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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatcctgcaatatctttgactctatttaaaccaagtaaaggctgttaccattttaatgatcgtcttgtgctatgattgtagGCTACACCAGAGCTGGAGTATGGTAGAATGAACATTGGTAGCCGTCCATCAAAGCGTAAGCCAAGTGGGGGAATTGAATCGCTCCGTGCAATCCCATGGA

Basic information

species Vitis vinifera
transcript Vv19s0014g01390.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0014g01390.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA13G34560.1 (Glycine max), 3'ss of exon 9
-----gtaagtatcctgca-atatctttgactc-----tatttaaaccaagtaaaggctgttaccattttaatgatcgtcttgtgctatgatt---gtagGCTACACCAGAGCTGGAGTATGGTAGAATGAACATTGGTAGCCGTCCATCAAAGCGTAAGCCAAGTGGGGGAATTGAATCGCTCCGTGCAATCCCATGGA
      |||    ||  || ||||  |||| ||       | |     |   ||  | | ||   ||  | |  |||    |   || || ||   |||||||||||| ||| |||||||||| || ||||||||||| || || ||| ||||| | ||||| ||||| || |||||| | || |||||||| || ||||
agtccttaaaaggcccccagatataattgaatcatcaacttctctgttagtaaattgatatttaaatgatgacaatcactgtcaactttgtttcatgtagGCTACACCGGAGTTGGAGTATGGAAGGATGAACATTGGAAGTCGACCAGCAAAGAGAAAGCCTAGTGGAGGCATTGAAACACTGCGTGCAATACCTTGGA

upper sequence: Vv19s0014g01390.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA12G35840.1 (Glycine max), 3'ss of exon 8
-----gtaagtatcctgcaatat--ctttgactcta---tttaaaccaagtaaag-gctgttaccattttaatgatcgtcttgtgctatgatt---gtagGCTACACCAGAGCTGGAGTATGGTAGAATGAACATTGGTAGCCGTCCATCAAAGCGTAAGCCAAGTGGGGGAATTGAATCGCTCCGTGCAATCCCATGGA
      |||   |||    || |   |||  |   |   | | |   |||||||  |   ||   ||  | |  |||    |   || || ||   |||||||||||||||| |||||||||| || ||||| ||||| || || ||| ||||| | |  || ||||| || |||||| | || |||||||| || ||||
gtcctttaaaggtcccaagatctaattttatcatcaacttctcatttaagtaaaatgacatttaaatgatgacaatcactgtcaactttgtttcatgtagGCTACACCAGAGTTGGAGTATGGAAGGATGAATATTGGAAGTCGACCAGCAAAGAGAAGACCTAGTGGAGGCATTGAAACACTGCGTGCAATACCTTGGA
















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|27755048|gb|CB035803.1|CB035803
EST:     ATCGTTCAGTTGTTTTCCAAGAACCTCGATTTGTTGAGTATTTCCGCCTT                         GCTACACCAGAGCTGGAGTATGGTAGAATGAACATTGGTAGCCGTCCATCA
genomic: ATCGTTCAATTGTTTTCCAAGAACCTCGATTTGTTGAGTATTTCCGCCTTgtaagtatcc ... atgattgtagGCTACACCAGAGCTGGAGTATGGTAGAATGAACATTGGTAGCCGTCCATCA
EST: gi|27585946|gb|CB008641.1|CB008641
EST:     ATCGTTCAATTGTTTTCCAAGAACCTCGATTTGTTGAGTATTTCCGCCTT                         GCTACACCAGAGCTGGAGTATGGTAGAATGAACATTGGTAGCCGTCCATCA
genomic: ATCGTTCAATTGTTTTCCAAGAACCTCGATTTGTTGAGTATTTCCGCCTTgtaagtatcc ... atgattgtagGCTACACCAGAGCTGGAGTATGGTAGAATGAACATTGGTAGCCGTCCATCA
EST: gi|110718456|gb|EE095313.1|EE095313
EST:     ATCGTTCAATTGTTTTCCAAGAACCTCGATTTGTTGAGTATTTCCGCCTT                         GCTACACCAGAGCTGGAGTATGGTAGAATGAACATTGGTAGCCGTCCATCA
genomic: ATCGTTCAATTGTTTTCCAAGAACCTCGATTTGTTGAGTATTTCCGCCTTgtaagtatcc ... atgattgtagGCTACACCAGAGCTGGAGTATGGTAGAATGAACATTGGTAGCCGTCCATCA
EST: gi|110361120|gb|EC924573.1|EC924573
EST:     TGAGTATTTCCGCCTT                         GCTACACCAGAGCTGGAGTATGGTAGAATGAACATTGGTAGCCGTCCATCA
genomic: TGAGTATTTCCGCCTTgtaagtatcc ... atgattgtagGCTACACCAGAGCTGGAGTATGGTAGAATGAACATTGGTAGCCGTCCATCA
EST: gi|27584127|gb|CB006822.1|CB006822
EST:     ATCGTTCAATTGTTTTCCAAGAACCTCGATTTGTTGAGTATTTCCGCCTT                         GCTACACCAGAGCTGGAGTATGGTAGAATGAACATTGGTAGCCGTCCATCA
genomic: ATCGTTCAATTGTTTTCCAAGAACCTCGATTTGTTGAGTATTTCCGCCTTgtaagtatcc ... atgattgtagGCTACACCAGAGCTGGAGTATGGTAGAATGAACATTGGTAGCCGTCCATCA
EST: gi|34544610|gb|CF512842.1|CF512842
EST:     ATCGTTCAATTGTTTTCCAAGAACCTCGATTTGTTGAGTATTTCCGCCTT                         GCTACACCAGAGCTGGAGTATGGTAGAATGAACATTGGTAGCCGTCCATCA
genomic: ATCGTTCAATTGTTTTCCAAGAACCTCGATTTGTTGAGTATTTCCGCCTTgtaagtatcc ... atgattgtagGCTACACCAGAGCTGGAGTATGGTAGAATGAACATTGGTAGCCGTCCATCA
EST: gi|156735834|gb|EV239955.1|EV239955
EST:     ATCGTTCAGTTGTTTTCCAAGAACCTCGATTTGTTGAGTATTTCCGCCTT                         GCTACACCAGAGCTGGAGTATGGTAGAATGAACATTGGTAGCCGTCCATCA
genomic: ATCGTTCAATTGTTTTCCAAGAACCTCGATTTGTTGAGTATTTCCGCCTTgtaagtatcc ... atgattgtagGCTACACCAGAGCTGGAGTATGGTAGAATGAACATTGGTAGCCGTCCATCA
EST: gi|71884541|gb|DT033596.1|DT033596
EST:     ATCGTTCAATTGTTTTCCAAGAACCTCGATTTGTTGAGTATTTCCGCCTT                         GCTACACCAGAGCTGGAGTATGGTAGAATGAACATTGGTAGCCGTCCATCA
genomic: ATCGTTCAATTGTTTTCCAAGAACCTCGATTTGTTGAGTATTTCCGCCTTgtaagtatcc ... atgattgtagGCTACACCAGAGCTGGAGTATGGTAGAATGAACATTGGTAGCCGTCCATCA
EST: gi|33409891|gb|CF215518.1|CF215518
EST:     ATCGTTCAATTGTTTTCCAGGAACCTCGATTTGTTGAGTATTTCCGCCTT                         GCTACACCAGAGCTGGAGTATGGTAGAATGAACATTGGTAGCCGTCCATCA
genomic: ATCGTTCAATTGTTTTCCAAGAACCTCGATTTGTTGAGTATTTCCGCCTTgtaagtatcc ... atgattgtagGCTACACCAGAGCTGGAGTATGGTAGAATGAACATTGGTAGCCGTCCATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaccaagtaaaggctgttaccattttaatgatcgtcttgtgctatgattgtagGCTACACCAGAGCTGGAGTATGGTAGAATGAACATTGGTAGCCGTCCATCAAAGCGTAAGCCAAGTGGGGGAATTGAATCGCTCCGTGCAATCCCATGGA
                        ttttaat  putative branch site (score: 3)
                       attttaatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatcctgcaatatctttgactctatttaaaccaagtaaaggctgttaccattttaatgatcgtcttgtgctatgattgtagGCTACACCAGAGCTGGAGTATGGTAGAATGAACATTGGTAGCCGTCCATCAAAGCGTAAGCCAAGTGGGGGAATTGAATCGCTCCGTGCAATCCCATGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA