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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTTCCTTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGTgtatgccattataacttttgacatctttgtgttgttctttctttaacatgcttttgtttgtcatgcatctatcgttgtgatgtctattaatatcaatctt...

Basic information

species Glycine max
transcript GLYMA16G06850.2
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G06850.3 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM2G130230_T02 (Zea mays), 5'ss of exon 12
GTGTTCCTTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGTgtatgccattataacttttgacatctttgtgt-tgttctttctttaacatgcttttgtttgtcatgcatctatcgttgtgatgtctattaatatcaatctt-
||||||||||||| || ||||| || || ||| | | ||| |  || |||||  |  |||| ||||||||||||||||||||||| ||||| |   |||||    || |||| | ||  |    ||   || | ||  ||||   |     |   | | | || |   | | ||   |    |||||||   | ||  
GTGTTCCTTTCATTCTTAAAGCTGGTAAAGCATTGAGTTCAAAGAAAGCAGAAGTTCGGGTGCAATTCAAGGATGTCCCTGGTGACATTTTTAGAAgtatgtgcatagaactatagaagttaacgttcatggtgttagtttactcttagcatagat-ttaggctttgtttgatgcactaga-attaatagttagctgc

upper sequence: GLYMA16G06850.3 (Glycine max), 5'ss of exon 12
lower sequence: Vv14s0171g00490.t01 (Vitis vinifera), 5'ss of exon 12
GTGTTCCTTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGTgtatgccattataacttttgacatctttgtgttgttctttctttaacatgcttttgtttgtcatgcatctatcgttgtgatgtc-tattaatatcaatctt
|||||||||| ||||| ||||||||||| ||||||||||| || |||||||| ||  |  |||||||||||||||| ||||||||||| | ||  |||||| ||| | | |||||   || |||   |  ||  || |   |  |    ||  ||  | || || | |  |   | | || ||| ||  | ||  | 
GTGTTCCTTTTATACTTAAAGCAGGGAAAGCACTAAATTCAAGGAAGGCAGAAATTCGCATTCAATTCAAGGATGTTCCTGGTGATATCTACAGATgtatggcatcagaccttttagtat-tttacttgatttcttttcacatgtttggtttatttacttgaatatcttctcaagttttcatatcaaacttaagttc
















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|15815763|gb|BI788038.1|BI788038
EST:     GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCGAGT                         GTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAG
genomic: GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGTgtatgccatt ... acaattttagGTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAG
EST: gi|6566164|gb|AW233801.1|AW233801
EST:     GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGT                         GTAAAAAGCAGGGGAGAAATGAGTTTGTTATCCGCCTACAGCCTTCAGAAG
genomic: GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGTgtatgccatt ... acaattttagGTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAG
EST: gi|37995859|gb|CF807448.1|CF807448
EST:     GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGT                         GTAAAAAGCAGGGGAGAAATGAGTTTGTTATCCGCCTACAGCCTTCAGAAG
genomic: GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGTgtatgccatt ... acaattttagGTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAG
EST: gi|37995462|gb|CF807051.1|CF807051
EST:     GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGT                         GTAAAAAGCAGGGGAGAAATGAGTTTGTTATCCGCCTACAGCCTTCAGAAG
genomic: GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGTgtatgccatt ... acaattttagGTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAG
EST: gi|151395248|gb|EV265119.1|EV265119
EST:     GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGT                         GTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAG
genomic: GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGTgtatgccatt ... acaattttagGTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAG
EST: gi|37994622|gb|CF806296.1|CF806296
EST:     GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGT                         GTAAAAAGCAGGGGAGAAATGAGTTTGTTATCCGCCTACAGCCTTCAGAAG
genomic: GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGTgtatgccatt ... acaattttagGTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAG
EST: gi|15661712|gb|BI699083.1|BI699083
EST:     GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGT                         GTAAAAAGCAGGGGAGAAATGAGTTTGTTATCCGCCTACAGCCTTCAGAAG
genomic: GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGTgtatgccatt ... acaattttagGTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTTCCTTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGTgtatgccattataacttttgacatctttgtgttgttctttctttaacatgcttttgtttgtcatgcatctatcgttgtgatgtctattaatatcaatctt

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