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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTGTGACAGAAGTTTTAAAATCTGCAAATATTAAAGTTAAAGTTGATGACTCAGATCAGAGAACCCCTGGATGGAAATTCAATTTCTGGGAGATGAAGgtctgtacattcttgaatcaatcctcgcataacctagtgttatcaaaggcaattgcttgggtcgcctaggccatcaggtcaggtggggcagataaaactc...

Basic information

species Vitis vinifera
transcript Vv16s0050g00960.t01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g00960.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G107089_T02 (Zea mays), 5'ss of exon 7
ATCTGTGACAGAAGTTTTAAAATCTGCAAATATTAAAGTTAAAGTTGATGACTCAGATCAGAGAACCCCTGGATGGAAATTCAATTTCTGGGAGATGAAGgtctgtacattcttgaatcaatcctcgcataacctagtgttatcaaaggcaattgcttgggtcgcctaggccatcaggtcaggtggggcagataaaactc----
 || ||   | || |  | |||   |||   |||| ||||||||| || |||||||| | | |||| ||||||||||||||||||  ||  |||||||| ||   |    | |  | ||       | |  ||  || | |   ||   |  | |  | | || || |     ||    ||  |  ||      |  ||     
TTCAGTTCAAAAAATACTCAAAGAAGCAGGAATTAGAGTTAAAGTGGACGACTCAGAGCTGCGAACTCCTGGATGGAAATTCAATCACTATGAGATGAAAgtaattg---tttctactcttatagtggaagactcagagctgcgaacttctgt-gtgttgttcacccatttgctcttagcatatttggtttcatatgctttcag

upper sequence: Vv16s0050g00960.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA09G24670.1 (Glycine max), 5'ss of exon 8
ATCTGTGACAGAAGTTTTAAAATCTGCAAATATTAAAGTTAAAGTTGATGACTCAGATCAGAGAACCCCTGGATGGAAATTCAATTTCTGGGAGATGAAGgtctg-tacattcttgaatcaatcctcgcat-----aacctagtgttatcaaaggcaattgcttgggtcgcctaggcc-atcaggtcaggtggggcagataaaactc--------------------------
|||||| | ||| ||| |  ||    |    |||||||||||| |||| ||||||||||| |||||||||||||||||||||||||||||||| |||||||| || |  |  ||||||   |   ||   |      ||| | |  |    |  ||  |  ||   |  ||     |  |||  ||   | |   | ||| | | |                           
ATCTGTAAAAGATGTTCTTCAAAGATCTGGGATTAAAGTTAAACTTGACGACTCAGATCAAAGAACCCCTGGATGGAAATTCAATTTCTGGGAAATGAAGgtttggtgtaaacttgaacggaaattcaatttctgggaccaaataatgcgcattgctttgtctcatgctgcaggatcttatcctgttttgagtatctgattatatttatatcatttacttcttcatatttcag

upper sequence: Vv16s0050g00960.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA16G29890.1 (Glycine max), 5'ss of exon 8
ATCTGTGACAGAAGTTTTAAAATCTGCAAATATTAAAGTTAAAGTTGATGACTCAGATCAGAGAACCCCTGGATGGAAATTCAATTTCTGGGAGATGAAGgtctgtacatt--cttgaatcaatcctcgcat-----aacctagtgttatcaaaggcaattgcttgggtcgcctaggccatcag-gtcaggtggggcagataaaactc-------------
|||||| | ||| ||| |  ||    |    |||||||||||| |||| ||||||||||| ||||| |||||||||||||||||||||||||| |||||||| |||   |   |||||||  |   ||   |      ||| | |  |    |  ||  | |||   |  ||     |  | || ||  | |       |||  | |              
ATCTGTAAAAGATGTTCTTCAAAGATCTGGGATTAAAGTTAAACTTGACGACTCAGATCAAAGAACTCCTGGATGGAAATTCAATTTCTGGGAAATGAAGgtttgtttttaaacttgaatggaaattcaatttctgggaccaaataatgcgcattgctttggctcatgctgcaggatctttgagtgtttgattatatttatatcatttacttcatatttag

upper sequence: Vv16s0050g00960.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: AT5G52520.1 (Arabidopsis thaliana), 5'ss of exon 8
ATCTGTGACAGAAGTTTTAAAATCTGCAAATATTAAAGTTAAAGTTGATGACTCAGATCAGAGAACCCCTGGATGGAAATTCAATTTCTGGGAGATGAAGgtctgtacat-tcttgaatcaatcctcgca-taacctagtgttatcaaaggcaattgcttgggtcgc---ctaggccatcaggtcaggtggggcagataaaactc----------
||| |||| ||||| | |  || ||||   | ||| ||||||| |||||||| ||||||| |||||||| |||||||| |||||||||||||| ||||||||  |||  | ||||  |  ||  | | || ||   |  | || |  |  | ||    ||  ||        | ||  | |                | || ||           
ATCAGTGAAAGAAGCTCTCCAAACTGCTGGTGTTAGAGTTAAACTTGATGACACAGATCAAAGAACCCCAGGATGGAAGTTCAATTTCTGGGAAATGAAGgttcgtaactatcttagaaaaaaacacacactagaatcattttctggagtgaaaagattttcgtgatatttcaagctcttataatttacatttggtttgaacctttggtttgtag

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|110711045|gb|EE087798.1|EE087798
EST:     CTCAAATCAGAGAACCCCTGTGATG-AAATTCAATTTCTGGGAGATGAAG                         GGAATTCCTTTAAGGAATGAGATTGGTCC
genomic: CTCAGATCAGAGAACCCCTG-GATGGAAATTCAATTTCTGGGAGATGAAGgtctgtacat ... ggtttttcagGGAGTTCCTTTAAGGATTGAAATTGGTCC
EST: gi|30330458|gb|CD013720.1|CD013720
EST:     ACTCAGATCAGAGAACCCCTGGATGGAAATTCAATTTCTGGGAGATGAAG                         GGAGTTCCTTTAAGGATTGAAATTGGTCCTCGTGATGTTTCAAGCGGGAGT
genomic: ACTCAGATCAGAGAACCCCTGGATGGAAATTCAATTTCTGGGAGATGAAGgtctgtacat ... ggtttttcagGGAGTTCCTTTAAGGATTGAAATTGGTCCTCGTGATGTTTCAAGCGGGAGT
EST: gi|351023829|gb|FQ448380.1|FQ448380
EST:     ACTCAGATCAGAGAACCCCTGGATGGAAATTCAATTTCTGGGAGATGAAG                         GGAGTTCCTTTAAGGATTGAAATTGGTCCTCGTGATGTTTCAAGCGGGAGT
genomic: ACTCAGATCAGAGAACCCCTGGATGGAAATTCAATTTCTGGGAGATGAAGgtctgtacat ... ggtttttcagGGAGTTCCTTTAAGGATTGAAATTGGTCCTCGTGATGTTTCAAGCGGGAGT
EST: gi|351033120|gb|FQ446473.1|FQ446473
EST:     ACTCAGATCAGAGAACCCCTGGATGGAAATTCAATTTCTGGGAGATGAAG                         GGAGTTCCTTTAAGGATTGAAATTGGTCCTCGTGATGTTTCAAGCGGGAGT
genomic: ACTCAGATCAGAGAACCCCTGGATGGAAATTCAATTTCTGGGAGATGAAGgtctgtacat ... ggtttttcagGGAGTTCCTTTAAGGATTGAAATTGGTCCTCGTGATGTTTCAAGCGGGAGT
EST: gi|27586757|gb|CB009452.1|CB009452
EST:     ACTCAGATCAGAGAACCCCTGGATGGAAATTCAATTTCTGGGAGATGAAG                         GGAGTTCCTTTAAGGATTGAAATTGGTCCTCGTGATGTTTCAAGCG
genomic: ACTCAGATCAGAGAACCCCTGGATGGAAATTCAATTTCTGGGAGATGAAGgtctgtacat ... ggtttttcagGGAGTTCCTTTAAGGATTGAAATTGGTCCTCGTGATGTTTCAAGCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTGTGACAGAAGTTTTAAAATCTGCAAATATTAAAGTTAAAGTTGATGACTCAGATCAGAGAACCCCTGGATGGAAATTCAATTTCTGGGAGATGAAGgtctgtacattcttgaatcaatcctcgcataacctagtgttatcaaaggcaattgcttgggtcgcctaggccatcaggtcaggtggggcagataaaactc

- - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaggcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtgggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gataaaa