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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAATGACCAGCAGGGAATACTTGGATGACCAAGATGCTGAAGAACCAGATGATTTTATTATTTCACTCACTGCACAGgtcagtaagttttcctgctccttttttagggcaagtagcggccaatatcacattgttggccctgcaaaaggcatgtttatatatatttcaacctgtcaaa...

Basic information

species Vitis vinifera
transcript Vv13s0019g04770.t01
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g04770.t01 (Vitis vinifera), 5'ss of exon 20
lower sequence: GLYMA20G32370.1 (Glycine max), 5'ss of exon 22
GAAATGACCAGCAGGGAATACTTGGATGACCAAGATGCTGAAGAACCAGATGATTTTATTATTTCACTCACTGCACAGgtcagtaagttttcctgctccttttttagggcaagtagcggccaatatcacattgttggccctgcaaaaggcatgtttatatat-atttcaacctgtcaaa-------
|||||| | |  |  ||||||||||||||||||||||||||||| || ||||| || || ||||| ||||||||||||||  ||       | | ||   ||| || |    ||       ||  ||  | |  |   ||||  |  |  |||   ||  |  |||   |  |   | |       
GAAATGGCAAATACAGAATACTTGGATGACCAAGATGCTGAAGAGCCGGATGACTTCATCATTTCGCTCACTGCACAGgtgtgt-------ctttctatctttgtatgatttgtcttcatgaagttcttagttgta-tcctgggatggatatggaaatgaaccattgggagttacaagagtaatgt

upper sequence: Vv13s0019g04770.t01 (Vitis vinifera), 5'ss of exon 20
lower sequence: GLYMA10G35190.2 (Glycine max), 5'ss of exon 19
GAAATGACCAGCAGGGAATACTTGGATGACCAAGATGCTGAAGAACCAGATGATTTTATTATTTCACTCACTGCACAGgtcagtaagttt-tcctgctccttttttagggcaagtagcggccaatatcacattgt--tggccctgcaaaaggcatgtttatatatatttcaacctgtcaaa
|||||| | |  |  ||||||||||||||||||||||||||||| || ||||| || || ||||| ||||||||||||||  ||   | | || |  |   ||||     || | ||     | |   |   ||   |||   || ||| |     ||   |  ||    |      |   
GAAATGGCAAATACAGAATACTTGGATGACCAAGATGCTGAAGAGCCGGATGACTTCATCATTTCGCTCACTGCACAGgtgtgtctttctatctttgtatgttttgtcttcatgaagttcttagttgtatcctgggatggatatggaaatgaaccattgggagttacaagagtaatac---

upper sequence: Vv13s0019g04770.t01 (Vitis vinifera), 5'ss of exon 20
lower sequence: PP1S4_346V6.1 (Physcomitrella patens), 5'ss of exon 23
GAAATGACCAGCAGGGAATACTTGGATGACCAAGATGCTGAAGAACCAGATGATTTTATTATTTCACTCACTGCACAGgtcagtaagttttcctgctccttttttagggcaagtagcggccaa-tatcacattgttggccctgcaaaaggcatgttta--tatatatttcaacctgtcaaa
   ||| |  | || | |||  ||  |||||||||||||||||||||||| ||||| ||| ||   |||||  | |||||    |   | |||| ||| | ||| | | |  |    ||     |||      ||| |   || ||  |  |  || |  || |         ||      
AGCATGGCGGGAAGAGTATATGTGACTGACCAAGATGCTGAAGAACCAGAAGATTTCATTGTTGGTCTCACAACCCAGgtatacattctgtcct-ctcttctttcaagtcgtgcgtaggatggctattggggggtttgtt-tgaaactgcaactttgagctacaagcactggactacttt-

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|110363229|gb|EC926805.1|EC926805
EST:     ACCAAGATGCTGAAGAACCAGATGATTTTATTATTTCACTCACTGCACAG                         ATAACACGGAGGGATGAGGAAATGGCTCCTTTTGTTGCTGGAGTGAAACGG
genomic: ACCAAGATGCTGAAGAACCAGATGATTTTATTATTTCACTCACTGCACAGgtcagtaagt ... taacccatagATAACACGGAGGGATGAGGAAATGGCTCCTTTTGTTGCTGGAGTGAAACGG
EST: gi|110717691|gb|EE093767.1|EE093767
EST:     ACCAAGATGCTGAAGAACCAGATGATTTTATTATTTCACTCACTGCACAG                         ATAACACGGAGGGATGAGGAAATGGCTCCTTTTGTTGCTGGAGTGAAACGG
genomic: ACCAAGATGCTGAAGAACCAGATGATTTTATTATTTCACTCACTGCACAGgtcagtaagt ... taacccatagATAACACGGAGGGATGAGGAAATGGCTCCTTTTGTTGCTGGAGTGAAACGG
EST: gi|30303826|gb|CB980620.1|CB980620
EST:     TTCACTCACTGCACAG                         ATAACACGGAGGGATGAGGAAATGGCTCCTTTTGTTGCTGGAGTGAAACGG
genomic: TTCACTCACTGCACAGgtcagtaagt ... taacccatagATAACACGGAGGGATGAGGAAATGGCTCCTTTTGTTGCTGGAGTGAAACGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAATGACCAGCAGGGAATACTTGGATGACCAAGATGCTGAAGAACCAGATGATTTTATTATTTCACTCACTGCACAGgtcagtaagttttcctgctccttttttagggcaagtagcggccaatatcacattgttggccctgcaaaaggcatgtttatatatatttcaacctgtcaaa

- - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agggcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcaaaag