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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGGGTCACCCCTGAAAGTGTTATTTACAGCTTTGGTACTGTCCTTTTGGATCTGCTAAGTGGAAAGCATATCCCGCCAAGTCATgtgagtcaattatacttgtgatgaacttatatgcttagttaatattacagatagcttcatttttgtttgacaatctggaaaccatgatcttgtggttgca...

Basic information

species Vitis vinifera
transcript Vv03s0038g03270.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g03270.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA02G48030.1 (Glycine max), 5'ss of exon 3
GAAGGGTCACCCCTGAAAGTGTTATTTACAGCTTTGGTACTGTCCTTTTGGATCTGCTAAGTGGAAAGCATATCCCGCCAAGTCATgtgagtcaattatacttgtgatgaacttatatgcttagttaa-tattacagatagcttc-atttttgtttgacaatctggaaaccatgatcttgtggttgca---
|||||||||| ||||||||||| |||||||||||||| || || ||| | || || || ||||| ||||| ||||| || |||||||| | |   || ||    | |    |   | |  | |  ||| || |    | | || | |  ||      |||||      || |   |||| |   | ||   
GAAGGGTCACGCCTGAAAGTGTCATTTACAGCTTTGGAACCGTTCTTCTAGACCTCCTCAGTGGCAAGCACATCCCTCCCAGTCATgtaactgccttctatcatttacctgcccctttcttcacctaactactttgcaaaactcccaccttctgcaaacaatt-----actagtttcttcttagttcactt

upper sequence: Vv03s0038g03270.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA14G00540.1 (Glycine max), 5'ss of exon 3
GAAGGGTCACCCCTGAAAGTGTTATTTACAGCTTTGGTACTGTCCTTTTGGATCTGCTAAGTGGAAAGCATATCCCGCCAAGTCATgtgagtcaattatacttgtgatgaacttatatgcttagtta---atattacagatagcttcatttttgtttgacaatctggaaaccatgatcttgtggttgca
|||||||||| ||||||||||| |||||||||||||| || || ||| | || || || ||||| ||||| ||||| || ||||| || | |   || ||    | ||   |   | |  | |  ||   | |  ||| |||  ||||||    |||  |||     |  ||   | | |       | 
GAAGGGTCACGCCTGAAAGTGTCATTTACAGCTTTGGAACCGTTCTTCTAGACCTCCTCAGTGGCAAGCACATCCCTCCCAGTCAAgtaactgccttctatcctttatctgcacctttcttcacctaaacacaggacaaataa-ttcattaaaatttt-caaatgaaacccccctaccctcaatcaac-

upper sequence: Vv03s0038g03270.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT4G35230.1 (Arabidopsis thaliana), 5'ss of exon 5
GAAGGGTCACCCCTGAAAGTGTTATTTACAGCTTTGGTACTGTCCTTTTGGATCTGCTAAGTGGAAAGCATATCCCGCCAAGTCATgtgagtcaattatacttgtgatgaacttatatgcttagttaatattacagatagcttcatttttgtttgacaatctggaaacca-tgatcttgtggttgca---
|||| || || |||||||||||||  || |||||||| ||||||||| ||||| |||| || ||||| || ||||| ||||| ||||| |||    |||  || || |  | |   |||  | || | || |||  |||  |   |||| ||   |  ||||    |    | ||  | | |||  |   
GAAGAGTGACACCTGAAAGTGTTACGTATAGCTTTGGAACTGTCCTTCTGGATTTGCTTAGCGGAAAACACATCCCTCCAAGCCATgtaagttc-ctatctttatgttttagtaggatgaattgt-actactactaata--tgtgttttggtgaaattatcttctcattggtcatgcttttgttttaagt

upper sequence: Vv03s0038g03270.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: PP1S178_86V6.1 (Physcomitrella patens), 5'ss of exon 6
GAAGGGTCACCCCTGAAAGTGTTATTTACAGCTTTGGTACTGTCCTTTTGGATCTGCTAAGTGGAAAGCATATCCCGCCAAGTCATgtgagtca----attatacttgtgat----gaacttatatgcttagttaatatt--------acagatagcttcatttttgtttgacaatctggaaaccatgatcttgtggttgca--------------------------
| ||||| || |||||||||||||||||||||| ||| ||||| ||  | |||||| | ||||| |||||| | || || ||||| || |||      ||  |     ||||    | | || | |  ||  |    ||         ||  || || |  ||||| ||      | |        | || | | | |   |                          
GTAGGGTGACACCTGAAAGTGTTATTTACAGCTATGGAACTGTTCTACTAGATCTGTTGAGTGGGAAGCATCTACCTCCTAGTCACgtaagtgctgacatagtgaccctgatttccgcagttgtgttgtttatcgtaatctatgatgaaccaatggcatgtttttttttatttttttttattttttttatttagcgttaatattttcctgaagcaagtgctcttgcag

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|110396180|gb|EC961861.1|EC961861
EST:     TTGGATCTGCTAAGTGGAAAGCATATCCCGCCAAGTCAT                         GCTCTTGATTTGATAAGGGACAAAAATATCATCCTTCTGATGGACTCACAT
genomic: TTGGATCTGCTAAGTGGAAAGCATATCCCGCCAAGTCATgtgagtcaat ... ttgttttcagGCTCTTGATTTGATAAGGGACAAAAATATCATCCTTCTGATGGACTCACAT
EST: gi|30325969|gb|CD009231.1|CD009231
EST:     GTACTGTCCTTTTGGATCTGCTAAGTGGAAAGCATATCCCGCCAAGTCAT                         GCTCTTGATTTGATAAGGGACAAAAATATCATCCTTCTGATGGACTCACAT
genomic: GTACTGTCCTTTTGGATCTGCTAAGTGGAAAGCATATCCCGCCAAGTCATgtgagtcaat ... ttgttttcagGCTCTTGATTTGATAAGGGACAAAAATATCATCCTTCTGATGGACTCACAT
EST: gi|33405090|gb|CF210717.1|CF210717
EST:     TGCTAAGTGGAAAG-ATATCCCGCCAAGTCAT                         GCTCTTGATTTGATAA-GGATCAAAAATATCATCCTTCTGATGGACTCACA
genomic: TGCTAAGTGGAAAGCATATCCCGCCAAGTCATgtgagtcaat ... ttgttttcagGCTCTTGATTTGATAAGGGA-CAAAAATATCATCCTTCTGATGGACTCACA
EST: gi|30328105|gb|CD011367.1|CD011367
EST:     GTACTGTCCTTTTGGATCTGCTAAGTGGAAAGCATATCCCGCCAAGTCAT                         GCTCTTGATTTGATAAGGGACAAAAATATCATCCTTCTGATGGACTCACAT
genomic: GTACTGTCCTTTTGGATCTGCTAAGTGGAAAGCATATCCCGCCAAGTCATgtgagtcaat ... ttgttttcagGCTCTTGATTTGATAAGGGACAAAAATATCATCCTTCTGATGGACTCACAT
EST: gi|30136281|gb|CB921619.1|CB921619
EST:     GTACTGTCCTTTTGGATCTGCTAAGTGGAAAGCATATCCCGCCAAGTCAT                         GCTCTTGATTTGATAAGGGACAAAAATATCATCCTTCTGATGGACTCACAT
genomic: GTACTGTCCTTTTGGATCTGCTAAGTGGAAAGCATATCCCGCCAAGTCATgtgagtcaat ... ttgttttcagGCTCTTGATTTGATAAGGGACAAAAATATCATCCTTCTGATGGACTCACAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGGGTCACCCCTGAAAGTGTTATTTACAGCTTTGGTACTGTCCTTTTGGATCTGCTAAGTGGAAAGCATATCCCGCCAAGTCATgtgagtcaattatacttgtgatgaacttatatgcttagttaatattacagatagcttcatttttgtttgacaatctggaaaccatgatcttgtggttgca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaacca