Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcattgtcagagctgggttgtctaaagaaatttaactgaaattctaagcagtttctaccaaatggtttgctcatagatcaaatttcacattcttgcgcagGATAAAGCAAGGGATATCCTGAAGAACGCTCCTGGTGTGGTGGTTATTGATGAGCGGCCATCCAATAACTTTCCTACCCCATTAGAGGTATCAAACAAAG

Basic information

species Vitis vinifera
transcript Vv01s0011g05860.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g05860.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G05250.1 (Glycine max), 3'ss of exon 5
-tcattgtcagagctgggttgtctaaagaaatttaactgaaattctaagcagtttctaccaaatggtttgctcatagatcaaatttcacattc---ttgcgcagGATAAAGCAAGGGATATCCTGAAGAACGCTCCTGGTGTGGTGGTTATTGATGAGCGGCCATCCAATAACTTTCCTACCCCATTAGAGGTATCAAACAAAG
 | |||  ||   |     | | | ||     |  |||    |   ||    | || |  |  |  | |  |  | ||     |||    ||    ||   ||||| |  ||||| ||||| |||||||| ||||| ||||| |||||||||||||| ||   ||||||| | |||||||| ||||| || || |||||||| |
attatttgcatgcccaaaatctatgaaa----tgcacttgcgtgagaaaagttctccaaaagttaatatcttatttgagttcctttgttttttaatttcttcagGACACTGCAAGAGATATTCTGAAGAATGCTCCAGGTGTAGTGGTTATTGATGATCGTGAATCCAATCATTTTCCTACTCCATTGGAAGTTTCAAACAAGG
















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|110684881|gb|EE062668.1|EE062668
EST:     GTGCGCATGCTGAAAGTGTTAATCTCCAGTTTGAGAATCCC-TTGATGAG                         GAAAAA-CAAGGGATATCCCTGA-GAACGCTCC
genomic: GTGCGCATGCTGAGAGTGTTAATCTCCAGTTTGAGAATCCCCTTGATGAGgtacaatgat ... tcttgcgcagGATAAAGCAAGGGATATCC-TGAAGAACGCTCC
EST: gi|26265064|gb|CA816127.1|CA816127
EST:     GTGCGCATGCTGAGAGTGTTAATCTCCAGTTTGAGAATCCCCTTGATGAG                         GATAAAGCAAGGGATATCCTGAAGAACGCTCCTGGTGTGGTGGTTATTGAT
genomic: GTGCGCATGCTGAGAGTGTTAATCTCCAGTTTGAGAATCCCCTTGATGAGgtacaatgat ... tcttgcgcagGATAAAGCAAGGGATATCCTGAAGAACGCTCCTGGTGTGGTGGTTATTGAT
EST: gi|34546869|gb|CF515101.1|CF515101
EST:     GTGCGCATGCTGAGAGTGTTAATCTCCAGTTTGAGAATCCCCTTGATGAG                         GATAAAGCAAGGGATATCCTGAAGAACGCTCCTGGTGTGGTGGTTATTGAT
genomic: GTGCGCATGCTGAGAGTGTTAATCTCCAGTTTGAGAATCCCCTTGATGAGgtacaatgat ... tcttgcgcagGATAAAGCAAGGGATATCCTGAAGAACGCTCCTGGTGTGGTGGTTATTGAT
EST: gi|26267158|gb|CA818221.1|CA818221
EST:     GTGCGCATGCTGAGAGTGTTAATCTCCAGTTTGAGAATCCCCTTGATGAG                         GATAAAGCAAGGGATATCCTGAAGAACGCTCCTGGTGTGGTGGTTATTGAT
genomic: GTGCGCATGCTGAGAGTGTTAATCTCCAGTTTGAGAATCCCCTTGATGAGgtacaatgat ... tcttgcgcagGATAAAGCAAGGGATATCCTGAAGAACGCTCCTGGTGTGGTGGTTATTGAT
EST: gi|34546690|gb|CF514922.1|CF514922
EST:     GTGCGCATGCTGAGAGTGTTAATCTCCAGTTTGAGAATCCCCTTGATGAG                         GATAAAGCAAGGGATATCCTGAAGAACGCTCCTGGTGTGGTGGTTATTGAT
genomic: GTGCGCATGCTGAGAGTGTTAATCTCCAGTTTGAGAATCCCCTTGATGAGgtacaatgat ... tcttgcgcagGATAAAGCAAGGGATATCCTGAAGAACGCTCCTGGTGTGGTGGTTATTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagcagtttctaccaaatggtttgctcatagatcaaatttcacattcttgcgcagGATAAAGCAAGGGATATCCTGAAGAACGCTCCTGGTGTGGTGGTTATTGATGAGCGGCCATCCAATAACTTTCCTACCCCATTAGAGGTATCAAACAAAG
                                          cattctt  CT-rich tract
                               atcaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcattgtcagagctgggttgtctaaagaaatttaactgaaattctaagcagtttctaccaaatggtttgctcatagatcaaatttcacattcttgcgcagGATAAAGCAAGGGATATCCTGAAGAACGCTCCTGGTGTGGTGGTTATTGATGAGCGGCCATCCAATAACTTTCCTACCCCATTAGAGGTATCAAACAAAG

-cattgtc
- - - - -gagctgg
- - - - - - - - - - - -aaagaaa
- - - - - - - - - - - - - - - - -aactgaaa
- - - - - - - - - - - - - - - - - - - - - -ctaagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctcata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atcaaat