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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTTCTCCTGATTCTTCTTCCTTGAGCCAGATTTTGCAAAACCCTGTTATGATGCAGATGATGCAGAATATCATGTCTGATCCACAGTCCATGAACCAGgtacggtatttcttaacttattttgttatataactttgatgatgttagagtcataacttcagatcattctgtaatttaaaatgtccacag

Basic information

species Oryza sativa
transcript LOC_Os10g39620.5
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g39620.6 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G170843_T02 (Zea mays), 5'ss of exon 3
TGGTTCTCCTGATTCTTCTTCCTTGAGCCAGATTTTGCAAAACCCTGTTATGATGCAGATGATGCAGAATATCATGTCTGATCCACAGTCCATGAACCAGgtacggtatttcttaacttattttgttatataactttgatgatgttagagtcataacttcagatcattctgtaatttaaaatgtccacag
|||||| ||||||  |||| | || || ||||| |||||||||||||  ||||| |||||||||||||| || |||||||| |||||| ||||||||||||||    |  |  |  |   ||||  | |     |||    |||||  | |  | || |  |||  || |||   |     || | ||||
TGGTTCACCTGATGTTTCTCCGTTCAGTCAGATGTTGCAAAACCCTGCAATGATACAGATGATGCAGAACATTATGTCTGACCCACAGACCATGAACCAGgtagttcaacttatgccaactttttctgtgctcttttttgtatgttgcaattctgacattggattgttttgtt-ctcgccttggctacag

upper sequence: LOC_Os10g39620.6 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G136769_T01 (Zea mays), 5'ss of exon 3
TGGTTCTCCTGATTCTTCTTCCTTGAGCCAGATTTTGCAAAACCCTGTTATGATGCAGATGATGCAGAATATCATGTCTGATCCACAGTCCATGAACCAGgta---cggtatttcttaacttattttgttatataactttgatgatgttagagtcataacttcagatcattctgtaatttaaaat-gtccacag
|||||||||||||  ||||   || || ||||| |||||||||||||  |||||||||||||||||||  || |||||||| |||||| ||||||||||||||   |    | |   |||||||| | ||   |   |||   ||||||  | |  | || |  |||| || |||  | |    | | ||||||
TGGTTCTCCTGATGTTTCTCTTTTCAGTCAGATGTTGCAAAACCCTGCAATGATGCAGATGATGCAGAGCATTATGTCTGACCCACAGACCATGAACCAGgtagttcaacttgtgccaacttattct-ttgcgttcttttttggatgttgcaattctgacattggatcgttttgtgttctctccttggccacag
















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|58665177|gb|CK053863.1|CK053863
EST:     TGATGCAGATGATGCAGAATATCATGTCTGATCCACAGTCCATGAACCAG                         TTGCTTAACTTCAACCCAAATACACGCAACCTCATGGAATCAAACACTCAG
genomic: TGATGCAGATGATGCAGAATATCATGTCTGATCCACAGTCCATGAACCAGgtacggtatt ... atgtccacagTTGCTTAACTTCAACCCAAATACACGCAACCTCATGGAATCAAACACTCAG
EST: gi|33812321|gb|CF332050.1|CF332050
EST:     TGATGCAGATGATGCAGAATATCATGTCTGATCCACAGTCCATGAACCAG                         TTGCTTAACTTCAACCCAAATACACGCAACCTCATGGAATCAAACACTCAG
genomic: TGATGCAGATGATGCAGAATATCATGTCTGATCCACAGTCCATGAACCAGgtacggtatt ... atgtccacagTTGCTTAACTTCAACCCAAATACACGCAACCTCATGGAATCAAACACTCAG
EST: gi|58676841|gb|CK065528.1|CK065528
EST:     TGATGCAGATGATGCAGAATATCATGTCTGATCCACAGTCCATGAACCAG                         TTGCTTAACTTCAACCCAAATACACGCAACCTCATGGAATCAAACACTCAG
genomic: TGATGCAGATGATGCAGAATATCATGTCTGATCCACAGTCCATGAACCAGgtacggtatt ... atgtccacagTTGCTTAACTTCAACCCAAATACACGCAACCTCATGGAATCAAACACTCAG
EST: gi|58597929|gb|CK008457.1|CK008457
EST:     TGATGCAGATGATGCAGAATATCATGTCTGATCCACAGTCCATGAACCAG                         TTGCTTAACTTCA
genomic: TGATGCAGATGATGCAGAATATCATGTCTGATCCACAGTCCATGAACCAGgtacggtatt ... atgtccacagTTGCTTAACTTCA
EST: gi|58681884|gb|CK070571.1|CK070571
EST:     TGATGCAGATGATGCAGAATATCATGTCTGATCCACAGTCCATGAACCAG                         TTGCTTAACTTCAACCCAAATACACGCAACCTCATGGAATCAAACACTCAG
genomic: TGATGCAGATGATGCAGAATATCATGTCTGATCCACAGTCCATGAACCAGgtacggtatt ... atgtccacagTTGCTTAACTTCAACCCAAATACACGCAACCTCATGGAATCAAACACTCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTTCTCCTGATTCTTCTTCCTTGAGCCAGATTTTGCAAAACCCTGTTATGATGCAGATGATGCAGAATATCATGTCTGATCCACAGTCCATGAACCAGgtacggtatttcttaacttattttgttatataactttgatgatgttagagtcataacttcagatcattctgtaatttaaaatgtccacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG