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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatcagccagcaataacaattggctaatgatagcttgttactttggcgataataagttatcgtttaactctgacgatgatgttatttgtgtttgttcagTGGATCTTCTGGGTGGGCCCCCTGATCGGCGCCGCCATCGCCGCCGCCTACCACCAGTACGTGCTGAGGGCCAGCGCCGCCAAGCTCGGGTCCTACCGGA

Basic information

species Oryza sativa
transcript LOC_Os02g41860.2
intron # 3
splice site 3'
intron type U2

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|29672611|gb|CB668886.1|CB668886
EST:     GCTTGGGAACCGCGGTTATCTACAACAAGGACAAGGCCTGGGATGACCAA                         TGGATCTTCTGGGTGGGCCCCCTGATCGGCGCCGCCATCGCCGCCGCCTAC
genomic: GCTTGGGAACCGCGGTTATCTACAACAAGGACAAGGCCTGGGATGACCAAgtgcgtaccc ... gtttgttcagTGGATCTTCTGGGTGGGCCCCCTGATCGGCGCCGCCATCGCCGCCGCCTAC
EST: gi|117222050|gb|CT852596.1|CT852596
EST:     GCTTGGGAGCCGCGGTTATCTACAACAAGGACAAGGCCTGGGATGACCAA                         TGGATCTTCTGGGTGGGCCCCCTGATCGGCGC-GCCATCGCCGCCGC-TAC
genomic: GCTTGGGAACCGCGGTTATCTACAACAAGGACAAGGCCTGGGATGACCAAgtgcgtaccc ... gtttgttcagTGGATCTTCTGGGTGGGCCCCCTGATCGGCGCCGCCATCGCCGCCGCCTAC
EST: gi|58613123|gb|CK040835.1|CK040835
EST:     GCTTGGGAGCCGCGGTTATCTACAACAAGGACAAGGCCTGGGATGACCAA                         TGGATCTTCTGGGTGGGCCCCCTGATCGGCGCCGCCATCGCCGCCGCCTAA
genomic: GCTTGGGAACCGCGGTTATCTACAACAAGGACAAGGCCTGGGATGACCAAgtgcgtaccc ... gtttgttcagTGGATCTTCTGGGTGGGCCCCCTGATCGGCGCCGCCATCGCCGCCGCCTAC
EST: gi|29687215|gb|CB683490.1|CB683490
EST:     GCTTGGGAACCGCGGTTATCTACAACAAGGACAAGGCCTGGGATGACCAA                         TGGATCTTCTGGGTGGGCCCCCTGATCGGCGCCGCCATCGCCGCCGCCTAC
genomic: GCTTGGGAACCGCGGTTATCTACAACAAGGACAAGGCCTGGGATGACCAAgtgcgtaccc ... gtttgttcagTGGATCTTCTGGGTGGGCCCCCTGATCGGCGCCGCCATCGCCGCCGCCTAC
EST: gi|86547122|gb|CI187328.1|CI187328
EST:     GCTTGGGAACCGCGGTTATCTACAACAAGGACAAGGCCTGGGATGACCAA                         TGGATCTTCTGGGTGGGCCCCCTGATCGGCGCCGCCATCGCCGCCGCCTAC
genomic: GCTTGGGAACCGCGGTTATCTACAACAAGGACAAGGCCTGGGATGACCAAgtgcgtaccc ... gtttgttcagTGGATCTTCTGGGTGGGCCCCCTGATCGGCGCCGCCATCGCCGCCGCCTAC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 74 (upstream exon), 68 (downstream exon)
Score: 109

CCATCTGGCCACCATCCCCATCACCGGCACCGGCATTAACCCGGCGAGGAGCTTGGGAACCGCGGTTATCTACAACAAGGACAAGGCCTGGGATGACCAAgtgcgtaccc ... gtttgttcagTGGATCTTCTGGGTGGGCCCCCTGATCGGCGCCGCCATCGCCGCCGCCTACCACCAGTACGTGCTGAGGGCCAGCGCCGCCAAGCTCGGGTCCTACCGGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcgataataagttatcgtttaactctgacgatgatgttatttgtgtttgttcagTGGATCTTCTGGGTGGGCCCCCTGATCGGCGCCGCCATCGCCGCCGCCTACCACCAGTACGTGCTGAGGGCCAGCGCCGCCAAGCTCGGGTCCTACCGGA
                       ctctgac  putative branch site (score: 109)
                                              tttgttc  putative PPT
     taataagttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatcagccagcaataacaattggctaatgatagcttgttactttggcgataataagttatcgtttaactctgacgatgatgttatttgtgtttgttcagTGGATCTTCTGGGTGGGCCCCCTGATCGGCGCCGCCATCGCCGCCGCCTACCACCAGTACGTGCTGAGGGCCAGCGCCGCCAAGCTCGGGTCCTACCGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT