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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgattatctaaacgcactagttcttgcatgcctgatatattccaaaacactgtgaataccctaaatcagtttttaattactgtgatatatcgattgatttgtcatggtttcctgatctctcagAACAAAGCGTGGAATATTTTCTGATGAGAGGTGTTCTGAACTACATTGGTAGTGTAGATGTAAG

Basic information

species Oryza sativa
transcript LOC_Os01g56630.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56630.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G079389_T01 (Zea mays), 3'ss of exon 2
gtaattgattatctaaacgcacta-gttcttgcatgcctgatatattccaaaacactgtgaataccctaaatc--agttttta-attactgtg---atatatcgat-----------tgatttgtcatggtttcctgatctctcagAACAAAGCG-TGGAATATTTTCTGATGAGAGGTGTTCTGAACTACATTGGTAGTGTAGATGTAAG
||||| ||||||| | |  ||||| | |  |   |  ||| | |||| |||| |  |||   | |  ||||    | | | || ||| || |     |  || |             |||| | | ||| |  | |||||  | |  | ||  || |||| |||||||||||||||||||| ||| |||| ||||||||||| ||||||||
gtaatcgattatccacatccactaagattctctgtctctggtctattgcaaagcg-tgtttcttctgtaaactgtaatatctatattgctatacgagtgaattggccaaaattcttatgatctttgatgttcccttgatccttgaagAAAACACGGTGGAGTATTTTCTGATGAGAGGTGTGCTGGACTATATTGGTAGTGTGGATGTAAG
















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|300215697|gb|HO088323.1|HO088323
EST:     AAGTCTTGAAATTGACAAGGATGAGAAGGGGCTGGAAAATTTTCCTTCTG                         AACAAAGCGTGGAATATTTTCTGATGAGAGGTGTTCTGAACTACATTGGTA
genomic: AAGTCTTGAAATTGACAAGGATGAGAAGGGGCTGGAAAATTTTCCTTCTGgtaattgatt ... gatctctcagAACAAAGCGTGGAATATTTTCTGATGAGAGGTGTTCTGAACTACATTGGTA
EST: gi|33679098|gb|CF307337.1|CF307337
EST:     AAGTCTTGAAATTGACAAGGATGAGAAGGGGCTGGAAAATTTTCCTTCTG                         AACAAAGCGTGGAATATTTTCTGATGAGAGGTGTTCTGAACTACATTGGTA
genomic: AAGTCTTGAAATTGACAAGGATGAGAAGGGGCTGGAAAATTTTCCTTCTGgtaattgatt ... gatctctcagAACAAAGCGTGGAATATTTTCTGATGAGAGGTGTTCTGAACTACATTGGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttttaattactgtgatatatcgattgatttgtcatggtttcctgatctctcagAACAAAGCGTGGAATATTTTCTGATGAGAGGTGTTCTGAACTACATTGGTAGTGTAGATGTAAG
                                         tcctgat  putative branch site (score: 3)
                                       tttcctgatctctc  CT-rich tract
     taattact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattgattatctaaacgcactagttcttgcatgcctgatatattccaaaacactgtgaataccctaaatcagtttttaattactgtgatatatcgattgatttgtcatggtttcctgatctctcagAACAAAGCGTGGAATATTTTCTGATGAGAGGTGTTCTGAACTACATTGGTAGTGTAGATGTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG