACAGAAAGTCGACGTGTATAGCTT
genomic: CAAACAGAAGGAATGACACCAGAGACAGGGACATACCGCTGGATGGCCCCgtaagccttt ... caacctgcagGGAGATGATCCAGCACAGGCCTTACACACAGAAAGTCGACGTGTATAGCTT
EST: gi|351030921|gb|FQ438957.1|FQ438957
EST:     CAAACAGAAGGAATGACACCAGAGACAGGGACATACCGCTGGATGGCCCC                         GGAGATGATCCAGTACAGGCCTTACACACAGAAAGTCGACGTGTATAGCTT
genomic: CAAACAGAAGGAATGACACCAGAGACAGGGACATACCGCTGGATGGCCCCgtaagccttt ... caacctgcagGGAGATGATCCAGCACAGGCCTTACACACAGAAAGTCGACGTGTATAGCTT
EST: gi|34548573|gb|CF516805.1|CF516805
EST:     CAAACAGAAGGAATGACACCAGAGACAGGGACATACCGCTGGATGGCCCC                         GGAGATGATCCAGCACAGGCCTTACACACAGAAAGTCGACGTGTATAGCTT
genomic: CAAACAGAAGGAATGACACCAGAGACAGGGACATACCGCTGGATGGCCCCgtaagccttt ... caacctgcagGGAGATGATCCAGCACAGGCCTTACACACAGAAAGTCGACGTGTATAGCTT
EST: gi|351023295|gb|FQ432678.1|FQ432678
EST:     CAAACAGAAGGAATGACACCAGAGACAGGGACATACCGCTGGATGGCCCC                         GGAGATGATCCAGTACAGGCCTTACACACAGAAAGTCGACGTGTATAGCTT
genomic: CAAACAGAAGGAATGACACCAGAGACAGGGACATACCGCTGGATGGCCCCgtaagccttt ... caacctgcagGGAGATGATCCAGCACAGGCCTTACACACAGAAAGTCGACGTGTATAGCTT
EST: gi|349832844|gb|FQ422966.1|FQ422966
EST:     CAAACAGAAGGAATGACACCAGAGACAGGGACATACCGCTGGATGGCCCC                         GGAGATGATCCAGTACAGGCCTTACACACAGAAAGTCGACGTGTATAGCTT
genomic: CAAACAGAAGGAATGACACCAGAGACAGGGACATACCGCTGGATGGCCCCgtaagccttt ... caacctgcagGGAGATGATCCAGCACAGGCCTTACACACAGAAAGTCGACGTGTATAGCTT
EST: gi|18459681|gb|BM437959.1|BM437959
EST:     CAAACAGAAGGAATGACACCAGAGACAGGGACATACCGCTGGATGGCCCC                         GGAGATGATCCAGCACAGGCCTTACACACAGAAAGTCGACGTGTATAGCTT
genomic: CAAACAGAAGGAATGACACCAGAGACAGGGACATACCGCTGGATGGCCCCgtaagccttt ... caacctgcagGGAGATGATCCAGCACAGGCCTTACACACAGAAAGTCGACGTGTATAGCTT
EST: gi|349812421|gb|FQ407040.1|FQ407040
EST:     CAAACAGAAGGAATGACACCAGAGACAGGGACATACCGCTGGATGGCCCC                         GGAGATGATCCAGTACAGGCCTTACACACAGAAAGTCGGCGTGTATAGCTT
genomic: CAAACAGAAGGAATGACACCAGAGACAGGGACATACCGCTGGATGGCCCCgtaagccttt ... caacctgcagGGAGATGATCCAGCACAGGCCTTACACACAGAAAGTCGACGTGTATAGCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGACAAGTCCATCAAAATTGCAGACTTTGGGGTTGCTCGAATAGAGGTGCAAACAGAAGGAATGACACCAGAGACAGGGACATACCGCTGGATGGCCCCgtaagccttttgattcttttcctgtctagatttgtctttagtttttcattactctcttttaaaattcactgggatgctttgcaatctcttgatttgtggt

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA