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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actaatctactcatacctatcatattcatgcaactattgtatttgtgttccctaattttgtctcttctttttcatgtttgctgcttgttttctcctggagATATGTGAGAATCATCCTCAGGGAGTTGTTTTGGTAAGATTCAAGGATAGGAAGGATGCCCAAAAGTGCATAGAATTGATGAACGGACGATG

Basic information

species Glycine max
transcript GLYMA20G36110.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G36110.1 (Glycine max), 3'ss of exon 12
lower sequence: AT5G16260.1 (Arabidopsis thaliana), 3'ss of exon 13
--actaatct-actcatacctatcatattcatgcaac------tattgtatttgtgttccct--aattttgtctcttctttttcatgtttgctgcttgttttctcctggagATATGTGAGAATCATCCTCAGGGAGTTGTTTTGGTAAGATTCAAGGATAGGAAGGATGCCCAAAAGTGCATAGAATTGATGAACGGACGATG
| |||| | | | | |||| || | | | || || | || || ||| | ||| | | | | |||| | || |||||||| ||||||| ||||| |||||| | ||||||||||||||| ||| ||||| || || || |||||| |||||||| |||||
gtaataatatgatttctttttatcttaagctggtggtcttgcttgctgcatatagctttgtggaaaacttgagattattttggagtaccaatcgaatctcttctt-tacagGTATGTGAGCATCATCCACAGGGTGTTGTTCTTGTAAGATTCAAGGATCGGAGAGATGCACAGAAATGTATAGAAGCAATGAACGGTCGATG

upper sequence: GLYMA20G36110.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv00s0220g00010.t01 (Vitis vinifera), 3'ss of exon 8
-actaatctactcatacctatcatattcatgcaactattgtatttgtgttccctaattttgtctcttctttttcatgtttgctgcttgttttctcctggagATATGTGAGAATCATCCTCAGGGAGTTGTTTTGGTAAGATTCAAGGATAGGAAGGATGCCCAAAAGTGCATAGAATTGATGAACGGACGATG
|| | | | ||| || | ||| | | ||||||||| | || | ||| | ||||| | |||| || | || || | ||||||| ||| || ||||| || |||||||||| | |||||||||| |||||| || ||||||||||| |||||||| ||| ||||
ccttatgagatttactgttatgatttacatttgaactgtcaatttgtgttatatgtttcatggattcatttcttatgttctat-cttggttctacttgcagGTTTGTGAGAGTCACCCACAGGGTGTAGTTTTGGTAAAGTATAAGGATAGGAGGGATGCGCAGAAGTGCATAGAGTTGATGAATGGAAGATG

upper sequence: GLYMA20G36110.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv00s0499g00010.t01 (Vitis vinifera), 3'ss of exon 12
-actaatctactcatacctatcatattcatgcaactattgtatttgtgttccctaattttgtctcttctttttcatgtttgctgcttgttttctcctggagATATGTGAGAATCATCCTCAGGGAGTTGTTTTGGTAAGATTCAAGGATAGGAAGGATGCCCAAAAGTGCATAGAATTGATGAACGGACGATG
|| | | | ||| || | ||| | | ||||||||| | || | ||| | ||||| | |||| || | || || | ||||||| ||| || ||||| || |||||||||| | |||||||| | |||||| || ||||||||||| |||||||| ||| ||||
ccttatgagatttactgttatgatttacatttgaactgtcaatttgtgttatatgtttcatggattcatttcttatgttctat-cttggttctacttgcagGTTTGTGAGAGTCACCCACAGGGTGTAGTTTTGGTAAAGTATAAGGATAGAAGGGATGCGCAGAAGTGCATAGAGTTGATGAATGGAAGATG

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|5688095|gb|AI941110.1|AI941110
EST:     AAGATGTTAAAGAGGAGTGTACAAAGCTTGGTCCTGTGGATTCAGTCAAG                         ATATGTGAGAATCATCCTCAGGGAGTTGTTTTGGTAAGATTCAAGGATAGG
genomic: AAGATGTTAAAGAGGAGTGTACAAAGCTTGGTCCTGTGGATTCAGTCAAGgtagttaatc ... tctcctggagATATGTGAGAATCATCCTCAGGGAGTTGTTTTGGTAAGATTCAAGGATAGG
EST: gi|9984040|gb|BE658148.1|BE658148
EST:     AAGATGTTAAAGAGGAGTGTACAAAGCTTGGTCCTGTGGATTCAGTCAAG                         ATATGTGAGAATCATCCTCAGGGAGTTGTTTTGGTAAGATTCAAGGATAGG
genomic: AAGATGTTAAAGAGGAGTGTACAAAGCTTGGTCCTGTGGATTCAGTCAAGgtagttaatc ... tctcctggagATATGTGAGAATCATCCTCAGGGAGTTGTTTTGGTAAGATTCAAGGATAGG
EST: gi|22928101|gb|BU545240.1|BU545240
EST:     AAGATGTTAAAGAGGAGTGTACAAAGCTTGGTCCTGTGGATTCAGTCAAG                         ATATGTGAGAATCATCCTCAGGGAGTTGTTTTGGTAAGATTCAAGGATAGG
genomic: AAGATGTTAAAGAGGAGTGTACAAAGCTTGGTCCTGTGGATTCAGTCAAGgtagttaatc ... tctcctggagATATGTGAGAATCATCCTCAGGGAGTTGTTTTGGTAAGATTCAAGGATAGG
EST: gi|19052889|gb|BM731556.1|BM731556
EST:     AAGATGTTAAAGAGGAGTGTACAAAGCTTGGTCCTGTGGATTCAGTCAAG                         ATATGTGAGAATCATCCTCAGGGAGTTGTTTTGGTAAGATTCAAGGATAGG
genomic: AAGATGTTAAAGAGGAGTGTACAAAGCTTGGTCCTGTGGATTCAGTCAAGgtagttaatc ... tctcctggagATATGTGAGAATCATCCTCAGGGAGTTGTTTTGGTAAGATTCAAGGATAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttccctaattttgtctcttctttttcatgtttgctgcttgttttctcctggagATATGTGAGAATCATCCTCAGGGAGTTGTTTTGGTAAGATTCAAGGATAGGAAGGATGCCCAAAAGTGCATAGAATTGATGAACGGACGATG
    ccctaat  putative branch site (score: 3)
 tctcttctttttcatg  putative PPT
 taattttgt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actaatctactcatacctatcatattcatgcaactattgtatttgtgttccctaattttgtctcttctttttcatgtttgctgcttgttttctcctggagATATGTGAGAATCATCCTCAGGGAGTTGTTTTGGTAAGATTCAAGGATAGGAAGGATGCCCAAAAGTGCATAGAATTGATGAACGGACGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG