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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTCAATGTCACTGAGGCAACAATTGCAAGATTCTGGAAGGAAGCCTGTTGCGGCCCAACATTACAACAAGGGTGATAAAGATGGAACAAGCACTGGCAGgcatgtttaaatttttcacttttcatttaggtgtcagatatgattgcttgactttgtttgcacttactccctccatcccaaaatataagaacctaggacc...

Basic information

species Oryza sativa
transcript LOC_Os12g07450.3
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g07450.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G096070_T01 (Zea mays), 5'ss of exon 4
ATTCAATGTCACTGAGGCAACAATTGCAAGATTCTGGAAGGAAGCCTGTTGCGGCCCAACATTACAACAAGGGTGATAAAGATGGAACAAGCACTGGCAGgcatgttt-aaatttttcacttttcatttaggtgtcagatatgattgcttgactttgtttgcacttactccctccatcccaaaatata-agaacctaggacc---------------------------------------
|||||||||| ||||||||||| || |||||| ||||||| || || || || || | ||||||||| ||||||||||||||||   ||  || ||| ||| ||| || ||| ||| || | || ||||   || || || ||||  | |    |  |||  | |||    |    | |  ||||||  |||    | |                                          
ATTCAATGTCGCTGAGGCAACAGTTACAAGATCCTGGAAGAAAACCCGTGGCAGCTCTACATTACAATAAGGGTGATAAAGATGTCTCACCCAATGGAAGgtatgcttgaaagtttccattattaatttgaatgacacatctgat-acatatggtcttttcaatttatcgacgttgttcataaatatttagattacatgtttgtttatattactgctctgtgattttgatatcatatttag
















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|29670875|gb|CB667150.1|CB667150
EST:     GCGGCCCAACATTACAACAAGGGTGATAAAGATGGAACAAGCACTGGCAG                         CCGATGCACTTCTGTTGCATGGGTACCGGAGCGTGAAGGAATCTTTGTTGT
genomic: GCGGCCCAACATTACAACAAGGGTGATAAAGATGGAACAAGCACTGGCAGgcatgtttaa ... tttttggcagCCGATGCACTTCTGTTGCATGGGTACCGGAGCGTGAAGGAATCTTTGTTGT
EST: gi|29665681|gb|CB661956.1|CB661956
EST:     CGGCCCAACATTACAACAAGAGGTGATAAAGATGGAACAAGCACTGGCAG                         CCGATGCACTTCTGTTGCATGGGTACCGGAGCGTGAAGGAATCTTTAGTTG
genomic: CGGCCCAACATTACAACAAG-GGTGATAAAGATGGAACAAGCACTGGCAGgcatgtttaa ... tttttggcagCCGATGCACTTCTGTTGCATGGGTACCGGAGCGTGAAGGAATCTTT-GTTG
EST: gi|33687920|gb|CF316159.1|CF316159
EST:     GCGGCCCAACATTACAACAAGGGTGATAAAGATGGAACAAGCACTGGCAG                         CCGATGCACTTCTGTTGCATGGGTACCGGAGCGTGAAGGAATCTNTGTTGT
genomic: GCGGCCCAACATTACAACAAGGGTGATAAAGATGGAACAAGCACTGGCAGgcatgtttaa ... tttttggcagCCGATGCACTTCTGTTGCATGGGTACCGGAGCGTGAAGGAATCTTTGTTGT
EST: gi|58684188|gb|CK072875.1|CK072875
EST:     GCGGCCCAACATTACAACAAGGGTGATAAAGATGGAACAAGCACTGGCAG                         CCGATGCACTTCTGTTGCATGGGTACCGGAGCGTGAAGGAATCTTTGTTGT
genomic: GCGGCCCAACATTACAACAAGGGTGATAAAGATGGAACAAGCACTGGCAGgcatgtttaa ... tttttggcagCCGATGCACTTCTGTTGCATGGGTACCGGAGCGTGAAGGAATCTTTGTTGT
EST: gi|66927819|gb|CX114667.1|CX114667
EST:     GCGGCCCAACATTACAACAAGGGTGATAAAGATGGAACAAGCACTGGCAG                         CCGATGCACTTCTGTTGCATGGGTACCGGAGCGTGAAGGAATCTTTGTTGT
genomic: GCGGCCCAACATTACAACAAGGGTGATAAAGATGGAACAAGCACTGGCAGgcatgtttaa ... tttttggcagCCGATGCACTTCTGTTGCATGGGTACCGGAGCGTGAAGGAATCTTTGTTGT
EST: gi|218478110|gb|FG955323.1|FG955323
EST:     GCGGCCCAACATTACAACAAGGGTGATAAAGATGGAACAAGCACTGGCAG                         CCGATGCACTTCTGTTGCATGGGTACCGGAGCGTGAAGGAATCTTTGTTGT
genomic: GCGGCCCAACATTACAACAAGGGTGATAAAGATGGAACAAGCACTGGCAGgcatgtttaa ... tttttggcagCCGATGCACTTCTGTTGCATGGGTACCGGAGCGTGAAGGAATCTTTGTTGT
EST: gi|58685449|gb|CK074136.1|CK074136
EST:     TAAAGATGGAACAAGCACTGGCAG                         CCGATGCACTTCTGTTGCATGGGTACCGGAGCGGGAAGGAATC-TTGTTGT
genomic: TAAAGATGGAACAAGCACTGGCAGgcatgtttaa ... tttttggcagCCGATGCACTTCTGTTGCATGGGTACCGGAGCGTGAAGGAATCTTTGTTGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTCAATGTCACTGAGGCAACAATTGCAAGATTCTGGAAGGAAGCCTGTTGCGGCCCAACATTACAACAAGGGTGATAAAGATGGAACAAGCACTGGCAGgcatgtttaaatttttcacttttcatttaggtgtcagatatgattgcttgactttgtttgcacttactccctccatcccaaaatataagaacctaggacc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA