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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtagcatttcttaaaaccacattagccaagacatttttttctcattgccatcatgggagaatgcttcactcctgtttaccctgctaatcaccggtgaatctacagGATTATACAGCCAAGCTTTCTGACTTTGGGCTTGCAAAAGCTGGACCACAAGGTGATGAGACCCATGTATCAACTCGTGTAATGGGTACCTATGGTTATG

Basic information

species Vitis vinifera
transcript Vv08s0056g00150.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0056g00150.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os11g02830.2 (Oryza sativa), 3'ss of exon 4
-gtaagtagcatttcttaaaaccacattagccaagacatttttttctcattgccatcatgggagaatgcttcactcctgtttaccctgctaatcaccggtgaatc-------tacagGATTATACAGCCAAGCTTTCTGACTTTGGGCTTGCAAAAGCTGGACCACAAGGTGATGAGACCCATGTATCAACTCGTGTAATGGGTACCTATGGTTATG
  | |||||||||||||   |  |  ||           ||| |  ||  |||     | || ||||   | | |  | || |   |   | | | |  | | |         |||||||||||| || || || ||||||||||| || ||||||||||| ||| |||| ||| | ||||||||||||||||| || ||||| || ||||||||||
gttgagtagcatttcttgccaatatcttgttttttttcctttctcttctatgcatctgttgg-gaatatgtaaatatttttcataatagcatttatcttttatttgcacttacacagGATTATACTGCTAAACTCTCTGACTTTGGTCTGGCAAAAGCTGGCCCAGAAGGCGATCAAACCCATGTATCAACTCGGGTGATGGGAACATATGGTTATG

upper sequence: Vv08s0056g00150.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os12g02810.1 (Oryza sativa), 3'ss of exon 4
-gtaagtagcatttcttaaaaccacattagccaagacatttttttctcattgccatcatgggagaatgcttcactcctgtttaccctgctaatcaccggtgaatc-------tacagGATTATACAGCCAAGCTTTCTGACTTTGGGCTTGCAAAAGCTGGACCACAAGGTGATGAGACCCATGTATCAACTCGTGTAATGGGTACCTATGGTTATG
  | |||||||||||||   |     || |        ||  |||||| |        | || ||||   | | |  | || |   |   | | | |  | | |         |||||||||||| || || || ||||||||||| || ||||||||||| ||| |||| ||| | |||||||||||||| || || ||||| || ||||||||||
gttgagtagcatttcttgtcaatgtctt-gttttttttttcctttctcttctatgctgttgg-gaatatgtaaatatttttcataataacatttatcttttatttacacttacacagGATTATACTGCTAAACTCTCTGACTTTGGTCTGGCAAAAGCTGGCCCAGAAGGCGATCAAACCCATGTATCAACACGGGTGATGGGAACATATGGTTATG

upper sequence: Vv08s0056g00150.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G007283_T02 (Zea mays), 3'ss of exon 4
-----gtaagtagcatttcttaaaaccacattagccaagacatttttttctcattgccatcatgggagaatgcttcactcctgtttaccctgctaatc-----accggtgaatctacagGATTATACAGCCAAGCTTTCTGACTTTGGGCTTGCAAAAGCTGGACCACAAGGTGATGAGACCCATGTATCAACTCGTGTAATGGGTACCTATGGTTATG
     ||    | || ||| | |  |  | ||  ||      |||   |  |||||| |||||   |   |  | ||    |||||  | |  | |||           |   | |||||||||||| || ||||| ||||||||||| || ||||||||||| ||  |||||||| |||||||||||||||| || || ||||| ||||| |||||||
gttgagtgttaaccacttcctcatgcttccttctcc----tttttcagttccattgctatcatccaatggtaatacatatatgtttgacatatttatcttcttgtttccgttgccacagGATTATACTGCTAAGCTGTCTGACTTTGGCCTGGCAAAAGCTGGCCCTGAAGGTGATCAGACCCATGTATCAACACGGGTGATGGGAACCTACGGTTATG

upper sequence: Vv08s0056g00150.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G099754_T01 (Zea mays), 3'ss of exon 4
-----gtaagtagcatttcttaaaaccacattagccaagacatttttttctcattgccatcatgggagaatgcttcactcctgtttaccctgctaatcaccggtgaatctacagGATTATACAGCCAAGCTTTCTGACTTTGGGCTTGCAAAAGCTGGACCACAAGGTGATGAGACCCATGTATCAACTCGTGTAATGGGTACCTATGGTTATG
     ||    | || ||  |    ||   | ||      |  |    ||  || |  ||   |     ||| || ||   | |||| | | ||  |  ||     | |  ||||||||||| ||||| || ||||||||||| || ||||||| ||| ||  |||||||| |||| ||||| || || || || ||||| ||||| |||||||
gttgagtgccaatcactttcttctcccttttcagttctatcgataccatccaatgggaat---gcacatatgtttgaca--tatttatcttcctgtttcccatc--acccgcagGATTATACTGCCAAACTGTCTGACTTTGGCCTCGCAAAAGATGGCCCTGAAGGTGATCAGACGCATGTGTCGACACGGGTGATGGGAACCTACGGTTATG

upper sequence: Vv08s0056g00150.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA09G40650.1 (Glycine max), 3'ss of exon 4
gtaagtagc--atttcttaaaaccacattagccaagacatttttttctcattgccatcatgggagaatgcttcactcctgtttaccctgctaatcaccggtgaatctacagGATTATACAGCCAAGCTTTCTGACTTTGGGCTTGCAAAAGCTGGACCACAAGGTGATGAGACCCATGTATCAACTCGTGTAATGGGTACCTATGGTTATG
||||||  |  || | || ||   | ||||  |   |   || | | | || ||  | |||   || |   | | |  | || ||  || |   | |   |||  ||| |||| ||||||||||| |||||||| ||||| || || ||||| ||||||||||||||||| ||||||||||| || || || |||||||||||||||||||
gtaagtttctgatattttgaagtta-attaatctgta---ttgtattttatggctgttatgatggagttact-attttttttcactgtgtt---cccaaatga--ctatagGACTATACAGCCAAACTTTCTGATTTTGGACTAGCTAAAGCAGGACCACAAGGTGATGAAACCCATGTATCTACCCGAGTCATGGGTACCTATGGTTATG

upper sequence: Vv08s0056g00150.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA18G45200.1 (Glycine max), 3'ss of exon 4
-gtaagtagc--atttcttaaaaccacattagccaagacatttttttctcattgccatcatgggagaatgcttcactcctgtttaccctgctaatcaccggtgaatctacagGATTATACAGCCAAGCTTTCTGACTTTGGGCTTGCAAAAGCTGGACCACAAGGTGATGAGACCCATGTATCAACTCGTGTAATGGGTACCTATGGTTATG
 ||||||  |   | | || ||   | ||||  |       || | | |  | ||  | ||   | | |   | | |  | ||| | ||| |  || |   ||| | || |||| ||||||||||| |||||||| ||||| || || ||||| ||||||||||||||||| ||||||||||| || || || |||||||| ||||||||| 
cgtaagtttctggtattttgaagtta-attaatctgtg---ttgtattttgtggctgttataaaatagttactaattatttttttcactg-tgttcccaaatgactgtataGGACTATACAGCCAAACTTTCTGATTTTGGACTAGCTAAAGCAGGACCACAAGGTGATGAAACCCATGTATCCACCCGAGTGATGGGTACATATGGTTAT-

upper sequence: Vv08s0056g00150.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G01020.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagtagc-atttcttaaaaccacattagccaagacatttttttctcattgccatcatgggagaatgcttcactcctgtt-taccctgctaatcaccggtgaatctacagGATTATACAGCCAAGCTTTCTGACTTTGGGCTTGCAAAAGCTGGACCACAAGGTGATGAGACCCATGTATCAACTCGTGTAATGGGTACCTATGGTTATG
||||| ||  |||  ||     |   || |||||        || |||   |  ||   || | |    | |||  ||  | || |||        | | |||| || ||||| || || ||||||||||| || |||||  | || ||||||||||| || |||||||| ||||||||||||||||| || |||||||| ||||| ||||
gtaagcagttattcttttctttctgctttgccaaag------ttgctccaagatattg-ggaatacctttccacaactaatatatccttgattgggctgatgaaccttcagGACTACACCGCCAAGCTTTCAGATTTTGGCTTAGCTAAAGCTGGACCCCAGGGTGATGAAACCCATGTATCAACTCGAGTTATGGGTACTTATGGCTATG

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|110370255|gb|EC929228.1|EC929228
EST:     GGCCTGTAATCTATCGGGACTTCAAAACGTCTAATATATTATTAGACTCT                         GATTATACAGCCAAGCTTTCTGACTTTGGGCTTGCAAAAGCTGGACCACAA
genomic: GGCCTGTAATCTATCGGGACTTCAAAACGTCTAATATATTATTAGACTCTgtaagtagca ... gaatctacagGATTATACAGCCAAGCTTTCTGACTTTGGGCTTGCAAAAGCTGGACCACAA
EST: gi|351019747|gb|FQ439564.1|FQ439564
EST:     GGCCTGTAATCTATCGGGACTTCAAAACGTCTAATATATTATTAGACTCT                         GATTATACAGCCAAGCTTTCTGACTTTGGGCTTGCAAAAGCTGGACCACAA
genomic: GGCCTGTAATCTATCGGGACTTCAAAACGTCTAATATATTATTAGACTCTgtaagtagca ... gaatctacagGATTATACAGCCAAGCTTTCTGACTTTGGGCTTGCAAAAGCTGGACCACAA
EST: gi|110696363|gb|EE072413.1|EE072413
EST:     GGCCTGTAATCTATCGGGACTTCAAAACGTCT-A-ATATTATTAGACTCT                         GATTATACAGCCAAGCTTTCTGACTTTGGGCTTGCAAAAGCTGGACCACAA
genomic: GGCCTGTAATCTATCGGGACTTCAAAACGTCTAATATATTATTAGACTCTgtaagtagca ... gaatctacagGATTATACAGCCAAGCTTTCTGACTTTGGGCTTGCAAAAGCTGGACCACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatgggagaatgcttcactcctgtttaccctgctaatcaccggtgaatctacagGATTATACAGCCAAGCTTTCTGACTTTGGGCTTGCAAAAGCTGGACCACAAGGTGATGAGACCCATGTATCAACTCGTGTAATGGGTACCTATGGTTATG
                               tgctaat  putative branch site (score: 2)