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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTCTTGTTTTATCATGTGTTTGCAAAGGAGTTGAAACCACACAAGCCCCTGACAAAGTTCATGTGCGTCAAAGGGATTGTTTTCTTCTGCTTTTGGCAGgtacaacttcacatccccttccttcttaattgctttgtaaaagttgttgaagagcattggataacttgaaagtaaaatttctatggttgaaccccttcta...

Basic information

species Vitis vinifera
transcript Vv00s0404g00020.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0404g00020.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G025242_T02 (Zea mays), 5'ss of exon 4
TGTCTTGTTTTATCATGTGTTTGCAAAGGAGTTGAAACCACACAAGCCCCTGACAAAGTTCATGTGCGTCAAAGGGATTGTTTTCTTCTGCTTTTGGCAGgtacaacttcacatccccttccttcttaattgctttgtaaaagttgttgaagagcattggataacttgaa--agtaaaatttctatggttgaaccccttcta---
 ||  | || || ||  ||||||| || ||| ||  ||| |||||||| ||  |||||||| ||||| ||||||||||||| |||||||  || ||||||||| |    || |||  || |   || ||| ||  | |      |  |  ||    |  || | ||| |   |   || |||  | |  |||  | |||      
GGTTCTCTTCTACCACTTGTTTGCTAAAGAGCTGGCACCTCACAAGCCTCTTGCAAAGTTCTTGTGCATCAAAGGGATTGTCTTCTTCTCTTTCTGGCAGgtata----catatcatct-cgacctgaatggccgtttggttccttcttcagcttttctgaaagctttatttatataactttgcacgagtgattctcttgatttc

upper sequence: Vv00s0404g00020.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA15G07390.1 (Glycine max), 5'ss of exon 3
TGTCTTGTTTTATCATGTGTTTGCAAAGGAGTTGAAACCACACAAGCCCCTGACAAAGTTCATGTGCGTCAAAGGGATTGTTTTCTTCTGCTTTTGGCAGgtacaacttcacatccccttccttcttaattgctttgtaaaagttgttgaagagcattggataacttgaa--agtaaaatttctatggttgaaccccttcta
 ||  | ||||| ||||||||||| || ||  ||  |||||||||||| ||  | || ||| ||||| ||||||| ||||||||||||||||||||||||||| ||||    |||   |   |  | |  || |  |   |  |   |||  | | | |    |    ||  || | |    | |     |||     || |
GGTGGTCTTTTACCATGTGTTTGCTAAAGAACTGGCACCACACAAGCCTCTAGCGAAATTCTTGTGCATCAAAGGAATTGTTTTCTTCTGCTTTTGGCAGgta-aactcattatcatttatataatcatctgataagctgagttaaatgacca-cttagagccataaaaagcagcacagagccaacaagagaataaactcga

upper sequence: Vv00s0404g00020.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA13G31920.2 (Glycine max), 5'ss of exon 3
TGTCTTGTTTTATCATGTGTTTGCAAAGGAGTTGAAACCACACAAGCCCCTGACAAAGTTCATGTGCGTCAAAGGGATTGTTTTCTTCTGCTTTTGGCAGgtacaacttcacatccccttccttcttaattgctttgtaaaagttgttgaagagcattggataacttgaaagtaaaatttctatggttgaaccccttcta---
 ||  | ||||| ||||||||||| || ||  ||  ||||||||| || ||  | || ||| ||||| ||||||| |||||||||||||||||||||||||||  |  ||| |           |  ||   |     ||||  |||        || | || | |  |||  |           | ||   | |  | |   
GGTGGTCTTTTACCATGTGTTTGCTAAAGAACTGGCACCACACAAACCTCTAGCTAAATTCTTGTGCATCAAAGGAATTGTTTTCTTCTGCTTTTGGCAGgta--agctcatacagaaaaagaacaaaaaaacaaaa-aaaacctgtgtttacatatagaatcaatataaataattggactagctgatggttctcaaccattt

upper sequence: Vv00s0404g00020.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT1G11200.1 (Arabidopsis thaliana), 5'ss of exon 3
TGTCTTGTTTTATCATGTGTTTGCAAAGGAGTTGAAACCACACAAGCCCCTGACAAAGTTCATGTGCGTCAAAGGGATTGTTTTCTTCTGCTTTTGGCAGgtaca-acttcacatccccttccttcttaattgctttgtaaaagttgttgaagagcattggataacttgaaagtaaaat-ttctatggttgaaccccttcta-----
 ||    || || ||||| ||||| || |||||| | || || ||||| || |||||||||||||||||||||||||| || ||||||||||||||||||||| | |||| |  |||   |  |||||   ||| |   ||| |      || | ||   | |  ||    | ||   | ||| ||     |||    | |      
GGTGAAATTCTACCATGTTTTTGCTAAAGAGTTGGAGCCTCATAAGCCTCTTACAAAGTTCATGTGCGTCAAAGGGATAGTGTTCTTCTGCTTTTGGCAGgtaaatacttaatttccaactttttctt---tgcctgccaaatgcc----aaaatcacaagttctctgcctactagtttcttcaatcaactaactgagtttgatgag

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|351025607|gb|FQ426621.1|FQ426621
EST:     GACAAAGTTCATGTGCGTCAAAGGGATTGTTTTTCT-CTGCTTTTGGCAG                         GGCATTGTGCTCGAGATTCTAGTTGCACTGGG
genomic: GACAAAGTTCATGTGCGTCAAAGGGATTGTTTT-CTTCTGCTTTTGGCAGgtacaacttc ... ccacatgcagGGCATAGTGCTCGAGATTCTAGTTGCACTGGG
EST: gi|110720058|gb|EE097300.1|EE097300
EST:     TGACAAAGTTCATGTGCGTCAAAGGGATTGTTTTCTTCTGCTTTTGGCAG                         GGCATTGTGCTCGAGATTCTAGTTGCACTGGGCATCATTCGATCACACCAT
genomic: TGACAAAGTTCATGTGCGTCAAAGGGATTGTTTTCTTCTGCTTTTGGCAGgtacaacttc ... ccacatgcagGGCATAGTGCTCGAGATTCTAGTTGCACTGGGCGTCATTCGATCACACCAT
EST: gi|351030194|gb|FQ432132.1|FQ432132
EST:     TGACAAAGTTCATGTGCGTCAAAGGGATTGTTTTCTTCTGCCTTTGGCAG                         GGCATTGTGCTCGAG
genomic: TGACAAAGTTCATGTGCGTCAAAGGGATTGTTTTCTTCTGCTTTTGGCAGgtacaacttc ... ccacatgcagGGCATAGTGCTCGAG
EST: gi|161718894|gb|FC067003.1|FC067003
EST:     TGACAAAGTTCATGTGCGTCAAAGGGATTGTTTTCTTCTGCTTTTGGCAG                         GGCAT-GTGCTCGAGAT-CTAGT-GCACTGG-CATCAT-CGATCACAC-AT
genomic: TGACAAAGTTCATGTGCGTCAAAGGGATTGTTTTCTTCTGCTTTTGGCAGgtacaacttc ... ccacatgcagGGCATAGTGCTCGAGATTCTAGTTGCACTGGGCGTCATTCGATCACACCAT
EST: gi|351039382|gb|FQ461249.1|FQ461249
EST:     TGACAAAGTTCATGTGCGTCAAAGGGATTGTTTTCTTCTGCTTTTGGCAG                         GGCATTGTGCTCGAGATTCTAGTTGCACTGGGCGTCATT
genomic: TGACAAAGTTCATGTGCGTCAAAGGGATTGTTTTCTTCTGCTTTTGGCAGgtacaacttc ... ccacatgcagGGCATAGTGCTCGAGATTCTAGTTGCACTGGGCGTCATT
EST: gi|30127638|gb|CB912977.1|CB912977
EST:     TGACAAAGTTCATGTGCGTCAAAGGGATTGTTTTCTTCTGCTTTTGGCAG                         GGCATTGTGCTCGAGATTCTAGTTGCACTGGGCGTCATTCGATCACACCAT
genomic: TGACAAAGTTCATGTGCGTCAAAGGGATTGTTTTCTTCTGCTTTTGGCAGgtacaacttc ... ccacatgcagGGCATAGTGCTCGAGATTCTAGTTGCACTGGGCGTCATTCGATCACACCAT
EST: gi|33404104|gb|CF209731.1|CF209731
EST:     GACAAAGTTCATGTGNCG-CAAAGGGNTTGTTTTCTTCTGCTTTTNGCAG                         GGCATTGTGCTCGAGATTCTA
genomic: GACAAAGTTCATGTG-CGTCAAAGGGATTGTTTTCTTCTGCTTTTGGCAGgtacaacttc ... ccacatgcagGGCATAGTGCTCGAGATTCTA
EST: gi|33404188|gb|CF209815.1|CF209815
EST:     TGACAAAGTTCATGTGCGTCAAAGGGATTGTTTTCTTCTGCTTTTGGCAG                         GGCATTGTGCTCGAGATTCTAGTTGCACTGGGCATCATTCGATCACACCAT
genomic: TGACAAAGTTCATGTGCGTCAAAGGGATTGTTTTCTTCTGCTTTTGGCAGgtacaacttc ... ccacatgcagGGCATAGTGCTCGAGATTCTAGTTGCACTGGGCGTCATTCGATCACACCAT
EST: gi|30124784|gb|CB910123.1|CB910123
EST:     TGACAAAGTTCATGTGCGTCAAAGGGATTGTTTTCTTCTGCTTTTGGCAG                         GGCATTGTGCTCGAGATTCTAGTTGCACTGGGCGTCATTCGATCACACCAT
genomic: TGACAAAGTTCATGTGCGTCAAAGGGATTGTTTTCTTCTGCTTTTGGCAGgtacaacttc ... ccacatgcagGGCATAGTGCTCGAGATTCTAGTTGCACTGGGCGTCATTCGATCACACCAT
EST: gi|110381469|gb|EC934548.1|EC934548
EST:     TGACAAAGTTCATGTGCGTCAAAGGGATTGTTTTCTTCTGCTTTTGGCAG                         GGCATTGTGCTCGAGATTCTAGTTGCACTGGGCATCATTCGATCACACCAT
genomic: TGACAAAGTTCATGTGCGTCAAAGGGATTGTTTTCTTCTGCTTTTGGCAGgtacaacttc ... ccacatgcagGGCATAGTGCTCGAGATTCTAGTTGCACTGGGCGTCATTCGATCACACCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTCTTGTTTTATCATGTGTTTGCAAAGGAGTTGAAACCACACAAGCCCCTGACAAAGTTCATGTGCGTCAAAGGGATTGTTTTCTTCTGCTTTTGGCAGgtacaacttcacatccccttccttcttaattgctttgtaaaagttgttgaagagcattggataacttgaaagtaaaatttctatggttgaaccccttcta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtaaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggataac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agtaaaa