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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgttttgttttgtttgtttccgacatgaacggtgaatatttcaactgtttttttttgtagtgtggtataccatgtttgactattagtttaacttgttagAAGGAGTATAATGGGTGAACAATTGGGGCTGCTAAAAGTCATTGTTGTGCAAGGGAAAAGGTTGGTGATCCGGGATTTCAAGACCAGTGATCCTTATGTT

Basic information

species Glycine max
transcript GLYMA15G12690.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G12690.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G47710.1 (Arabidopsis thaliana), 3'ss of exon 1
ttgttttgttttgtttgtttccgacatgaacggtgaatatttcaactgtttttttttgtagtgtggtat--accatgtttgactattagtttaacttgttagAAGGAG-TATAATGGGTGAACAATTGGGGCTGCTAAAAGTCATTGTTGTGCAAGGGAAAAGGTTGGTGATCCGGGATTTCAAGACCAGTGATCCTTATGTT--
|  | ||    || ||||  |  | |   || ||   |  || | || | || ||    ||  | || |  |  |  ||  |   || ||   |  |||| | || |  |   ||||| || | | | || |||||  | || | |||| | ||||| || |   |||||||||| ||||||||| | ||||||||||||||   
tcatattcaactgattgt--ctaataaagacagt---tgctttagctctgttattcacgaggattgtctcaagaagtttctaaagttggtagcatgtgtttgtagAATCTGAGATGGGCGAGCCACTAGGACTGCTCCAGGTGACTGTTATTCAAGGAAAGAAACTGGTGATCCGAGATTTCAAGTCAAGTGATCCTTATGTGAT
















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|207814138|gb|GD783931.1|GD783931
EST:     ACAAATCACAACATATCCATTG                         AAGGAGTATAATGGGTGAACAATTGGGGCTGCTAAAAGTCATTGTTGTGCA
genomic: ACAAATCACAACATATCCATTGgtgagttcca ... aacttgttagAAGGAGTATAATGGGTGAACAATTGGGGCTGCTAAAAGTCATTGTTGTGCA
EST: gi|120529482|gb|EH257616.1|EH257616
EST:     AACATATCCATT-                         --GGAGTATAATGGGTGAACAATTGGGGCTGCTAAAAGTCATTGTTGTGCA
genomic: AACATATCCATTGgtgagttcca ... aacttgttagAAGGAGTATAATGGGTGAACAATTGGGGCTGCTAAAAGTCATTGTTGTGCA
EST: gi|193651902|gb|FK597243.1|FK597243
EST:     ATTCACAAATCACAACATATCCATTG                         AAGGAGTATAATGGGTGAACAATTGGGGCTGCTAAAAGTCATTGTTGTGCA
genomic: ATTCACAAATCACAACATATCCATTGgtgagttcca ... aacttgttagAAGGAGTATAATGGGTGAACAATTGGGGCTGCTAAAAGTCATTGTTGTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtttttttttgtagtgtggtataccatgtttgactattagtttaacttgttagAAGGAGTATAATGGGTGAACAATTGGGGCTGCTAAAAGTCATTGTTGTGCAAGGGAAAAGGTTGGTGATCCGGGATTTCAAGACCAGTGATCCTTATGTT
                                         gtttaac  putative branch site (score: 3)
                                    tattagtttaactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgttttgttttgtttgtttccgacatgaacggtgaatatttcaactgtttttttttgtagtgtggtataccatgtttgactattagtttaacttgttagAAGGAGTATAATGGGTGAACAATTGGGGCTGCTAAAAGTCATTGTTGTGCAAGGGAAAAGGTTGGTGATCCGGGATTTCAAGACCAGTGATCCTTATGTT

-tgttttg
- - - - - - - -tgtttcc
- - - - - - - - - - - - catgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgtggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccatgtt