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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttgtctcatctcaaatcagcacttgatttgttcactgtttgcatgctattaatccatccacgctatatctttgcagTGTAAAAACAGCAGCTGGGGTTAAAGTAATTGATTTTGGATCAGCATGCTTGGAGGGTAAAACCATTTACTCGTATATTCAG

Basic information

species Oryza sativa
transcript LOC_Os02g47410.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g47410.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G849796_T01 (Zea mays), 3'ss of exon 6
gttagttgtctcatctcaa-atcagcacttgatttgttcactgtttgcatgctattaatccatccacgctatatctttgcagTGTAAAAACAGCAGCTGGGGTTAAAGTAATTGATTTTGGATCAGCATGCTTGGAGGGTAAAACCATTTACTCGTATATTCAG
|| |||||  || |||||   ||||   |  ||||  ||| |   || |  ||| | |   |    || || |  ||| ||||||||||||||||| ||| || ||||||||||||||||||||||  ||| ||||||||||||||||||| || |||||||||
gtgagttgattcttctcactgtcagtgttgaatttcatcaat-cctgtagcctaatgactaa---gcggta-acttttacagTGTAAAAACAGCAGTTGGAGTGAAAGTAATTGATTTTGGATCAGTGTGCATGGAGGGTAAAACCATTTATTCATATATTCAG
















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|58607868|gb|CK035901.1|CK035901
EST:     GGCATTATTCATTGTGATCTAAAACCGGAAAATATTCTCATAACTCCAAA                         TGTAAAAACAGCAGCTGGGGTTAAAGTAATTGATTTTGGATCAGCATGCTT
genomic: GGCATTATTCATTGTGATCTAAAACCGGAAAATATTCTCATAACTCCAAAgttagttgtc ... atctttgcagTGTAAAAACAGCAGCTGGGGTTAAAGTAATTGATTTTGGATCAGCATGCTT
EST: gi|29638402|gb|CB643411.1|CB643411
EST:     GGCATTATTCATTGTGATCTAAAACCGGAAAATATTCTCATAACTCCAAA                         TGTAAAAACAGCAGCTGGGGTTAAAGTAATTGATTTTGGATCAGCATGCTT
genomic: GGCATTATTCATTGTGATCTAAAACCGGAAAATATTCTCATAACTCCAAAgttagttgtc ... atctttgcagTGTAAAAACAGCAGCTGGGGTTAAAGTAATTGATTTTGGATCAGCATGCTT
EST: gi|58673354|gb|CK062040.1|CK062040
EST:     GGCATTATTCATTGTGATCTAAAAGCGGAAAATATTCTCATAACTCCCAA                         TGT-AAAACAGCAGCTGGGGTTAAAGTAATTGATTTTGGATCAGCATGCTT
genomic: GGCATTATTCATTGTGATCTAAAACCGGAAAATATTCTCATAACTCCAAAgttagttgtc ... atctttgcagTGTAAAAACAGCAGCTGGGGTTAAAGTAATTGATTTTGGATCAGCATGCTT
EST: gi|58610888|gb|CK038600.1|CK038600
EST:     GGCATTATTCATTGTGATCTAAAACCGGAAAATATTCTCATAACTCCAAA                         TGTAAAAACAGCAGCTGGGGTTAAAGTAATTGATTTTGGATCAGCATGCTT
genomic: GGCATTATTCATTGTGATCTAAAACCGGAAAATATTCTCATAACTCCAAAgttagttgtc ... atctttgcagTGTAAAAACAGCAGCTGGGGTTAAAGTAATTGATTTTGGATCAGCATGCTT
EST: gi|58666776|gb|CK055462.1|CK055462
EST:     GGCATTATTCATTGTGATCTAAAACCGGAAAATATTCTCATAACTCCAAA                         TGTAAAAAACAGCAGCTGGGGTTAAAGTAATTGATTTCGGATCAGCATGCT
genomic: GGCATTATTCATTGTGATCTAAAACCGGAAAATATTCTCATAACTCCAAAgttagttgtc ... atctttgcagTGTAAAAA-CAGCAGCTGGGGTTAAAGTAATTGATTTTGGATCAGCATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgatttgttcactgtttgcatgctattaatccatccacgctatatctttgcagTGTAAAAACAGCAGCTGGGGTTAAAGTAATTGATTTTGGATCAGCATGCTTGGAGGGTAAAACCATTTACTCGTATATTCAG
                         tattaat  putative branch site (score: 2)
                                            tatcttt  putative PPT
                                          tatatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagttgtctcatctcaaatcagcacttgatttgttcactgtttgcatgctattaatccatccacgctatatctttgcagTGTAAAAACAGCAGCTGGGGTTAAAGTAATTGATTTTGGATCAGCATGCTTGGAGGGTAAAACCATTTACTCGTATATTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG