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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCGAGATATTCAGGCATGGGAATATATTCCTCTTGGTCCATTTCTTGGCAAGAGTTTTGgtaagatgtttcaaataattacttaatatcttttaagtcctatggaaaaaagctgggcatttggacttgtgcagtatatccaacgtggatgattgcatgtaccatttgctctagatataaactatcactttacagttgttatttacttattttagagttaaccatcctttagggtgctaactaaaattatacag

Basic information

species Glycine max
transcript GLYMA09G01270.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G01270.1 (Glycine max), 5'ss of exon 8
lower sequence: AT1G12050.1 (Arabidopsis thaliana), 5'ss of exon 8
CTCGAGATATTCAGGCATGGGAATATATTCCTCTTGGTCCATTTCTTGGCAAGAGTTTTGgtaagatgtttcaaataattacttaatatcttttaagtcctatggaaaaaagctgggcatttggacttgtgcagtatatccaacgtggatg-attgcatgtaccatttgctctagatataaactatcactttacagttgttatttacttattttagagttaaccatcctttagggtgctaactaaaattatacag
|| | ||||||||||| ||||| ||| | ||||||||||| || || || |||||||||||| |||| |||    | | |||||   || |  |     |||    ||  |  ||||||   | ||||   | ||  ||      | | ||  ||| |                                                                                                 
CTAGGGATATTCAGGCGTGGGAGTATGTACCTCTTGGTCCTTTCCTGGGGAAGAGTTTTGgtgagatatttggcttcaatactttg-atttcatttcctctagttgaagtatatgggcaaa-gaactt---cggtgaatgttgtcttgttgtgttgtag------------------------------------------------------------------------------------------------

upper sequence: GLYMA09G01270.1 (Glycine max), 5'ss of exon 8
lower sequence: Vv00s0187g00300.t01 (Vitis vinifera), 5'ss of exon 5
CTCGAGATATTCAGGCATGGGAATATATTCCTCTTGGTCCATTTCTTGGCAAGAGTTTTGgtaagatgtttcaaata-attacttaatatcttttaagtcctatggaaaaaagctgggcatttggacttgtgcagtatatccaacgtggatgattgcatgtaccatttgctctagatataaactatcactttacagttgttatttacttattttagagttaaccatcctttagggtgctaactaaaattatacag
|  ||||||||||||||||||||||| | |||||||| || |||||||| |||||||||||||||| ||   |  |  ||| ||| ||| |||| || |||             |  || | | |  |  || || | |  ||   |  ||  ||   |   ||  ||    |||                                                                                
CAAGAGATATTCAGGCATGGGAATATGTGCCTCTTGGGCCTTTTCTTGGGAAGAGTTTTGgtaagaagtcatatttttattgcttcata-ctttcaattcc-----------atttagcctctaggttcttgtagcagaatca---tacatttttatcttggcctctt----tag--------------------------------------------------------------------------------
















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|298195581|gb|HO043972.1|HO043972
EST:     TCAGGCATGGGAATATATTCCTCTTGGTCCATTTCTTGGCAAGAGTTTTG                         GCACAACAATATCACCTTGGATTGTGACCTTGGAAGCATTAGAACCTTTTG
genomic: TCAGGCATGGGAATATATTCCTCTTGGTCCATTTCTTGGCAAGAGTTTTGgtaagatgtt ... aattatacagGCACAACAATATCACCTTGGATTGTGACCTTGGAAGCATTAGAACCTTTTG
EST: gi|151405820|gb|EV275635.1|EV275635
EST:     CAGGCATGGGAATATATTCCTCTTGGTCCATTTTCTTGGCAAGAGTTTTG                         GCACAACAATATCACCTTGGATTGTGACCTTGGAAGCATTAGAAC
genomic: CAGGCATGGGAATATATTCCTCTTGGTCCATTT-CTTGGCAAGAGTTTTGgtaagatgtt ... aattatacagGCACAACAATATCACCTTGGATTGTGACCTTGGAAGCATTAGAAC
EST: gi|193724130|gb|FK656410.1|FK656410
EST:     TCAGGCATGGGAATATATTCCTCTTGGTCCATTTCTTGGCAAGAGTTTTG                         GCACAACAATATCACCTTGGATTGTGACCTTGGAAGCATTAGAACCTTTTG
genomic: TCAGGCATGGGAATATATTCCTCTTGGTCCATTTCTTGGCAAGAGTTTTGgtaagatgtt ... aattatacagGCACAACAATATCACCTTGGATTGTGACCTTGGAAGCATTAGAACCTTTTG
EST: gi|6567242|gb|AW234853.1|AW234853
EST:     TCAGGCATGGGAATATATTCCTCTTGGTCCATTTCTTGGCAAGAGTTTTG                         GCACAACAATATCACCTTGGATTGTGACCTTGGAAGCATTAGAACCTTTTG
genomic: TCAGGCATGGGAATATATTCCTCTTGGTCCATTTCTTGGCAAGAGTTTTGgtaagatgtt ... aattatacagGCACAACAATATCACCTTGGATTGTGACCTTGGAAGCATTAGAACCTTTTG
EST: gi|7232656|gb|AW568010.1|AW568010
EST:     TCAGGCATGGGAATATATTCCTCTTGGTCCATTTCTTGGCAAGAGTTTTG                         GCACAACAATATCACCTTGGATTGTGACCTTGGAAGCATTAGAACCTTTTG
genomic: TCAGGCATGGGAATATATTCCTCTTGGTCCATTTCTTGGCAAGAGTTTTGgtaagatgtt ... aattatacagGCACAACAATATCACCTTGGATTGTGACCTTGGAAGCATTAGAACCTTTTG
EST: gi|7232634|gb|AW567988.1|AW567988
EST:     TCAGGCATGGGAATATATTCCTCTTGGTCCATTTCTTGGCAAGAGTTTTG                         GCACAACAATATCACCTTGGATTGTGACCTTGGAAGCATTAGAACCTTTTG
genomic: TCAGGCATGGGAATATATTCCTCTTGGTCCATTTCTTGGCAAGAGTTTTGgtaagatgtt ... aattatacagGCACAACAATATCACCTTGGATTGTGACCTTGGAAGCATTAGAACCTTTTG
EST: gi|298184616|gb|HO029829.1|HO029829
EST:     TTAGGCATGGGAATATATTCCTCTTGGTCCATTTCTTGGCAAGAGTTTTG                         GCACAACAATATCACCCTGGATTGTGACCTTGGAAGCATTAGAACCTTTTG
genomic: TCAGGCATGGGAATATATTCCTCTTGGTCCATTTCTTGGCAAGAGTTTTGgtaagatgtt ... aattatacagGCACAACAATATCACCTTGGATTGTGACCTTGGAAGCATTAGAACCTTTTG
EST: gi|213601975|gb|DB976222.1|DB976222
EST:     TCAGGCATGGGAATATATTCCTCTTGGTCCATTTCTTGGCAAGAGTTTTG                         GCACAACAATATCACCTTGGATTGTGACCTTGGAAGCATTAGAACCTTTTG
genomic: TCAGGCATGGGAATATATTCCTCTTGGTCCATTTCTTGGCAAGAGTTTTGgtaagatgtt ... aattatacagGCACAACAATATCACCTTGGATTGTGACCTTGGAAGCATTAGAACCTTTTG
EST: gi|10847964|gb|BF071656.1|BF071656
EST:     TCAGGCATGGGAATATATTCCTCTTGGTCCATTTCTTGGCAAGAGTTTTG                         GCACAACAATATCACCTTGGATTGTGACCTTGGAAGCATTAGAACCTTTTG
genomic: TCAGGCATGGGAATATATTCCTCTTGGTCCATTTCTTGGCAAGAGTTTTGgtaagatgtt ... aattatacagGCACAACAATATCACCTTGGATTGTGACCTTGGAAGCATTAGAACCTTTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCGAGATATTCAGGCATGGGAATATATTCCTCTTGGTCCATTTCTTGGCAAGAGTTTTGgtaagatgtttcaaataattacttaatatcttttaagtcctatggaaaaaagctgggcatttggacttgtgcagtatatccaacgtggatgattgcatgtaccatttgctctagatataaactatcactttacagttgttatttacttattttagagttaaccatcctttagggtgctaactaaaattatacag

- - - - - - - - - - - - - - - - - - - - - - - - GCAAGA