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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGTATCCATATGAAGAAATTTTGAGGACCTTTCACAATCAGACAAGCATAATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAACAGAACCAAAGgtaacagttcttacttcaaacctttccaccagacatcagaattcatgactttccaatttctgttctgatgcgaatgttggtattttgtgagcccag

Basic information

species Glycine max
transcript GLYMA09G02160.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G02160.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os03g21210.1 (Oryza sativa), 5'ss of exon 4
GGGTATCCATATGAAGAAATTTTGAGGACCTTTCACAATCAGACAAGCATAATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAACAGAACCAAAGgtaacagttcttactt--caaacctttccaccagacatcagaattcatgactttccaatttct--gttctgatgcgaatgttggtattttgtgagcccag--
|| |||||||||||||| ||  | ||||| || |||||||| |||||||| || |||||||| ||||| ||| ||||||     || ||||| || ||||||   |  |   |||     || |   |   || ||||  |  ||  |||      | || ||  |  |   |     | |    |   | |  ||  |   
GGTTATCCATATGAAGAGATCCTCAGGACATTCCACAATCAAACAAGCATTATTATGTGCTCTTATCTTCCAATTTTCAAGTCTTTCAACAGGACAAAAGgtttgaccttgaactcactgaatcacacagtcacacattgg--tttgtgaacagttagttacttaggccctgtttagttctccaaaaacttttcgcaaaaac

upper sequence: GLYMA09G02160.1 (Glycine max), 5'ss of exon 4
lower sequence: AT5G49720.1 (Arabidopsis thaliana), 5'ss of exon 4
GGGTATCCATATGAAGAAATTTTGAGGACCTTTCACAATCAGACAAGCATAATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAACAGAACCAAAGgtaacagttcttacttcaaacctttccaccagacatcagaattca--tgactttccaatttctgttct-gatgcgaatgttggtatttt--gtgagcccag
|| |||||||||||||||||| | |||||||| ||||||||||| |||||| |||||||||| ||  | ||  ||||||  |  |||||||||||||| ||| |     ||| |  |     | ||  ||    || | | | ||  ||     |   ||  ||||   |||    |   ||  || ||  ||  |  |||
GGATATCCATATGAAGAAATTCTAAGGACCTTCCACAATCAGACCAGCATAGTCATGTGCTCATACTTGCCTATTTTCAACAAATTTAACAGAACCAATGgttagttaccttccagctttaatgtctgcctctaataaaactccaactgtggggcttgttcttgtttcagatatctaaaatgaaatctttggtatgtgcag

upper sequence: GLYMA09G02160.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv12s0035g02180.t01 (Vitis vinifera), 5'ss of exon 4
GGGTATCCATATGAAGAAATTTTGAGGACCTTTCACAATCAGACAAGCATAATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAACAGAACCAAAGgtaac--agttcttacttca--aacctttccaccagacatcagaattcatgactttccaatttctgttctgatgcgaatgttggtattttgtgagcccag-----
||||||||||||||||||||| ||||||| ||||||||||| || |||||||| |||||||| || |||||  |||||||||||||||||||||| ||||||| |  || |  || |||   |||||| |     |   |  | ||    |  |  |||| ||     |  |  |  |   |  | ||||| |  |||       
GGGTATCCATATGAAGAAATTCTGAGGACATTTCACAATCAAACCAGCATAATTATGTGCTCATACCTACCGATTTTCACAAGCTTTAACAGAACAAAAGgtaccccagctaatatttcgtcaaccttacagtttg--gtggggatg---ggttgcccaagtttaacacaaaaacttaatgtaatgttttgggtaccccttgcag

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|4296298|gb|AI442455.1|AI442455
EST:     ATCATGTGCTCCTATCTACCAGGTTTT-ACAAGCTNTAACAGAACCAAAG                         GTGGCTTGATTCAATTAAACCATGGTAGGCCTCAGCCTCTCCAATATGTGG
genomic: ATCATGTGCTCCTATCTACCAG-TTTTCACAAGCTTTAACAGAACCAAAGgtaacagttc ... gtgagcccagGTGGCTTGATTCAATTAAACCATGGTAGGCCTCAGCCTCTCCAATATGTGG
EST: gi|37994320|gb|CF806066.1|CF806066
EST:     AATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAACAGAACCAAAG                         GTGGCTTGATTCAATTAAACCATGGTAGGCCTCAGCCTCTCCAATATGTGG
genomic: AATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAACAGAACCAAAGgtaacagttc ... gtgagcccagGTGGCTTGATTCAATTAAACCATGGTAGGCCTCAGCCTCTCCAATATGTGG
EST: gi|16106049|gb|BI893789.1|BI893789
EST:     AATCATGTGCTCCTATCTACCAGTTTTCATAT-CTTTAACAGAACCAAAG                         GTGGCTTGATTCAATTAAACCATGGTAGGCCTCAGCCTCTCCAATATGTGG
genomic: AATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAACAGAACCAAAGgtaacagttc ... gtgagcccagGTGGCTTGATTCAATTAAACCATGGTAGGCCTCAGCCTCTCCAATATGTGG
EST: gi|26048689|gb|CA785142.1|CA785142
EST:     AATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAACAGAACCAAAG                         GTGGCTTGATTCAATTAAACCATGGTAGGCCTCAGCCTCTCCAATATGTGG
genomic: AATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAACAGAACCAAAGgtaacagttc ... gtgagcccagGTGGCTTGATTCAATTAAACCATGGTAGGCCTCAGCCTCTCCAATATGTGG
EST: gi|5605872|gb|AI899970.1|AI899970
EST:     AATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAACAGAACCAAAG                         GTGGCTTGATTCAATTAAACCATGGTAGGCCTCAGCCTCTCCAATATGTGG
genomic: AATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAACAGAACCAAAGgtaacagttc ... gtgagcccagGTGGCTTGATTCAATTAAACCATGGTAGGCCTCAGCCTCTCCAATATGTGG
EST: gi|14990101|gb|BI315774.1|BI315774
EST:     AATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAACAGAACCAAAG                         GTGGCTTGATTCAATTAAACCAT
genomic: AATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAACAGAACCAAAGgtaacagttc ... gtgagcccagGTGGCTTGATTCAATTAAACCAT
EST: gi|207811648|gb|GD784017.1|GD784017
EST:     AATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAACAGAACCAAAG                         GTGGCTTGATTCAATTAAACCATGGTAGGCCTCAGCCTCTCCAATATGTGG
genomic: AATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAACAGAACCAAAGgtaacagttc ... gtgagcccagGTGGCTTGATTCAATTAAACCATGGTAGGCCTCAGCCTCTCCAATATGTGG
EST: gi|7588237|gb|AW704037.1|AW704037
EST:     AATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAACAGAACCAAAG                         GTGGCTTGATTCAATTAAACCATGGTAGGCCTCAGCCTCTCCAATATGTGG
genomic: AATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAACAGAACCAAAGgtaacagttc ... gtgagcccagGTGGCTTGATTCAATTAAACCATGGTAGGCCTCAGCCTCTCCAATATGTGG
EST: gi|33389935|gb|CA853142.1|CA853142
EST:     AATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAACAGAACCAAAG                         GTGGCTTGATTCAATTAAACCATGGTAGGCCTCAGCCTCTC
genomic: AATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAACAGAACCAAAGgtaacagttc ... gtgagcccagGTGGCTTGATTCAATTAAACCATGGTAGGCCTCAGCCTCTC
EST: gi|6454405|gb|AW185088.1|AW185088
EST:     AATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAACAGAACCAAAG                         GTGGCTTGATTCAATTAAACCATGGTAGGCCTCAGCCTCTCCAATATGTGG
genomic: AATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAACAGAACCAAAGgtaacagttc ... gtgagcccagGTGGCTTGATTCAATTAAACCATGGTAGGCCTCAGCCTCTCCAATATGTGG
EST: gi|21888159|gb|BQ741372.1|BQ741372
EST:     AATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAACAGAACCAAAG                         GTGGCTTGATTCAATTAAACCATGGTAGGCCTCAGCCTCTCCAATATGTGG
genomic: AATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAACAGAACCAAAGgtaacagttc ... gtgagcccagGTGGCTTGATTCAATTAAACCATGGTAGGCCTCAGCCTCTCCAATATGTGG
EST: gi|22525618|gb|BU084429.1|BU084429
EST:     GTGCTCCTATCTACCAGTTTTCACAAGCTTTAACAGAACCAAAG                         GTGGCTTGATTCAATTAAACCATGGTAGGCCTCAGCCTCTCCAATATGTGG
genomic: GTGCTCCTATCTACCAGTTTTCACAAGCTTTAACAGAACCAAAGgtaacagttc ... gtgagcccagGTGGCTTGATTCAATTAAACCATGGTAGGCCTCAGCCTCTCCAATATGTGG
EST: gi|21637832|gb|BM107987.1|BM107987
EST:     AATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAACAGAACCAAAR                         GTGGCTTGATTCAATTAAACCATGGTAGGCCTCAGCCTCTCCAATATGTGG
genomic: AATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAACAGAACCAAAGgtaacagttc ... gtgagcccagGTGGCTTGATTCAATTAAACCATGGTAGGCCTCAGCCTCTCCAATATGTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGTATCCATATGAAGAAATTTTGAGGACCTTTCACAATCAGACAAGCATAATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAACAGAACCAAAGgtaacagttcttacttcaaacctttccaccagacatcagaattcatgactttccaatttctgttctgatgcgaatgttggtattttgtgagcccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT