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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCACTAAGAAAAGCGATGTTTATAGTTTTGGTGTGCTACTGTTTGAACTTATCACTGGCAGGAATCCACAGCAAGGGCTCATGGAATATGTAAAACTAgtaagaacagtatctgcttgttggtttctatgtttgtgcttgtgctgtggtgcatgagtgtatcttgatgcgtttgaaaatatatgtaagcaaatacttaggattgacacagcatttttctggttatgattag

Basic information

species Glycine max
transcript GLYMA08G06620.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G06620.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv00s0361g00050.t01 (Vitis vinifera), 5'ss of exon 4
CTTCACTAAGAAAAGCGATGTTTATAGTTTTGGTGTGCTACTGTTTGAACTTATCACTGGCAGGAATCCACAGCAAGGGCTCATGGAATATGTAAAACTAgtaagaacagtatctgcttgttg--------------gtttctatgtttgtgcttgtgct--gtggtgcatg-agtgtatcttga--tgcgtttgaaa-atatatgtaagcaaatact--------taggattgacacagcatttttctggttatgattag
||||||||||||||| ||||||||||||||||| ||||| || |||||||| ||  | ||||||||||| |  || || ||||||||| ||||| |||| |||||  |  | |||      |                 | |||          | ||||  ||     |   | |    |||||  ||| | |||   ||||   |   || |||||         |  ||||    |  |  ||| ||   ||||  ||
CTTCACTAAGAAAAGTGATGTTTATAGTTTTGGCGTGCTGCTCTTTGAACTAATTGCAGGCAGGAATCCCCTACAGGGTCTCATGGAACATGTAGAACTTgtaagttctttctctatcatatacacaacaaccacatactcctagacaaaaaagtttgctaagtaactaacacaattggccttgagctgcttctgagttatatgcatcttcatatactatctatgacaacattgtagtattaactttatgtcaatgaacag

upper sequence: GLYMA08G06620.1 (Glycine max), 5'ss of exon 6
lower sequence: PP1S18_54V6.1 (Physcomitrella patens), 5'ss of exon 6
CTTCACTAAGAAAAGCGATGTTTATAGTTTTGGTGTGCTACTGTTTGAACTTATCACTGGCAGGAATCCACAGCAAGGGCTCATGGAATATGTAAAACTAgtaagaacagta-tctgcttgttggtttctat-gtttgtgcttgtgc-tgtggtgcatgagtg--tatcttgatgcgtttgaa-aatatatgtaagcaaatacttagga---ttgacacagcatttttctggtta-tgattag------------------------------------------------------
|||||||   ||||| |||||||||||||| |||||||| || ||||| |||||||||| | | || ||||| |||||| | ||||| || ||  | |||||| |  |   | ||  | | ||  ||| ||| ||   |  || ||  ||   | |  || |   | || |||    | ||   ||  | | |  |  ||   ||||     |||   ||| |  | ||   | | | |  ||                                                      
CTTCACTGCAAAAAGTGATGTTTATAGTTTCGGTGTGCTTCTTTTTGAGCTTATCACTGCCCGTAACCCACAACAAGGGTTAATGGACTACGTTCACCTAgtatgcccttgactcaacatctttctttttatcgtgcttagttatgaatggcctcctagaatacttgtcctgaattttctgtttaagttgtattggttaagggttagagggtttgtttcagtagctgtcacatcaatcacgagcgaaggatccaatctattcttacatgctgaggaatatgtgatctgtgaatgaag

upper sequence: GLYMA08G06620.1 (Glycine max), 5'ss of exon 6
lower sequence: PP1S18_53V6.1 (Physcomitrella patens), 5'ss of exon 6
CTTCACTAAGAAAAGCGATGTTTATAGTTTTGGTGTGCTACTGTTTGAACTTATCACTGGCAGGAATCCACAGCAAGGGCTCATGGAATATGTAAAACTAgtaagaacagta-tctgcttgttggtttctatgtttgtgcttgtgctgtggtgcatgagtgtatcttgatgcgtttgaaaatatatgtaagcaaatacttaggattgacacagcatttttctggttatgattag
|||||||   ||||| |||||||||||||| |||||||| || ||||| |||||||||| | | || ||||| |||||| | ||||| || ||  | |||||| |  |   | ||  | | ||  ||| ||   | ||||||     ||  || ||| |  |      || | | |    |  | | |    || |  |   | || |                          
CTTCACTGCAAAAAGTGATGTTTATAGTTTCGGTGTGCTTCTTTTTGAGCTTATCACTGCCCGTAACCCACAACAAGGGTTAATGGACTACGTTCACCTAgtatgcccttgactcaacatctttcttttta---tcgtgctta----gttatgaatg-gcctcctagaatacttgtcctgaattttctgtttaagttgtattggttaa--------------------------

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|6913046|gb|AW394510.1|AW394510
EST:     CCACAGCAAGGGCTCATGGAATATGTAAAACTA                         GCAGTCATGGAAAGCGAGGGTAAGGTTGGATGGGAAGAAATTGTGGACCCA
genomic: CCACAGCAAGGGCTCATGGAATATGTAAAACTAgtaagaacag ... ttatgattagGCAGTCATGGAAAGCGAGGGTAAGGTTGGATGGGAAGAAATTGTGGACCCA
EST: gi|10845425|gb|BF071104.1|BF071104
EST:     TTATCACTGGCAGGAATCCACAGCAAGGGCTCATGGAATATGTAAAACTA                         GCAGTCATGGAAAGCGAGGGTAAGGTTGGATGGGAAGAAATTGTGGACCCA
genomic: TTATCACTGGCAGGAATCCACAGCAAGGGCTCATGGAATATGTAAAACTAgtaagaacag ... ttatgattagGCAGTCATGGAAAGCGAGGGTAAGGTTGGATGGGAAGAAATTGTGGACCCA
EST: gi|16345462|gb|BI971057.1|BI971057
EST:     TTATCACTGGCAGGAATCCACAGCAAGGGCTCATGGAATATGTAAAACTA                         GCAGTCATGGAAAGCGAGGGTAAGGTTGGATGGGAAGAAATTGTGGACCCA
genomic: TTATCACTGGCAGGAATCCACAGCAAGGGCTCATGGAATATGTAAAACTAgtaagaacag ... ttatgattagGCAGTCATGGAAAGCGAGGGTAAGGTTGGATGGGAAGAAATTGTGGACCCA
EST: gi|208026987|gb|GD826813.1|GD826813
EST:     ATCACTGGCAGGAATCCACAGCAAGGGCTCATGGAATATGTAAAACTA                         GCAGTCATGGAAAGCGAGGGTAAGGTTGGATGGGAAGAAATTGTGGACCCA
genomic: ATCACTGGCAGGAATCCACAGCAAGGGCTCATGGAATATGTAAAACTAgtaagaacag ... ttatgattagGCAGTCATGGAAAGCGAGGGTAAGGTTGGATGGGAAGAAATTGTGGACCCA
EST: gi|193664890|gb|FK611634.1|FK611634
EST:     TTATCACTGGCAGGAATCCACAGCAAGGGCTCATGGAATATGTAAAACTA                         GCGGTCATGGAAAGCGAGGGTAAGGTTGGATGGGAAGAAATTGTGGACCCA
genomic: TTATCACTGGCAGGAATCCACAGCAAGGGCTCATGGAATATGTAAAACTAgtaagaacag ... ttatgattagGCAGTCATGGAAAGCGAGGGTAAGGTTGGATGGGAAGAAATTGTGGACCCA
EST: gi|8283551|gb|BE021110.1|BE021110
EST:     TTATCACTGGCAGGAATCCACAGCAAGGGCTCATGGAATATGTAATACTA                         GCAGTCATGGAAAGCGAGGGTAATGTTGGATGGGAAGAAATTGTGGACCCA
genomic: TTATCACTGGCAGGAATCCACAGCAAGGGCTCATGGAATATGTAAAACTAgtaagaacag ... ttatgattagGCAGTCATGGAAAGCGAGGGTAAGGTTGGATGGGAAGAAATTGTGGACCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCACTAAGAAAAGCGATGTTTATAGTTTTGGTGTGCTACTGTTTGAACTTATCACTGGCAGGAATCCACAGCAAGGGCTCATGGAATATGTAAAACTAgtaagaacagtatctgcttgttggtttctatgtttgtgcttgtgctgtggtgcatgagtgtatcttgatgcgtttgaaaatatatgtaagcaaatacttaggattgacacagcatttttctggttatgattag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA