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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTAATGGAATACTCCCACCTGTTAGATAAAGCAGATGAATGCGAGGATCCTTACATGCGATTGGTGTATGCTTgtgagtatattcttgcattaaatatttcagggcatacatgtattatctggttaatggtggaactttaatgttactaattgcag

Basic information

species Vitis vinifera
transcript Vv06s0004g04930.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g04930.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G114126_T01 (Zea mays), 5'ss of exon 4
TTAATGGAATACTCCCACCTGTTAGATAAAGCAGATGAATGCGAGGATCCTTACATGCGATTGGTGTATGCTTgtgagtatattcttgcattaaatatttcagggcataca-tgtattatc-tggttaa--tggtggaactttaatgttactaattgcag
|| ||||||||||   |  ||||||| |||||||||||||| |||||||| ||||||||  |||| ||||||||||||| |  || | |  |     || ||   | | |  ||   |||| ||||| |  ||   || || | |    | |  || |||
TTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCATACATGCGTATGGTTTATGCTTgtgagttttctccttcccttgcc-ttgcacaccgttcggtgccatatcatggttgacttgactgagctgttaatcaatttgtttcag

upper sequence: Vv06s0004g04930.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G174644_T01 (Zea mays), 5'ss of exon 4
TTAATGGAATACTCCCACCTGTTAGATAAAGCAGATGAATGCGAGGATCCTTACATGCGATTGGTGTATGCTTgtgagtatattcttgcattaaatatttcagggcatacatgtattatctggttaatggtggaactttaatgttactaattgcag
|| ||||||||||   |  ||||||| |||||||||||||| |||||||| |||||| |  |||| ||||||||| ||| |  |  | |  |     || ||   ||| | | |   || |  |   ||   ||||| | |    | |  || |||
TTGATGGAATACTGTGAATTGTTAGACAAAGCAGATGAATGTGAGGATCCATACATGTGTATGGTTTATGCTTgtaagttttctgcttcccttccc-ttgcacaccattc-tatgccatatcatggttgcctgaactgttaatccatt--tttcag

upper sequence: Vv06s0004g04930.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA15G04210.1 (Glycine max), 5'ss of exon 4
TTAATGGAATACTCCCACCTGTTAGATAAAGCAGATGAATGCGAGGATCCTTACATGCGATTGGTGTATGCTTgtgagtatattcttgcattaaatatttcaggg-catacatgtattatct-ggttaatgg--tggaactttaatgttactaattgcag--------------
|| ||||| |||||| ||||||||||| | ||||||||||| ||||| || ||||||||  |||||||||| ||||||| ||||  | |  |   ||||||   | |||   |  ||| | | | | ||| |  | ||| ||| || |||    |    |              
TTGATGGAGTACTCCTACCTGTTAGATCAGGCAGATGAATGTGAGGACCCATACATGCGGCTGGTGTATGCATgtgagt-tatttgttccctttgtatttctctgtcattttttaattgttttgatcaattgaattgaattttcatcttaaaggtaatggagggtgttgtaaac

upper sequence: Vv06s0004g04930.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA12G06690.1 (Glycine max), 5'ss of exon 4
TTAATGGAATACTCCCACCTGTTAGATAAAGCAGATGAATGCGAGGATCCTTACATGCGATTGGTGTATGCTTgtgagtatattcttgcattaaatatttcagggcatacatgtattatctggtta-atggtggaactttaatgttact--aattgcag--------------
|| ||||| |||||| || |||||||| ||||||||||||  |||||||| |||||||| || || |||||  |||||||  || || | ||     ||||       ||   ||||  |   | | || |   |    |  ||    |  | ||  ||              
TTGATGGAGTACTCCTACTTGTTAGATCAAGCAGATGAATCAGAGGATCCATACATGCGGTTAGTTTATGCAAgtgagtaattttttccttttttattttctcttttaactcttatttcccaatcacattgaaaagtcgtcctggggatatagttttagataggaatgaatgg

upper sequence: Vv06s0004g04930.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA11G14770.1 (Glycine max), 5'ss of exon 4
TTAATGGAATACTCCCACCTGTTAGATAAAGCAGATGAATGCGAGGATCCTTACATGCGATTGGTGTATGCTTgtgagtatattcttgcattaaatatttcagggcatacatgtattatctggttaatggtgga---actttaatgttactaattgcag----------------
|| ||||| |||||| || |||||||| ||||||||||||  |||||||| |||||||  || || |||||  |||||| |||| || |  |   |||||       ||  | | ||  | |   ||| |   |   |   | | | || || ||  ||                
TTGATGGAGTACTCCTACTTGTTAGATCAAGCAGATGAATCAGAGGATCCATACATGCAGTTAGTTTATGCAAgtgagt-tattttttccctttttattttctcttttaactcttttcccagtcgaattgaaaagtcatcctgaggata-tagttttagataagaatgaatggca

upper sequence: Vv06s0004g04930.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT5G59420.1 (Arabidopsis thaliana), 5'ss of exon 4
TTAATGGAATACTCCCACCTGTTAGATAAAGCAGATGAATGCGAGGATCCTTACATGCGATTGGTGTATGCTTgtgagta----tattcttgcattaaatattt-cagggcatacatgtattatctggttaatggtggaactttaatgttactaattgcag-------------------
 ||||||| || || ||  |||| ||| |||||||||||||||| ||||| ||| |||| || || ||||||||| ||||    ||||    ||  ||| | |   |  |  | |     || |  | |  ||| |   | ||| |  || ||  | |  |                   
ATAATGGAGTATTCTCATTTGTTGGATCAAGCAGATGAATGCGAAGATCCATACTTGCGTTTAGTATATGCTTgtaagtattagtatttacacacaaaaaactcgtattgacttccgactttgtaagatgtatgttaagagttttacttttcttgtggttgtacgtgaatttttatatag

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|30133371|gb|CB918710.1|CB918710
EST:     AGATAAAGCAGATGAATGCGAGGATCCTTACATGCGATTGGTGTATGCTT                         CATCATGGGCTATATCTGTCTATTATGCCTACCAACGAACTTGGAAGCCTT
genomic: AGATAAAGCAGATGAATGCGAGGATCCTTACATGCGATTGGTGTATGCTTgtgagtatat ... ctaattgcagCATCATGGGCTATATCTGTCTATTATGCCTACCAACGAACTTGGAAGCCTT
EST: gi|30252454|gb|CB970005.1|CB970005
EST:     AGATAAAGCAGATGAATGCGAGGATCCTTACATGCGATTGGTGTATGCTT                         CATCATGGGCTATATCTGTCTATTATGCCTACCAACGAACTTGGAAGCCTT
genomic: AGATAAAGCAGATGAATGCGAGGATCCTTACATGCGATTGGTGTATGCTTgtgagtatat ... ctaattgcagCATCATGGGCTATATCTGTCTATTATGCCTACCAACGAACTTGGAAGCCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTAATGGAATACTCCCACCTGTTAGATAAAGCAGATGAATGCGAGGATCCTTACATGCGATTGGTGTATGCTTgtgagtatattcttgcattaaatatttcagggcatacatgtattatctggttaatggtggaactttaatgttactaattgcag

- - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - GAGGAT