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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGAAAGTGGAGCAGTTTTGCCTCACTAGCCCAAATGACAATGATTCATGGGACATGCATGAGGAAATGCTGAAGAACTCTGAAGATTTCTACAAAGCGgtatgatacagccacagtgcccctcattaagcgactaatgtttaaggccactctggatgagtttaaatttcaaataaataataaatataaataaataata...

Basic information

species Glycine max
transcript GLYMA20G37700.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G37700.1 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os03g10190.1 (Oryza sativa), 5'ss of exon 7
TGAGAAAGTGGAGCAGTTTTGCCTCACTAGCCCAAATGACAATGATTCATGGGACATGCATGAGGAAATGCTGAAGAACTCTGAAGATTTCTACAAAGCGgtatgatacagccacagtgcccctcattaagcgactaatgtttaaggccactctgga-tgagtttaaatttcaaataaataataaata--taaataaataata
||| || | || || || || |||| || |||||||||||||| || ||||| |||||||| |||||| | || || || |||||||||||||| | |||| ||| | | | || |||||| || |||| || ||| | || ||| || || ||||| | | || | || | |
TGAAAAGATCGAACAATTCTGTGTCACAAGTCCAAATGACAATGAATCTTGGGAGATGCATGAAGAAATGATTAAAAATTCAGAAGATTTCTACAAGGAGgtagagatcagaagcttcgtacatc-ttaagcacct--tgtta-----catcctgaactgtcttttgatgtctaataatttcttcattgtccattatacag--

upper sequence: GLYMA20G37700.1 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os01g37837.1 (Oryza sativa), 5'ss of exon 7
TGAGAAAGTGGAGCAGTTTTGCCTCACTAGCCCAAATGACAATGATTCATGGGACATGCATGAGGAAATGCTGAAGAACTCTGAAGATTTCTACAAAGCGgtatgatacagccacagtgcccctcattaagcgactaatgtttaaggccactctggatgagtttaaatttcaaataaataataaatataaat-aaataata
|| || | ||||| || || | || || |||||||||||||| || ||||| |||||||| |||||| | || || || |||||||||||||| | |||| | | | | | || |||||| || |||| | || ||| | ||| | | || | | | | | | || | | |
CGAAAAGATTGAGCAATTCTGTGTTACAAGTCCAAATGACAATGAATCCTGGGAGATGCATGAAGAAATGATAAAAAATTCAGAAGATTTCTACAAGGAGgtagacatcggaagcttcacacatc-ttaagcacct--tgttacatgcggaactgtct---tttgatgtctaatcatttcttcattgtctattatacag--

upper sequence: GLYMA20G37700.1 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G172101_T01 (Zea mays), 5'ss of exon 7
TGAGAAAGTGGAGCAGTTTTGCCTCACTAGCCCAAATGACAATGATTCATGGGACATGCATGAGGAAATGCTGAAGAACTCTGAAGATTTCTACAAAGCGgtatgatacagc-cacagtgcccctcattaagcgactaatgtttaaggccactctggatgagtttaaatttcaaataaataataaatataaataaataata
||| ||| | || || || ||| | || |||||||||||||| ||||| ||||| |||||||| || ||||| || ||||| ||||||| ||| || | |||| | ||| ||| | | || | ||| | | | || | ||| | || ||||||| | | ||| | | |
TGAAAAAATCGAACAATTCTGCATTACAAGCCCAAATGACAACGATTCTTGGGAGATGCATGAAGAGATGCTAAAAAACTCAGAAGATTACTATAAGGAGgtaataatcagtatgttgtgatctttataac----ctagtttgt----cctccctgagtt-gtctaaatttttatttaatgtccatcttgcag--------

upper sequence: GLYMA20G37700.1 (Glycine max), 5'ss of exon 7
lower sequence: Vv14s0128g00370.t01 (Vitis vinifera), 5'ss of exon 7
TGAGAAAGTGGAGCAGTTTTGCCTCACTAGCCCAAATGACAATGATTCATGGGACATGCATGAGGAAATGCTGAAGAACTCTGAAGATTTCTACAAAGCGgtatgatacagccacagtgcccctcattaagcgactaatgtttaaggccactctggatgagtttaaatttcaaataaataataaatataaataaataata-
|||||||||||||||||| ||| | || |||||||||| ||||| || ||||||||||||||||||||| | || ||||| || || || ||||| |||| | | | || | || | |||| | || | | | | | ||| | || || ||| || || || | | || |
TGAGAAAGTGGAGCAGTTCTGCATTACCAGCCCAAATGGAAATGACTCTTGGGACATGCATGAGGAAATGATTAAAAACTCAGAGGACTTTTACAAGATGgtacaagaattcttcatttccatcagaaagaggacttttagttt-gcctttttttcttatgttgctttatctaacaaaaaagttttaacaaaagaaaagac

upper sequence: GLYMA20G37700.1 (Glycine max), 5'ss of exon 7
lower sequence: PP1S13_192V6.2 (Physcomitrella patens), 5'ss of exon 5
TGAGAAAGTGGAGCAGTTTTGCCTCACTAGCCCAAATGACAATGATTCATGGGACATGCATGAGGAAATGCTGAAGAACTCTGAAGATTTCTACAAAGCGgtat-gatacagccacagtgcccctcattaagcgactaatgtttaaggccactctggatgagtttaaatttcaaataaataataaatataaataaataata
|||||| ||||||||||| || | |||||||||||||| ||||| || ||||| ||||||| |||||| |||| ||||| ||||| ||||| || ||||| | | | || | | | | | ||| || | | | || || | | || | | | | | | | | | | || |
TGAGAAGGTGGAGCAGTTCTGTATTACTAGCCCAAATGATAATGACTCTTGGGAAGTGCATGAAGAAATGTTGAAAAACTCAGAAGAATTCTATCAACAGgtattggtgctcacaaacttctcatgtttagctgaggactttagcagttggctgtag-tggatatcttatcgaccaagttggcgattctcgttgaagttca

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|192299348|gb|FG988719.1|FG988719
EST:     GGGACATACATGAGGAAATGCTGAAGAACTCTGAAGATTTCTACAAAGCG                         TTAAACCTTCCCTATCAAGTTGTTTCC
genomic: GGGACATGCATGAGGAAATGCTGAAGAACTCTGAAGATTTCTACAAAGCGgtatgataca ... tttactgcagTTAAACCTTCCCTATCAAGTTGTTTCC
EST: gi|151396984|gb|EV266857.1|EV266857
EST:     GGGACATGCATGAGGAAATGCTGAAGAACTCTGAAGATTTCTACAAAGCG                         TTAAACCTTCCCTATCAAGTTGTTTCCATTGTATCTGGTGCTTTGAATGAT
genomic: GGGACATGCATGAGGAAATGCTGAAGAACTCTGAAGATTTCTACAAAGCGgtatgataca ... tttactgcagTTAAACCTTCCCTATCAAGTTGTTTCCATTGTATCTGGTGCTTTGAATGAT
EST: gi|9564750|gb|BE474259.1|BE474259
EST:     GGGACATGCATGAGGAAATGCTGAAGAACTCTGAAGATTTCTACAAAGCG                         TTAAACCTTCCCTATCAAGTTGTTTCCATTGTATCTGGTGCTTTGAATGAT
genomic: GGGACATGCATGAGGAAATGCTGAAGAACTCTGAAGATTTCTACAAAGCGgtatgataca ... tttactgcagTTAAACCTTCCCTATCAAGTTGTTTCCATTGTATCTGGTGCTTTGAATGAT
EST: gi|192296773|gb|FG993071.1|FG993071
EST:     GGGACATGCATGAGGAAATGCTGAAGAACTCTGAAGATTTCTACAAAGCG                         TTAAACCTTCCCTATCAAGTTGTTTCCATTGTATCTGGTGCTTTGAATGAT
genomic: GGGACATGCATGAGGAAATGCTGAAGAACTCTGAAGATTTCTACAAAGCGgtatgataca ... tttactgcagTTAAACCTTCCCTATCAAGTTGTTTCCATTGTATCTGGTGCTTTGAATGAT
EST: gi|15286655|gb|BI470546.1|BI470546
EST:     TGAAGATTTCTACAAAGCG                         TTAAACCTTCCCTATCAAGTTGTTTCCATTGTATCTGGTGCTTTGAATGAT
genomic: TGAAGATTTCTACAAAGCGgtatgataca ... tttactgcagTTAAACCTTCCCTATCAAGTTGTTTCCATTGTATCTGGTGCTTTGAATGAT
EST: gi|192296772|gb|FG993070.1|FG993070
EST:     GGGACATGCATGAGGAAATGCTGAAGAACTCTGAAGATTTCTACAAAGCG                         TTAAACCTTCCCTATCAAGTTGTTTCCATTGTATCTGGTGCTTTGAATGAT
genomic: GGGACATGCATGAGGAAATGCTGAAGAACTCTGAAGATTTCTACAAAGCGgtatgataca ... tttactgcagTTAAACCTTCCCTATCAAGTTGTTTCCATTGTATCTGGTGCTTTGAATGAT
EST: gi|13788033|gb|BG650625.1|BG650625
EST:     GGGACATGCATGAGGAAATGCTGAAGAACTCTGAAGATTTCTACAAAGCG                         TTAAATCTTCCCTATCAAGTTGTTTCCATTGTATCTGGTGCATTGAATGAT
genomic: GGGACATGCATGAGGAAATGCTGAAGAACTCTGAAGATTTCTACAAAGCGgtatgataca ... tttactgcagTTAAACCTTCCCTATCAAGTTGTTTCCATTGTATCTGGTGCTTTGAATGAT
EST: gi|15814019|gb|BI786294.1|BI786294
EST:     GGGACATGCATGAGGAAATGCTGAAGAACTCTGAAGATTTCTACAAAGCG                         TTAAACCTTCCCTATCAAGTTGTTTCCATTGTATCTGGTGCTTTGAATGAT
genomic: GGGACATGCATGAGGAAATGCTGAAGAACTCTGAAGATTTCTACAAAGCGgtatgataca ... tttactgcagTTAAACCTTCCCTATCAAGTTGTTTCCATTGTATCTGGTGCTTTGAATGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAGAAAGTGGAGCAGTTTTGCCTCACTAGCCCAAATGACAATGATTCATGGGACATGCATGAGGAAATGCTGAAGAACTCTGAAGATTTCTACAAAGCGgtatgatacagccacagtgcccctcattaagcgactaatgtttaaggccactctggatgagtttaaatttcaaataaataataaatataaataaataata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcccctc