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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACACCACTTAGTGGAAGCTCTTTGTCACCTCCTTTCCCACCATGCACTTTAAGAACAGCACTAACTCGGTATGCAGATGTTTTGAGTTCTCCCAAAAAGgttagtttctttcctcaagtcaatatatcaaaataatttttttattgatgaaatttgagttcgctaattttttagtactaattgtttgaatgcgtttattttccag

Basic information

species Vitis vinifera
transcript Vv11s0052g00880.t01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0052g00880.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA17G07050.2 (Glycine max), 5'ss of exon 10
CACACCACTTAGTGGAAGCTCTTTGTCACCTCCTTTCCCACCATGCACTTTAAGAACAGCACTAACTCGGTATGCAGATGTTTTGAGTTCTCCCAAAAAGgt--tagtttctttcctcaag-tcaatatatcaaaa--taatttttttattgatgaaatttgagttcgctaattttttagtactaattgtttgaatgcgtttattttccag
|| ||||| ||| |||||||| ||| ||||| | |||||||| || ||| ||||||||||||| || || |||||||||||||||||||| |||||||||||  | ||||    | | | | ||  |  ||  |||  | ||   |||||   |  ||      ||| ||        | || ||||  ||| ||      ||||||||||
CAAACCACGTAGCGGAAGCTCCTTGCCACCTACATTCCCACCCTGTACTCTAAGAACAGCACTTACACGATATGCAGATGTTTTGAGTTCACCCAAAAAGgtgcttgttttgagcttgatgctcccttaatttaaaccttatccctttatctttctaag--agattcactctgccacaattaataatacttttaaca----tattttccag

upper sequence: Vv11s0052g00880.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA13G00990.1 (Glycine max), 5'ss of exon 10
CACACCACTTAGTGGAAGCTCTTTGTCACCTCCTTTCCCACCATGCACTTTAAGAACAGCACTAACTCGGTATGCAGATGTTTTGAGTTCTCCCAAAAAGgt--tagtttc---tttcctcaagtcaatatatcaaaataatttttttattgatgaaatttgagttcgctaattttttagtactaattgtttgaatgcgtttattttccag
 | ||||||| |||||||||| ||| ||||| | |||||||| || ||| |||||| ||||||  | |  ||||| |||||||||||||| |||||||||||  | ||||     ||  |  |  |   || |||||   ||   |||||      ||      | |  ||  |    | || ||||  ||||||      ||||||||||
AAAACCACTTGGTGGAAGCTCCTTGCCACCTACATTCCCACCCTGTACTCTAAGAAAAGCACTTGCACAATATGCGGATGTTTTGAGTTCACCCAAAAAGgtgcttgttttgagcttgatgcacccttaatttcaaacatatccctttatctgctcaagagatttactttatgtcacaattaataatactttgaaca----tattttccag
















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|71856704|gb|DT005759.1|DT005759
EST:     TAAGAACAGCACTAACTCGGTATGCAGATGTTTTGAGTTCTCCCAAAAAG                         TCTGCTTTGGTTGCTCTAGCCGCCCATGCTTCTGATCCCAGTGAAGCTGAT
genomic: TAAGAACAGCACTAACTCGGTATGCAGATGTTTTGAGTTCTCCCAAAAAGgttagtttct ... tattttccagTCTGCTTTGGTTGCTCTAGCCGCCCATGCTTCTGATCCCAGTGAAGCTGAT
EST: gi|110695029|gb|EE072582.1|EE072582
EST:     TAAGAACAGCACTAACTCGGTATGCAGATGTTTTGAGTTCTCCCAAAAAG                         TCTGCTTTGGTTGCTCTAGCCGCCCATGCTTCTGATCCCAGTGAAGCTGAT
genomic: TAAGAACAGCACTAACTCGGTATGCAGATGTTTTGAGTTCTCCCAAAAAGgttagtttct ... tattttccagTCTGCTTTGGTTGCTCTAGCCGCCCATGCTTCTGATCCCAGTGAAGCTGAT
EST: gi|71862920|gb|DT011975.1|DT011975
EST:     TAAGAACAGCACTAACTCGGTATGCAGATGTTTTGAGTTCTCCCAAAAAG                         TCTGCTTTGGTTGCTCTAGCCGCCCATGCTTCTGATCCCAGTGAAGCTGAT
genomic: TAAGAACAGCACTAACTCGGTATGCAGATGTTTTGAGTTCTCCCAAAAAGgttagtttct ... tattttccagTCTGCTTTGGTTGCTCTAGCCGCCCATGCTTCTGATCCCAGTGAAGCTGAT
EST: gi|27582064|gb|CB004759.1|CB004759
EST:     GTTCTCCCAAAAAG                         TCTGCTTTGGTTGCTCTAGCCGCCCATGCTTCTGATCCCAGTGAAGCTGAT
genomic: GTTCTCCCAAAAAGgttagtttct ... tattttccagTCTGCTTTGGTTGCTCTAGCCGCCCATGCTTCTGATCCCAGTGAAGCTGAT
EST: gi|71865093|gb|DT014148.1|DT014148
EST:     TAAGAACAGCACTAACTCGGTATGCAGATGTTTTGAGTTCTCCCAAAAAG                         TCTGCTTTGGTTGCTCTAGCCGCCCATGCTTCTGATCCCAGTGAAGCTGAT
genomic: TAAGAACAGCACTAACTCGGTATGCAGATGTTTTGAGTTCTCCCAAAAAGgttagtttct ... tattttccagTCTGCTTTGGTTGCTCTAGCCGCCCATGCTTCTGATCCCAGTGAAGCTGAT
EST: gi|30300181|gb|CB976975.1|CB976975
EST:     TAAGAACAGCACTAACTCGGTATGCAGATGTTTTGAGTTCTCCCAAAAAG                         TCTGCTTTGGTTGCTCTAGCCGCCCATGCTTCTGATCCCAGTGAAGCTGAT
genomic: TAAGAACAGCACTAACTCGGTATGCAGATGTTTTGAGTTCTCCCAAAAAGgttagtttct ... tattttccagTCTGCTTTGGTTGCTCTAGCCGCCCATGCTTCTGATCCCAGTGAAGCTGAT
EST: gi|71861275|gb|DT010330.1|DT010330
EST:     TAAGAACAGCACTAACTCGGTATGCAGATGTTTTGAGTTCTCCCAAAAAG                         TCTGCTTTGGTTGCTCTAGCCGCCCATGCTTCTGATCCCAGTGAAGCTGAT
genomic: TAAGAACAGCACTAACTCGGTATGCAGATGTTTTGAGTTCTCCCAAAAAGgttagtttct ... tattttccagTCTGCTTTGGTTGCTCTAGCCGCCCATGCTTCTGATCCCAGTGAAGCTGAT
EST: gi|71864604|gb|DT013659.1|DT013659
EST:     TAAGAACAGCACTAACTCGGTATGCAGATGTTTTGAGTTCTCCCAAAAAG                         TCTGCTTTGGTTGCTCTAGCCGCCCATGCTTCTGATCCCAGTGAAGCTGAT
genomic: TAAGAACAGCACTAACTCGGTATGCAGATGTTTTGAGTTCTCCCAAAAAGgttagtttct ... tattttccagTCTGCTTTGGTTGCTCTAGCCGCCCATGCTTCTGATCCCAGTGAAGCTGAT
EST: gi|32270293|gb|CD719452.1|CD719452
EST:     TAAGAACAGCACTAACTCGGTATGCAGATGTTTTGAGTTCTCCCAAAAAG                         TCTGCTTTGGTTGCTCTAGCCGCCCATGCTTCTGATCCCAGTGAAGCTGAT
genomic: TAAGAACAGCACTAACTCGGTATGCAGATGTTTTGAGTTCTCCCAAAAAGgttagtttct ... tattttccagTCTGCTTTGGTTGCTCTAGCCGCCCATGCTTCTGATCCCAGTGAAGCTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACACCACTTAGTGGAAGCTCTTTGTCACCTCCTTTCCCACCATGCACTTTAAGAACAGCACTAACTCGGTATGCAGATGTTTTGAGTTCTCCCAAAAAGgttagtttctttcctcaagtcaatatatcaaaataatttttttattgatgaaatttgagttcgctaattttttagtactaattgtttgaatgcgtttattttccag

- - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG