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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTAGGAGAAAGTGTGCAAAAACCTTTACTATACTATAACAACAACTTGACTGGGACAATCACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAGAAGgtaaaatccttcttgtttctcagtcctgcatgatagaccttaactgtactgaaagaatattattaattctcaaactgctatggcaaccacccgtaatgtc...

Basic information

species Glycine max
transcript GLYMA01G43540.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G43540.2 (Glycine max), 5'ss of exon 3
lower sequence: AT1G64440.1 (Arabidopsis thaliana), 5'ss of exon 3
AGTAGGAGAAAGTGTGCAAAAACCTTTACTATACTATAACAACAACTTGACTGGGACAATCACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAGAAGgtaaaatccttcttgtttctcagtcctgcatgatagaccttaactgtactgaaagaatattattaattctcaaac-tgctatggcaaccacccgt-aatgtc------
||| || || || ||| ||||| | || || |||||||| ||||||| || ||| || || || |||||||| |||||||| || ||||| || |||||||||||| || ||| | || | | || | | | || ||| | | | |||| || | | | | | | | || ||
AGTTGGTGAGAGCGTGGCGAAACCACTTCTGTATTATAACAATAACTTGATTGCGACTATTACACTTTTGGAAGTAATGGCTGCACACGGATGTAAAAAGgtaaaatccccttttggtctgtattgcagatttttggtattccttatg-tatgtgagtat--gtgacagtgaaacatgatttaactttctctcattgatctcaatcag

upper sequence: GLYMA01G43540.2 (Glycine max), 5'ss of exon 3
lower sequence: Vv02s0025g01560.t01 (Vitis vinifera), 5'ss of exon 3
AGTAGGAGAAAGTGTGCAAAAACCTTTACTATACTATAACAACAACTTGACTGGGACAATCACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAGAAGgtaaaatccttcttgtttctcagtcctgcatgatagacctta-actgtactgaaagaatattattaattctcaaactgctatggcaaccacccgtaatgtc
||| || ||||||||||||||||| || || |||| | | |||||| | | ||| ||||| ||||||||||||||||||||||||||||||||||| |||||| | | | || || || | | | ||| | | | | || | | | | | || | | | |
AGTTGGTGAAAGTGTGCAAAAACCCTTGCTTTACTTTGATAACAACCTTATTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAGgtattgcctcttacactgct-gctctattattactcataatgtgttgttttccataactgttgcttctagttgagtagacatatgtaatgtctcagctatt

upper sequence: GLYMA01G43540.2 (Glycine max), 5'ss of exon 3
lower sequence: Vv02s0025g01580.t01 (Vitis vinifera), 5'ss of exon 3
AGTAGGAGAAAGTGTGCAAAAACCTTTACTATACTATAACAACAACTTGACTGGGACAATCACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAGAAGgtaaaatccttcttgtttctcagtcctgcatgatagaccttaactgtactgaaagaatattattaattctcaaactgctatggcaaccacccgtaatgtc-
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AGTTGGTGAAAGTGTGCAAAAACCATTGCTTTACTATGATAACAACCTTATTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAGgtattatctctggcactgctgctctattcatattcataatgcattgttttcata-actcttgcttcttgttgagtagacacatgtaatgtctcagctattt

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|209713128|gb|BW653837.1|BW653837
EST:     CTGGGACAATCACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAGAAG                         CTCGTGTTTTCATCTTCAGCAACTGTATATGGTTGGCCAAAGGAGGTTCCA
genomic: CTGGGACAATCACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAGAAGgtaaaatcct ... atgatttcagCTCGTGTTTTCATCTTCAGCAACTGTATATGGTTGGCCAAAGGAGGTTCCA
EST: gi|192299883|gb|FG990091.1|FG990091
EST:     CACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAGAAG                         CTCGTGTTTTCATCTTCAGCAACTGTATATGGTTGGCCAAAGGAGGTTCCA
genomic: CACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAGAAGgtaaaatcct ... atgatttcagCTCGTGTTTTCATCTTCAGCAACTGTATATGGTTGGCCAAAGGAGGTTCCA
EST: gi|192333229|gb|FK026110.1|FK026110
EST:     CTGGGACAATCACTCTATTGGAAGTCATGGCTGCCCATGGATACAAGAAG                         CTCGTGTTTTCATCTTCAGCAACTGTATATGGTTGGCC
genomic: CTGGGACAATCACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAGAAGgtaaaatcct ... atgatttcagCTCGTGTTTTCATCTTCAGCAACTGTATATGGTTGGCC
EST: gi|15000492|gb|BI321306.1|BI321306
EST:     CTGGGACAATCACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAGAAG                         CTCGTGTTTTCATCTTCAGCAACTGTATATGGTTGGCCAAAGGAGGTTCCA
genomic: CTGGGACAATCACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAGAAGgtaaaatcct ... atgatttcagCTCGTGTTTTCATCTTCAGCAACTGTATATGGTTGGCCAAAGGAGGTTCCA
EST: gi|15813402|gb|BI785677.1|BI785677
EST:     CTGGGACAATCACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAGAAG                         CTCGTGTTTTCATCTTCAGCAACTGTATATGGTTGGCCA
genomic: CTGGGACAATCACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAGAAGgtaaaatcct ... atgatttcagCTCGTGTTTTCATCTTCAGCAACTGTATATGGTTGGCCA
EST: gi|151398432|gb|EV268303.1|EV268303
EST:     CTGGGACAATCACTCTATTGGAAGTCATGGCTGCCCGTGGATGCAAGAAG                         CTCGTGTTTTCATCTTCAGCAACTGTATATGGTTGGCCAAAGGAGGTTCCA
genomic: CTGGGACAATCACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAGAAGgtaaaatcct ... atgatttcagCTCGTGTTTTCATCTTCAGCAACTGTATATGGTTGGCCAAAGGAGGTTCCA
EST: gi|12489618|gb|BG043139.1|BG043139
EST:     CTGGGACAATCACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAGAAG                         CTCGTGTTTTCATCTTCAGCAACTGTATATGGTTGGCCAAAGGAGGTTCCA
genomic: CTGGGACAATCACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAGAAGgtaaaatcct ... atgatttcagCTCGTGTTTTCATCTTCAGCAACTGTATATGGTTGGCCAAAGGAGGTTCCA
EST: gi|14991639|gb|BI317312.1|BI317312
EST:     CTGGGACAATCACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAGAAG                         CTCGTGTTTTCATCTTCAGCAACTGTATATGGTTGGCCAAAGGAGGTTCCA
genomic: CTGGGACAATCACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAGAAGgtaaaatcct ... atgatttcagCTCGTGTTTTCATCTTCAGCAACTGTATATGGTTGGCCAAAGGAGGTTCCA
EST: gi|209699775|gb|BW652120.1|BW652120
EST:     CTGGGACAATCACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAGAAG                         CTCGTGTTTTCATCTTCAGCAACTGTATATGGTTGGCCAAAGGAGGTTCCA
genomic: CTGGGACAATCACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAGAAGgtaaaatcct ... atgatttcagCTCGTGTTTTCATCTTCAGCAACTGTATATGGTTGGCCAAAGGAGGTTCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTAGGAGAAAGTGTGCAAAAACCTTTACTATACTATAACAACAACTTGACTGGGACAATCACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAGAAGgtaaaatccttcttgtttctcagtcctgcatgatagaccttaactgtactgaaagaatattattaattctcaaactgctatggcaaccacccgtaatgtc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccacccg