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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTAGGATATTGTGTGGTGTGGATCATGATGATTTGAAGCAGCTTTTCCATGTATCAAACACAATCAGAGACGCAgtaagttccccatattttgaaaaattcgtttggtttgatttgttcttgtttcgatccgtatttgaacccaatttctgtttgcaatcaacag

Basic information

species Vitis vinifera
transcript Vv00s0181g00080.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0181g00080.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA13G32000.1 (Glycine max), 5'ss of exon 2
ATTAGGATATTGTGTGGTGTGGATCATGATGATTTGAAGCAGCTTTTCCATGTATCAAACACAATCAGAGACGCAgtaagttcc--ccatattttgaaaaattcgtttggtttgatttgttcttgtttcgatccgtatttgaacccaatttctgtttgcaatcaacag
 |     | |||||||||||||||||||| || |||||||||||||| |||||||| || || || ||||| || ||| ||  |    | ||   || |||  | || |   || | | ||  |  || ||||   |||| |||   | || | ||  | ||   |||
GTCCAAGTGTTGTGTGGTGTGGATCATGAAGACTTGAAGCAGCTTTTTCATGTATCCAAAACGATTAGAGAAGCGgtatgtatcagtaacatgaggataaacgcattag---tggtgtatttgtaatttgatc---attttaacgttaattatattgtctat--gcag

upper sequence: Vv00s0181g00080.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA15G07320.1 (Glycine max), 5'ss of exon 2
ATTAGGATATTGTGTGGTGTGGATCATGATGATTTGAAGCAGCTTTTCCATGTATCAAACACAATCAGAGACGCAgta-agttccccatattttgaaaaattcgtttggtt-tgatttgttcttgtttcgatccgtatttgaac--ccaatttctgtttgcaatcaacag-
 || |  | | |||||||||||| ||||| |||||||||||||||||  |||| ||||  || || ||||| |  |   |  ||    |   ||| |  |||  | || || | ||||| |  | ||   ||| |||  |  |      ||| |   ||   ||    |  
GTTCGAGTGTCGTGTGGTGTGGACCATGAAGATTTGAAGCAGCTTTTTAATGTGTCAAGAACTATTAGAGAAgtggagtaactcgaggttaattgcattattgatgtgtttgtaatttgat--tattctaatcagtaactatattgtttattgcatattttgatggctaag
















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|27581698|gb|CB004393.1|CB004393
EST:     ATGATGATTTGAAGCAGCTTTTCCATGTATCAAACACAATCAGAGACGCA                         ACTTTGATAGCAAAGAAGTCGCATTTCGCATTTAGTACTCC
genomic: ATGATGATTTGAAGCAGCTTTTCCATGTATCAAACACAATCAGAGACGCAgtaagttccc ... caatcaacagACTTTGATAGCAAAGAAGTCGCATTTCGCATTTAGTACTCC
EST: gi|161720703|gb|FC070629.1|FC070629
EST:     ATGATGATTTGAAGCAGCTTTTCCATGTATCAAACACAATCAGAGACGCA                         ACTTTGATAGCAAAGAAGTCGCATTTCGCATTTAGTACTCCTTCAAAGGTA
genomic: ATGATGATTTGAAGCAGCTTTTCCATGTATCAAACACAATCAGAGACGCAgtaagttccc ... caatcaacagACTTTGATAGCAAAGAAGTCGCATTTCGCATTTAGTACTCCTTCAAAGGTA
EST: gi|161713350|gb|FC063361.1|FC063361
EST:     ATGATGATTTGAAGCAGCTTTTCCATGTATCAAACACAATCAGAGACGCA                         ACTTTGATAGCAAAGAAGTCGCATTTCGCATTTAGTACTCCTTCAAAGGTA
genomic: ATGATGATTTGAAGCAGCTTTTCCATGTATCAAACACAATCAGAGACGCAgtaagttccc ... caatcaacagACTTTGATAGCAAAGAAGTCGCATTTCGCATTTAGTACTCCTTCAAAGGTA
EST: gi|71876591|gb|DT025646.1|DT025646
EST:     ATGATGATTTGAAGCAGCTTTTCCATGTATCAAACACAATCAGAGACGCA                         ACTTTGATAGCAAAGAAGTCGCATTTCGCATTTAGTACTCCTTCAAAGGTA
genomic: ATGATGATTTGAAGCAGCTTTTCCATGTATCAAACACAATCAGAGACGCAgtaagttccc ... caatcaacagACTTTGATAGCAAAGAAGTCGCATTTCGCATTTAGTACTCCTTCAAAGGTA
EST: gi|71876309|gb|DT025364.1|DT025364
EST:     ATGATGATTTAAAGCAGCTTTTCCATGTATCAAACACAATCAGAGACGCA                         ACTTTGATAGCAAAGAAGTCGCATTTCGCATATAGTACTCCTTCAAAGGTA
genomic: ATGATGATTTGAAGCAGCTTTTCCATGTATCAAACACAATCAGAGACGCAgtaagttccc ... caatcaacagACTTTGATAGCAAAGAAGTCGCATTTCGCATTTAGTACTCCTTCAAAGGTA
EST: gi|26261757|gb|CA812820.1|CA812820
EST:     ATGATGATTTGAAGCAGCTTTTCCATGTATCAAACACAATCAGAGACGCA                         ACTTTGATAGCAAAGAAGTCGCATTTCGCATTTAGTACTCCTTCAAAGGTA
genomic: ATGATGATTTGAAGCAGCTTTTCCATGTATCAAACACAATCAGAGACGCAgtaagttccc ... caatcaacagACTTTGATAGCAAAGAAGTCGCATTTCGCATTTAGTACTCCTTCAAAGGTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTAGGATATTGTGTGGTGTGGATCATGATGATTTGAAGCAGCTTTTCCATGTATCAAACACAATCAGAGACGCAgtaagttccccatattttgaaaaattcgtttggtttgatttgttcttgtttcgatccgtatttgaacccaatttctgtttgcaatcaacag

- - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - GCAGCT