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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGCCTCAATGTTACTTCTATCATTGTCCTTCACGTGGAAGGCTTTGGCACCTTATTCAGGCCCTCTTGCTGTTGCTGGCACTGTTTTgtaagtggtttgtcatacgctttagtcaggccttttgctgattgtcattgttaactgttaatataacttgaatataattttatttag

Basic information

species Oryza sativa
transcript LOC_Os01g04190.3
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g04190.3 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G153704_T02 (Zea mays), 5'ss of exon 12
GCTGCCTCAATGTTACTTCTATCATTGTCCTTCACGTGGAAGGCTTTGGCACCTTATTCAGGCCCTCTTGCTGTTGCTGGCACTGTTTTgtaagtggtt-tg--tcatacgctttagtcaggccttttgctgattgtcattgttaactgttaatataacttgaatata--attttatttag
| ||| |||||| |||| ||| ||||||||||||| ||||| ||| ||||||||||||| ||  |||||||||||| |||||||||| ||||||| ||  ||  |||| |  |||  || |    | |    ||    |   | ||   || | || ||| || ||||  ||| | |  ||
GGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCACCTTATTCTGGTACTCTTGCTGTTGTTGGCACTGTTCTgtaagttgtcatgattcatcctgtttgttctgattctatttgaatgtataacttcaatgtttgacatgactggagtatatgattctgtgcag

upper sequence: LOC_Os01g04190.3 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G098011_T01 (Zea mays), 5'ss of exon 12
GCTGCCTCAATGTTACTTCTATCATTGTCCTTCACGTGGAAGGCTTTGGCACCTTATTCAGGCCCTCTTGCTGTTGCTGGCACTGTTTTgtaagtggtttgtcatacgctttagtcaggccttttgctgattgtcattg------ttaactgttaatataacttgaatataat-tttatttag
| ||| |||||| |||| ||| ||||||||||||| ||||| ||| ||||||||||||| ||   ||||||||||| |||||||||| ||||||| |||  | || |   ||  |  |    |||||||||| |  ||       | |  ||    | | || | | |  | | ||| |  ||
GGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCACCTTATTCTGGTATTCTTGCTGTTGTTGGCACTGTTCTgtaagttgttaatgattcatcttgtttgg--tctttgctgattctatttaaatgtataacttgaatgtttgacataactggagtatttgtgcag
















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|163921085|gb|EG710424.1|EG710424
EST:     AAGGCTTTGGCACCTTATTCAGGCCCTCTTGCTGTTGCTGGCACTGTTTT                         GT--GTGCTGTCTTTTGCTCTTGGAGCTGGCCCAGTTCCAGCATTGCTCCT
genomic: AAGGCTTTGGCACCTTATTCAGGCCCTCTTGCTGTTGCTGGCACTGTTTTgtaagtggtt ... ttttatttagGTATGTGCTGTCTTTTGCTCTTGGAGCTGGCCCAGTTCCAGCATTGCTCCT
EST: gi|38481055|gb|CF965144.1|CF965144
EST:     AAGGCTTTGGCACCTTATTCAGGCCCTCTTGCTGTTGCTGGCACTGTTTT                         GTATGTGCTGTCTTTTGCTCTTGGAGCTGGCCCAGTTCCAGCATTGCTCCT
genomic: AAGGCTTTGGCACCTTATTCAGGCCCTCTTGCTGTTGCTGGCACTGTTTTgtaagtggtt ... ttttatttagGTATGTGCTGTCTTTTGCTCTTGGAGCTGGCCCAGTTCCAGCATTGCTCCT
EST: gi|58598313|gb|CK008841.1|CK008841
EST:     AAGGCTTTGGCACCTTATTCAGGCCCTCTTGCTGTTGCTGGCACTGTTTT                         GTATGTGCTGTCTTTTGCTCTTGGAGCTGGCCCAGTTCCAGCATTGCTCCT
genomic: AAGGCTTTGGCACCTTATTCAGGCCCTCTTGCTGTTGCTGGCACTGTTTTgtaagtggtt ... ttttatttagGTATGTGCTGTCTTTTGCTCTTGGAGCTGGCCCAGTTCCAGCATTGCTCCT
EST: gi|27554385|gb|CA998285.1|CA998285
EST:     AAGGCTTTGGCACCTTATTCAGGCCCTCTTGCTGTTGCTGGCACTGTTTT                         GTATGTGCTGTCTTTTGCTCTTGGAGCTGGCCCAGTTCCAGCATTGCTCCT
genomic: AAGGCTTTGGCACCTTATTCAGGCCCTCTTGCTGTTGCTGGCACTGTTTTgtaagtggtt ... ttttatttagGTATGTGCTGTCTTTTGCTCTTGGAGCTGGCCCAGTTCCAGCATTGCTCCT
EST: gi|27576947|gb|CA999641.1|CA999641
EST:     AAGGCTTTGGCACCTTATTCAGGCCCTCTTGCTGTTGCTGGCACTGTTTT                         GTATGTGCTGTCTTTTGCTCTTGGAGCTGGCCCAGTTCCAGCATTGCTCCT
genomic: AAGGCTTTGGCACCTTATTCAGGCCCTCTTGCTGTTGCTGGCACTGTTTTgtaagtggtt ... ttttatttagGTATGTGCTGTCTTTTGCTCTTGGAGCTGGCCCAGTTCCAGCATTGCTCCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGCCTCAATGTTACTTCTATCATTGTCCTTCACGTGGAAGGCTTTGGCACCTTATTCAGGCCCTCTTGCTGTTGCTGGCACTGTTTTgtaagtggtttgtcatacgctttagtcaggccttttgctgattgtcattgttaactgttaatataacttgaatataattttatttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT