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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatcctatattttgccttcttttcattagaattggttgtttatgtctaaatgtcttaatttcttgttctgtaggtaacataaatattttactttgtacagGGTATGTGTACATTGACTCTCTCAGCAACAGTTCCTGCATTCAAGCCTGCTGATTGTGTGGGTTCAGTATGCCCTCCGGCTACCACAGCTCAGTATGCAG

Basic information

species Vitis vinifera
transcript Vv01s0011g06620.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g06620.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G26690.1 (Glycine max), 3'ss of exon 1
-------aatcctatattttgccttcttttcattagaattggttgtttatgtctaaatgtcttaatttcttgttctgtaggtaacataaatattttactttgtacagGGTATGTGTACATTGACTCTCTCAGCAACAGTTCCTGCATTCAAGCCTGCTGATTGTGTGGGTTCAGTATGCCCTCCGGCTACCACAGCTCAGTATGCAG
           | | |||      |   || |||| |  |     ||  ||| ||  ||||||  ||| ||||| |    || | ||        |||| ||| ||||| |||||||| ||||| || || ||| |  | |||||||| ||||||||||| ||| ||||||| ||||||||||| |||||| | || || ||||| |
tgacagtgtatcaaaattaaattcttacttaattacatatatgctttgttgtttagttgtctt--tttgttgttgtaatagtgatatgg-----ctactgtgtgcagGGGATGTGTACCTTGACACTTTCTGCATCTTTACCTGCATTGAAGCCTGCTGAATGTTTGGGTTCTGTATGCCCTCCAGCTACCCCTGCACAATATGCTG

upper sequence: Vv01s0011g06620.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G26670.1 (Glycine max), 3'ss of exon 3
--aatcctatattttgccttcttttcattagaattggttgtttatgtctaaatgtcttaatttct-tgttctgtaggtaacataaatattttactttgtacagGGTATGTGTACATTGACTCTCTCAGCAACAGTTCCTGCATTCAAGCCTGCTGATTGTGTGGGTTCAGTATGCCCTCCGGCTACCACAGCTCAGTATGCAG
    || |  ||||||  |||| | |||     ||| || | ||||  |   ||||     |||| |  |   |    ||  ||||        ||  | ||||| ||| ||||||||||||| || ||| |||||||||| || |||||||| || ||| ||||| | | ||| ||||| |||||  | || || ||||| |
tttgtcat-cattttgttttctgtacatctt--ttgcttctatatgctttgctgtccagtattctatacttgttttaaaatgtaaactggccgtttcattcagGGAATGGGTACATTGACTCTTTCTGCATCAGTTCCTGCCTTGAAGCCTGCAGAGTGTTTGGGTCCTGCATGTCCTCCAGCTACTCCTGCACAATATGCTG
















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|352794680|gb|FQ475178.1|FQ475178
EST:     ATTGTGGAAGATATTGGACAATCGCTGCTTTCTCCACAATATACTTCATC                         GGTATGTGTACATTGACTCTCTCAGCAACGGTTCCTGCATTCAAGCCTGCT
genomic: ATTGTGGAAGATATTGGACAATCGCTGCTTTCTCCACAATATACTTCATCgtaaatacta ... ctttgtacagGGTATGTGTACATTGACTCTCTCAGCAACAGTTCCTGCATTCAAGCCTGCT
EST: gi|352785794|gb|FQ475797.1|FQ475797
EST:     ATTGTGGAAGATATTGGACAATCGCTGCTTTCTCCACAATATACTTCATC                         GGTATGTGTACATTGACTCTCTCAGCAACAGTTCCTGCATTCAAGCCTGCT
genomic: ATTGTGGAAGATATTGGACAATCGCTGCTTTCTCCACAATATACTTCATCgtaaatacta ... ctttgtacagGGTATGTGTACATTGACTCTCTCAGCAACAGTTCCTGCATTCAAGCCTGCT
EST: gi|352769291|gb|FQ471440.1|FQ471440
EST:     ATTGTGGAAGATATTGGACAATCGCTGCTTTCTCCACAATATACTTCATC                         GGTATGTGTACATTGACTCTCTCAGCAACAGTTCCTGCATTCAAGCCTGCT
genomic: ATTGTGGAAGATATTGGACAATCGCTGCTTTCTCCACAATATACTTCATCgtaaatacta ... ctttgtacagGGTATGTGTACATTGACTCTCTCAGCAACAGTTCCTGCATTCAAGCCTGCT
EST: gi|352780890|gb|FQ466203.1|FQ466203
EST:     ATTGTGGAAGATATTGGACAATCGCTGCTTTCTCCACAATATACTTCATC                         GGTATGTGTACATTGACTCTCTCAGCAACAGTTCCTGCATTCAAGCCTGCT
genomic: ATTGTGGAAGATATTGGACAATCGCTGCTTTCTCCACAATATACTTCATCgtaaatacta ... ctttgtacagGGTATGTGTACATTGACTCTCTCAGCAACAGTTCCTGCATTCAAGCCTGCT
EST: gi|352773196|gb|FQ470811.1|FQ470811
EST:     ATTGTGGAAGATATTGGACAATCGCTGCTTTCTCCACAATATACTTCATC                         GGTATGTGTACATTGACTCTCTCAGCAACAGTTCCTGCATTCAAGCCTGCT
genomic: ATTGTGGAAGATATTGGACAATCGCTGCTTTCTCCACAATATACTTCATCgtaaatacta ... ctttgtacagGGTATGTGTACATTGACTCTCTCAGCAACAGTTCCTGCATTCAAGCCTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaaatgtcttaatttcttgttctgtaggtaacataaatattttactttgtacagGGTATGTGTACATTGACTCTCTCAGCAACAGTTCCTGCATTCAAGCCTGCTGATTGTGTGGGTTCAGTATGCCCTCCGGCTACCACAGCTCAGTATGCAG
                          aggtaac  putative branch site (score: 3)
                                        ttttacttt  putative PPT
                             taacataaatatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatcctatattttgccttcttttcattagaattggttgtttatgtctaaatgtcttaatttcttgttctgtaggtaacataaatattttactttgtacagGGTATGTGTACATTGACTCTCTCAGCAACAGTTCCTGCATTCAAGCCTGCTGATTGTGTGGGTTCAGTATGCCCTCCGGCTACCACAGCTCAGTATGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - tgccttc
- - - - - - - - - - - - - - - - tggttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acataaa