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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacagctgacatgggctcttttctgacagtccagactgatccatgtcgacttccctttttttttttatcttattatacctgtctgttcactgttcagGAAGCTTTAAGGTCAAGGGGCTTGAAGGATGATACAACATGCCTAGTTGTTGATATGATTCCATCAGATAATCCTGTCTTACCTCCAACACCAAAGAAGA

Basic information

species Vitis vinifera
transcript Vv14s0060g01580.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g01580.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA20G38270.1 (Glycine max), 3'ss of exon 6
gtaacagctgacatgggctctttt-ctgacagtccagactgatccatgtcgacttccctttttttttttatcttattatacctgtctgttcactgttcagGAAGCTTTAAGGTCAAGGGGCTTGAAGGATGATACAACATGCCTAGTTGTTGATATGATTCCATCAGATAATCCTGTCTTACCTCCAACACCAAAGAAGA
|| |  | | |   || |  | |  ||  |  | |||    ||  ||||    ||  ||| | |  |   |  | || | |   ||  ||   |   |||||||||||||||||||| ||  |||||||||||||||| ||||| ||||| ||||| ||||| |||||| |||| || || ||  |||  ||||  ||||
gtgat-gttaattgggccaatctcactatcttttcagg--aatggatgttccattatcttctctaatgctttgtgtttttctcttccattttttaa-cagGAAGCTTTAAGGTCAAGAGGTCTGAAGGATGATACAACTTGCCTCGTTGTAGATATTATTCCTTCAGATCATCCCGTGTTGCCAACAATTCCAAGAAAGA

upper sequence: Vv14s0060g01580.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA10G29060.1 (Glycine max), 3'ss of exon 6
gtaacagctgacatgggctctttt-ctgacagtccagactgatccatgtcgacttccctttttttttttatcttattatacctgtctgttcactgtt----cagGAAGCTTTAAGGTCAAGGGGCTTGAAGGATGATACAACATGCCTAGTTGTTGATATGATTCCATCAGATAATCCTGTCTTACCTCCAACACCAAAGAAGA
|| |  | | |   || |  | || ||  |  | |||    ||  ||||    ||  ||| | |  |  || || || |   | ||| |||  | ||    ||||||||| |||||||||| ||  |||||||||||||||| ||||| ||||| ||||| ||||| |||||| ||||| | |||||  |||  ||||  ||||
gtgattgttaattgggccaatcttactatcttttcagg--aatgaatgttccattatcttctctactcaatgtt-ttgtgtttttctcttccattttttaacagGAAGCTCTAAGGTCAAGAGGGCTGAAGGATGATACAACTTGCCTTGTTGTAGATATTATTCCTTCAGATCATCCTATGTTACCAGCAATTCCAAGAAAGA

upper sequence: Vv14s0060g01580.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA03G39260.1 (Glycine max), 3'ss of exon 6
gtaacagctgacatgggctcttttctgacagtccagactgatccatgtcgacttccctttttttttttatcttattatacctgtctgttcactgttcagGAAGCTTTAAGGTCAAGGGGCTTGAAGGATGATACAACATGCCTAGTTGTTGATATGATTCCATCAGATAATCCTGTCTTACCTCCAACACCAAAGAAGA
|| |    |      |||  | |||  | | |   || |||         |  | |  | |||| || || | ||| |   |||  |||   | | ||||||||| |||||||||| ||| | |||||||||||||| ||||| ||||| ||||| ||||| || ||    ||||| ||||| || |  ||||  ||||
gtgatgattagttctggcattcttcccatacta-ggaatga---------atgttcaatattttgttcat-tcattgt-tttgttcgttatttttccagGAAGCTCTAAGGTCAAGAGGCCTTAAGGATGATACAACCTGCCTTGTTGTAGATATTATTCCTTCGGACCTCCCTGTATTACCACCGATTCCAAGAAAGA

upper sequence: Vv14s0060g01580.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA19G41810.2 (Glycine max), 3'ss of exon 6
gtaacagctgacatgggctcttttctgacagtccagactgatccatgtcgacttccctttttttttttatcttattatacctgtctgttcactgttcagGAAGCTTTAAGGTCAAGGGGCTTGAAGGATGATACAACATGCCTAGTTGTTGATATGATTCCATCAGATAATCCTGTCTTACCTCCAACACCAAAGAAGA
|| |    |      |||  | |||      |    |  |||    ||         ||  |   || ||  | || | | | | |        | ||||||||| |||||||||| ||| | |||||||||||||| ||||| ||||| ||||| ||||| || ||    ||||| ||||| ||||  ||||  ||||
gtgatgattagttctggcattcttcccgtgctaggaatggatgttcgtga------tttagtacattcattgttttgttctttttt--------tccagGAAGCTCTAAGGTCAAGAGGCCTCAAGGATGATACAACTTGCCTTGTTGTAGATATTATTCCTTCGGACCTCCCTGTATTACCACCAATTCCAAGAAAGA

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|110398762|gb|EC965236.1|EC965236
EST:     AGTCTTGTCGGGGTTTGCCTGCAGAGCTTGCTGCAAAGCTGGTTGTTAAG                         GAAGCTTTAAGGTCAAGGGGCTTGAAGGATGATACAACATGTCTAGTTGTT
genomic: AGTCTTGTCGGGGTTTGCCTGCAGAGCTTGCTGCAAAGCTGGTTGTTAAGgtaacagctg ... cactgttcagGAAGCTTTAAGGTCAAGGGGCTTGAAGGATGATACAACATGCCTAGTTGTT
EST: gi|71874154|gb|DT023209.1|DT023209
EST:     AGTCTTGTCGGGGTTTGCCTGCAGAGCTTGCTGCAAAGCTGGTTGTTAAG                         GAAGCTTTAAGGTCAAGGGGCTTGAAGGATGATACAACATGCCTAGTTGTT
genomic: AGTCTTGTCGGGGTTTGCCTGCAGAGCTTGCTGCAAAGCTGGTTGTTAAGgtaacagctg ... cactgttcagGAAGCTTTAAGGTCAAGGGGCTTGAAGGATGATACAACATGCCTAGTTGTT
EST: gi|37189043|gb|CF608392.1|CF608392
EST:     AGTCTTGTCGGGGTTTGCCTGCAGAGCTTGCTGCAAAGCTGGTTGTTAAG                         GAAGCTTTAAGGTCAAGGGGCTTGAAGGATGATACAACATGCCTAGTTGTT
genomic: AGTCTTGTCGGGGTTTGCCTGCAGAGCTTGCTGCAAAGCTGGTTGTTAAGgtaacagctg ... cactgttcagGAAGCTTTAAGGTCAAGGGGCTTGAAGGATGATACAACATGCCTAGTTGTT
EST: gi|33402981|gb|CF208608.1|CF208608
EST:     AGTCTTGTCGGGGTTTGCCTGCAGAGCTTGCTGCAAAGCTGGTTGTTAAG                         GAAGCTTTAAGGTCAAGGGGCTTGAAGGATGATACAACATGTCTAGTTGTT
genomic: AGTCTTGTCGGGGTTTGCCTGCAGAGCTTGCTGCAAAGCTGGTTGTTAAGgtaacagctg ... cactgttcagGAAGCTTTAAGGTCAAGGGGCTTGAAGGATGATACAACATGCCTAGTTGTT
EST: gi|110687916|gb|EE065868.1|EE065868
EST:     AGTCTTGTCGGGGTTTGCCTGCAGAGCTTGCTGCAAAGCTGGTTGTTAAG                         GAAGCTTTAAGGTCGAGGGGCTTGAAGGATGATACAACATGCGTAGTTGTT
genomic: AGTCTTGTCGGGGTTTGCCTGCAGAGCTTGCTGCAAAGCTGGTTGTTAAGgtaacagctg ... cactgttcagGAAGCTTTAAGGTCAAGGGGCTTGAAGGATGATACAACATGCCTAGTTGTT
EST: gi|110384652|gb|EC949105.1|EC949105
EST:     TTGCCTGCAGAGCTTGCTGCAAAGCTGGTTGTTAAG                         GAAGCTTTAAGGTCAAGGGGCTTGAAGGATGATACAACATGTCTAGTTGTT
genomic: TTGCCTGCAGAGCTTGCTGCAAAGCTGGTTGTTAAGgtaacagctg ... cactgttcagGAAGCTTTAAGGTCAAGGGGCTTGAAGGATGATACAACATGCCTAGTTGTT
EST: gi|110388299|gb|EC953034.1|EC953034
EST:     AGTCTTGTCGGGGTTTGCCTGCAGAGCTTGCTGCAAAGCTGGTTGTTAAG                         GAAGCTTTAAGGTCAAGGGGCTTGAAGGATGATACAACATGCCTAGTTGTT
genomic: AGTCTTGTCGGGGTTTGCCTGCAGAGCTTGCTGCAAAGCTGGTTGTTAAGgtaacagctg ... cactgttcagGAAGCTTTAAGGTCAAGGGGCTTGAAGGATGATACAACATGCCTAGTTGTT
EST: gi|110362563|gb|EC926106.1|EC926106
EST:     AGTCTTGTCGGGGTTTGCCTGCAGAGCTTGCTGCAAAGCTGGTTGTTAAG                         GAAGCTTTAAGGTCAAGGGGCTTGAAGGATGATACAACATGCCTAGTTGTT
genomic: AGTCTTGTCGGGGTTTGCCTGCAGAGCTTGCTGCAAAGCTGGTTGTTAAGgtaacagctg ... cactgttcagGAAGCTTTAAGGTCAAGGGGCTTGAAGGATGATACAACATGCCTAGTTGTT
EST: gi|71890427|gb|DT039482.1|DT039482
EST:     AGTCTTGTCGGGGTTTGCCTGCAGAGCTTGCTGCAAAGCTGGTTGTTAAG                         GAAGCTTTAAGGTCA
genomic: AGTCTTGTCGGGGTTTGCCTGCAGAGCTTGCTGCAAAGCTGGTTGTTAAGgtaacagctg ... cactgttcagGAAGCTTTAAGGTCA
EST: gi|254914412|gb|GR906513.1|GR906513
EST:     AGTCTTGTCGGGGTTTGCCTGCGGAGCTTGCTGCAAAGCTGGTTGTTAAG                         GAAGCTTTAAGGTCGAGGGGCTTGAAGGATGATACAACATGCGTAGTTGTT
genomic: AGTCTTGTCGGGGTTTGCCTGCAGAGCTTGCTGCAAAGCTGGTTGTTAAGgtaacagctg ... cactgttcagGAAGCTTTAAGGTCAAGGGGCTTGAAGGATGATACAACATGCCTAGTTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtcgacttccctttttttttttatcttattatacctgtctgttcactgttcagGAAGCTTTAAGGTCAAGGGGCTTGAAGGATGATACAACATGCCTAGTTGTTGATATGATTCCATCAGATAATCCTGTCTTACCTCCAACACCAAAGAAGA
                                       tctgttc  CT-rich tract
        ttcccttttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacagctgacatgggctcttttctgacagtccagactgatccatgtcgacttccctttttttttttatcttattatacctgtctgttcactgttcagGAAGCTTTAAGGTCAAGGGGCTTGAAGGATGATACAACATGCCTAGTTGTTGATATGATTCCATCAGATAATCCTGTCTTACCTCCAACACCAAAGAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG