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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatgagtcattggtttttttgatgcaatattaatcttaatcttgacctctatggattctatatattgatgacttccttccattattcagGTTTATGCAAAGGTGAGTGGGGAACCTTCTTTGGAGGTACCAACTGTTGATGTAAGCTCCAAAGAATTCTATGGTGAAGGATATGATGACAGTGACAAGA

Basic information

species Vitis vinifera
transcript Vv03s0017g00680.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os01g73790.1 (Oryza sativa), 3'ss of exon 7
gtgaatgagtcattggtttttttgatgcaatattaatcttaatcttgacctctatggattctatatattgatgacttccttccattattcagGTTTATGCAAAGGTGAGTGGGGAACCTTCTTTGGAGGTACCAACTGTTGATGTAAGCTCCAAAGAATTCTATGGTGAAGGATATGATGACAGTGACAAGA
     |   ||||| |  |       ||||| ||  | | |   ||  |   ||   || |  ||  |   | || |  ||    | | ||||| |||||||| ||    || || ||  |  |||| | ||| |   |||| || || || ||  | ||||||||||||||||||||||| ||||| ||||
----gtacatcattagcgtg------gcaatgtttctttgagcgttt-ctgttactcatgccctaagtc--ttacatggttgtcctgtacagGTCTATGCAAATGTCTCAGGAGAGCCACCACTGGATGAACCTATGATTGACGTGAGTTCGAAGCAGTTCTATGGTGAAGGATATGATGATAGTGATAAGA

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA12G30490.1 (Glycine max), 3'ss of exon 7
gtgaatgagtca--ttggtttttttgatgcaatattaatcttaatcttgacctctatggattctatatattgatgacttccttccattattcagGTTTATGCAAAGGTGAGTGGGGAACCTTCTTTGGAGGTACCAACTGTTGATGTAAGCTCCAAAGAATTCTATGGTGAAGGATATGATGACAGTGACAAGA
|| |  |  | |  || | || ||||   | ||   ||| | || | ||   | |  |     |  | ||| ||   ||| ||| ||| | ||||||||| ||||||| ||||| ||| |  || ||||   ||| ||| ||||||| |||||||||||||| |||||||| ||||||||||| ||||||||||
gttagaggattaagtttgattgtttgtacctattagaatttcaa-catggtatttgggaccattcaacatttat--tttcgttcaattctgcagGTTTATTCAAAGGTAAGTGGAGAAGCACCTCTGGAAAAACCTACTATTGATGTGAGCTCCAAAGAATTTTATGGTGAGGGATATGATGATAGTGACAAGA

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA11G19550.2 (Glycine max), 3'ss of exon 6
gtgaatgagtcattggtttttttgatgcaatatta-atcttaatcttgacctctatggattctatatattgatgact-------tccttccattattcagGTTTATGCAAAGGTGAGTGGGGAACCTTCTTTGGAGGTACCAACTGTTGATGTAAGCTCCAAAGAATTCTATGGTGAAGGATATGATGACAGTGACAAGA
 |||   | |  ||  | || |      | | ||| |  |||  | ||   |    ||| |  ||  ||  ||   |       |  || |  ||| ||||||||  ||||||| ||||| ||||   ||   ||   ||| ||  ||||||| ||||| |||||||| |||||||| ||||||||||||||||||||||
atgatcaactttttattgttatgtgactactgttagaatttaggcatgttgttatgggaattcatgaatcaattgttattccattattttctatatacagGTTTACTCAAAGGTAAGTGGAGAACAAACTGCTGAAACACCTACCATTGATGTGAGCTCAAAAGAATTTTATGGTGAGGGATATGATGACAGTGACAAGA

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA11G19550.1 (Glycine max), 3'ss of exon 7
gtg-aatgagtcattggtttttttgatgcaa----tatta-atcttaatcttgacctctatggattctatatattgatgact-------tccttccattattcagGTTTATGCAAAGGTGAGTGGGGAACCTTCTTTGGAGGTACCAACTGTTGATGTAAGCTCCAAAGAATTCTATGGTGAAGGATATGATGACAGTGACAAGA
||| |||||   | |  || || | |||  |    | ||| |  |||  | ||   |    ||| |  ||  ||  ||   |       |  || |  ||| ||||||||  ||||||| ||||| ||||   ||   ||   ||| ||  ||||||| ||||| |||||||| |||||||| ||||||||||||||||||||||
gtggaatgatcaactttttattgttatgtgactactgttagaatttaggcatgttgttatgggaattcatgaatcaattgttattccattattttctatatacagGTTTACTCAAAGGTAAGTGGAGAACAAACTGCTGAAACACCTACCATTGATGTGAGCTCAAAAGAATTTTATGGTGAGGGATATGATGACAGTGACAAGA

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA12G08930.1 (Glycine max), 3'ss of exon 7
gtgaatgagtca--ttggtttttttgatgcaatattaatctta--atcttgac-----ctctatggattctatatattgat---gacttccttccatt----attcagGTTTATGCAAAGGTGAGTGGGGAACCTTCTTTGGAGGTACCAACTGTTGATGTAAGCTCCAAAGAATTCTATGGTGAAGGATATGATGACAGTGACAAGA
|||||    |||  ||  ||||| | ||   |   || | |||  || ||| |      | |  ||| |  ||  ||  ||    | | | |||||||    || ||||||||| ||||||| ||||| ||||   ||   ||   ||| || |||||||| ||||| |||||||| |||||||| ||||||||||| ||||||||||
gtgaaatgatcaagtttctttttattatttgactctactgttagaattttggcatgttgttttgggaattcatgaatcaattgttattccattccattctatatacagGTTTATTCAAAGGTAAGTGGCGAACAAACTCCTGAAACACCTACCGTTGATGTGAGCTCAAAAGAATTTTATGGTGAGGGATATGATGATAGTGACAAGA

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA17G05440.1 (Glycine max), 3'ss of exon 5
gtgaatgagtca--ttggtttttttgatgcaatattaatcttaatcttgacctctatggattctatatattgatgacttccttccattattcagGTTTATGCAAAGGTGAGTGGGGAACCTTCTTTGGAGGTACCAACTGTTGATGTAAGCTCCAAAGAATTCTATGGTGAAGGATATGATGACAGTGACAAGA
|| |  |  | |  || | || |||||  |  |   ||| | || | ||   | |  |     |  | ||| ||   ||  ||| ||||| ||||||||| ||||||| || || ||| |  || ||||   ||| ||| ||||||| || ||||||||||| |||||||| ||||||||||| ||||||||||
gttagaggattaagtttgattgtttgacccttttagaatttcaa-catggtatttgggaccgttcaacatttat--ttttgttcaattatgcagGTTTATTCAAAGGTTAGCGGAGAAGCACCTCTGGAAAAACCTACTATTGATGTGAGTTCCAAAGAATTTTATGGTGAGGGATATGATGATAGTGACAAGA

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 7
--gtgaatgagtcattggtttttttgatgcaatattaatcttaatcttgacctctatggattctatatattgatgacttccttccattattcagGTTTATGCAAAGGTGAGTGGGGAACCTTCTTTGGAGGTACCAACTGTTGATGTAAGCTCCAAAGAATTCTATGGTGAAGGATATGATGACAGTGACAAGA
  | | | ||   ||  |||       |   | | || | | | |  |  |       | ||||  ||  | |  ||       |||  |||||||||| ||||| |||||||| |||    |  | |||   ||||| |||||||| ||||||||||| || || || ||||| |||||||||||||||||||
gtgaggaagatggatcagttaggaaactatgaaaatagtttgatttct--ctgtcgctggttctcaattctcaaaacgaat---catgtttcagGTTTACGCAAAAGTGAGTGGAGAAGGAGCCATTGAGAGCCCAACGGTTGATGTTAGCTCCAAAGAGTTTTACGGGGAAGGTTATGATGACAGTGACAAGA

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT1G08200.1 (Arabidopsis thaliana), 3'ss of exon 7
gtgaatgagtcattggtttttttgatgcaat--attaatcttaatcttgacctctatgg-attctatatattgatgacttccttccattattcagGTTTATGCAAAGGTGAGTGGGGAACCTTCTTTGGAGGTACCAACTGTTGATGTAAGCTCCAAAGAATTCTATGGTGAAGGATATGATGACAGTGACAAGA
||||   |   ||||||  |    | | |    | | || ||       ||   ||| | |  |  |  | || ||     |    | |   ||||| || || || |||||||| ||  |  || | |||   |||||  | || || ||||||||||| || ||||| ||||| ||||||||||| |||||||
gtgagaaaa--attggtcatagataagaatctgagtgattttcgataaaactattatagcacacgctcaaatgttgcaaaacaaaaaatggacagGTCTACGCCAAAGTGAGTGGAGAGACAGCTATCGAGAGTCCAACGATCGACGTGAGCTCCAAAGAGTTTTATGGAGAAGGTTATGATGACAGCGACAAGA

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|110696696|gb|EE073040.1|EE073040
EST:     ACCCAAACAATGAAGCTACAGTTAAGCAGCTTGCAGAAATGATGACTGAG                         GTTTATGCAAAGGTGAGTGGGGAACCTTCTTTGGAGGTACCAACTGTTGAT
genomic: ACCCAAACAATGAAGCTACAGTTAAGCAGCTTGCAGAAATGATGACTGAGgtgaatgagt ... cattattcagGTTTATGCAAAGGTGAGTGGGGAACCTTCTTTGGAGGTACCAACTGTTGAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaatcttgacctctatggattctatatattgatgacttccttccattattcagGTTTATGCAAAGGTGAGTGGGGAACCTTCTTTGGAGGTACCAACTGTTGATGTAAGCTCCAAAGAATTCTATGGTGAAGGATATGATGACAGTGACAAGA
                            tattgat  putative branch site (score: 3)
                                     cttccttccattattc  putative PPT
                    attctatatattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaatgagtcattggtttttttgatgcaatattaatcttaatcttgacctctatggattctatatattgatgacttccttccattattcagGTTTATGCAAAGGTGAGTGGGGAACCTTCTTTGGAGGTACCAACTGTTGATGTAAGCTCCAAAGAATTCTATGGTGAAGGATATGATGACAGTGACAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA