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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attatattctcatttaaccctttcatcatttccaaatttcaattctatactttgcagacttgttactgatttagtgattccatgttcaatcttgtggcagTCAAGGATGCTTTTGCAACCAGAACTTGTTCTTGAAGATGTTAGTCAAGACCATGCACGCAAAACG

Basic information

species Glycine max
transcript GLYMA12G00830.5
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G00830.5 (Glycine max), 3'ss of exon 5
lower sequence: AT5G61500.1 (Arabidopsis thaliana), 3'ss of exon 6
attatattctcatttaaccctt-tcatcatttccaaatttcaattctatactt-tgcagacttgttactgatttagt--gattccatgttcaatcttgtggcagTCAAGGATGCTTTTGCAACCAGAACTTGTTCTTGAAGATGTTAGTCAAGACCATGCACGCAAAACG
| | || ||| | | | ||| ||| || | ||| | | | || | | || || | | | | | | ||||||| ||||||||||||| ||||||| |||||||| | || |||||||| ||||||||||| || ||||||
gtcttgtttcgttttgtttttcattaaaattcatgggttttgttttgttgcttgtttatatttcctgtt-atctacttaaaagctacgatgtatcttgt---agTCAAGGATGCTGCTGCAACCTGAACTTGTAATGGAGGATGTTAGCCAAGACCATGCTCGTAAAACG

upper sequence: GLYMA12G00830.5 (Glycine max), 3'ss of exon 5
lower sequence: PP1S62_116V6.1 (Physcomitrella patens), 3'ss of exon 8
attatattctcatttaaccctttcatcatttccaaatttcaattctatactttgcagacttgttactgatttagtgattccatgttcaat-cttgtggcagTCAAG----GATGCTT-TTGCAACCAGAACTTGTTCTTGAAGATGTTAGTCAAGACCATGCACGCAAAACG
| |||| ||| || | || ||| || || ||| |||| || |||||| || | || |||| | ||| | | || | | || | |||||||||||||| | || || ||||||||||||||||||||||| |||
----tcttctgattcaatttcgttttctttttttccgttt--ttgtatcttttgtcatggattttttgatttcaagaattcaccttcattgctttccacgtttcagACCCGTTATTTGCTTCAACCAGAACTTGTGTTGGAGGACGTTAGTCAAGACCATGCACGCAAGACG
















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|31312555|gb|CD397758.1|CD397758
EST:     ATGATAAATATTATCNAACACCACGAGTATGGCTTACTGGGTATGACGAG                         TCAAGGATGCTTTTGCAACCAGAACTTGTTCTTGAAGATGTTAGTCAAGAC
genomic: ATGATAAATATTATCAAACACCACGAGTATGGCTTACTGGGTATGACGAGgtttgtttta ... cttgtggcagTCAAGGATGCTTTTGCAACCAGAACTTGTTCTTGAAGATGTTAGTCAAGAC
EST: gi|207721023|gb|GD702724.1|GD702724
EST:     TAAATATTATCAAACACCACGAGTATGGCTTACTGGGTATGACGAG                         TCAAGGATGCTTTTGCAACCAGAACTTGTTCTTGAAGATGTTAGTCAAGAC
genomic: TAAATATTATCAAACACCACGAGTATGGCTTACTGGGTATGACGAGgtttgtttta ... cttgtggcagTCAAGGATGCTTTTGCAACCAGAACTTGTTCTTGAAGATGTTAGTCAAGAC
EST: gi|193369407|gb|FK336669.1|FK336669
EST:     ATATTATCAAACACCACGAGTATAGCTTACTGGGTATGACGAG                         TCAAGGATGCTTTTGCAACCAGAACTTGTTCTTGAAGATGTTAGTCAAGAC
genomic: ATATTATCAAACACCACGAGTATGGCTTACTGGGTATGACGAGgtttgtttta ... cttgtggcagTCAAGGATGCTTTTGCAACCAGAACTTGTTCTTGAAGATGTTAGTCAAGAC
EST: gi|192330861|gb|FK021620.1|FK021620
EST:     ATGATAAATATTATCAAACACCACGAGTATGGCTTACTGGGTATGACGAG                         TCAAGGATGCTTTTGCAACCAGAACTTGTTCTTGAAGATGTTAGTCAAGAC
genomic: ATGATAAATATTATCAAACACCACGAGTATGGCTTACTGGGTATGACGAGgtttgtttta ... cttgtggcagTCAAGGATGCTTTTGCAACCAGAACTTGTTCTTGAAGATGTTAGTCAAGAC
EST: gi|193463512|gb|FK427436.1|FK427436
EST:     ATGATAAATATTATCAAACACCACGAGTATGGCTTACTGGGTATGACGAG                         TCAAGGATGCTTTTGCAACCAGAACTTGTTCTTGAAGTTGTTAGTCAAGAC
genomic: ATGATAAATATTATCAAACACCACGAGTATGGCTTACTGGGTATGACGAGgtttgtttta ... cttgtggcagTCAAGGATGCTTTTGCAACCAGAACTTGTTCTTGAAGATGTTAGTCAAGAC
EST: gi|9820599|gb|BE556109.1|BE556109
EST:     TATCAACCACCACGAGTATGGCTTACTGGGTATGACGAG                         TCAAGAATGCTTTTGCACCCCGANCTTGTTCTTGAAGATGTTAGTCAAGAC
genomic: TATCAAACACCACGAGTATGGCTTACTGGGTATGACGAGgtttgtttta ... cttgtggcagTCAAGGATGCTTTTGCAACCAGAACTTGTTCTTGAAGATGTTAGTCAAGAC
EST: gi|19346154|gb|BM891034.1|BM891034
EST:     ATGATAAATATTATCAAACACCACGAGTATGGCTTACTGGGTATGACGAG                         TCAAGGATGCTTTTGCAACCAGAACTTGTTCTTGAAGATGTTAGTCAAGAC
genomic: ATGATAAATATTATCAAACACCACGAGTATGGCTTACTGGGTATGACGAGgtttgtttta ... cttgtggcagTCAAGGATGCTTTTGCAACCAGAACTTGTTCTTGAAGATGTTAGTCAAGAC
EST: gi|21887729|gb|BQ740942.1|BQ740942
EST:     ATGATAAATATTATCAAACACCACGAGTATGGCTTACTGGGTATGACGAG                         TCAAGGATGCTTTTGCAACCAGAACTTGTTCTTGAAGATGTTAGTCAAGAC
genomic: ATGATAAATATTATCAAACACCACGAGTATGGCTTACTGGGTATGACGAGgtttgtttta ... cttgtggcagTCAAGGATGCTTTTGCAACCAGAACTTGTTCTTGAAGATGTTAGTCAAGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatactttgcagacttgttactgatttagtgattccatgttcaatcttgtggcagTCAAGGATGCTTTTGCAACCAGAACTTGTTCTTGAAGATGTTAGTCAAGACCATGCACGCAAAACG
                  tactgat  putative branch site (score: 2)
 tgattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attatattctcatttaaccctttcatcatttccaaatttcaattctatactttgcagacttgttactgatttagtgattccatgttcaatcttgtggcagTCAAGGATGCTTTTGCAACCAGAACTTGTTCTTGAAGATGTTAGTCAAGACCATGCACGCAAAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG