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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAAGAAGGCCGCAGCACGAGCACACTCCAAAAATTTATCCTCATTCTGTGGAAGgtatgacaaacaatatctatttcctccctaacccttcttgattttttatttgttttttggatttaaaagttgttttattgcatatctgacctcttattac...

Basic information

species Oryza sativa
transcript LOC_Os02g02524.1
intron # 6
splice site 5'
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|88505777|gb|CI433283.1|CI433283
EST:     TTCTGTGGAAG                         GTTACTGGAGGAAACTGAGGATGAG
genomic: TTCTGTGGAAGgtatgacaaa ... catggtgcagGTTACTGGAGGAAACTGAGGATGAG
EST: gi|86539990|gb|CI180196.1|CI180196
EST:     AAGGCCGCAGCACGAGCACACTCCAAAAATTTATCCTCATTCTGTGGAAG                         GTTACTGGAGGAAACTGAGGATGAG
genomic: AAGGCCGCAGCACGAGCACACTCCAAAAATTTATCCTCATTCTGTGGAAGgtatgacaaa ... catggtgcagGTTACTGGAGGAAACTGAGGATGAG
EST: gi|88282038|gb|CI403434.1|CI403434
EST:     ATTTATCCTCATTCTGTGGAAG                         GTTACTGGAGGAAACTGAGGATGAG
genomic: ATTTATCCTCATTCTGTGGAAGgtatgacaaa ... catggtgcagGTTACTGGAGGAAACTGAGGATGAG
EST: gi|88527801|gb|CI455987.1|CI455987
EST:     TCATTCTGTGGAAG                         GTTACTGGAGGAAACTGAGGATGAG
genomic: TCATTCTGTGGAAGgtatgacaaa ... catggtgcagGTTACTGGAGGAAACTGAGGATGAG
EST: gi|427973|gb|D24119.1|D24119
EST:     ATTTATCCTCATTCTGTGGAAG                         GTTACTGGAGGANACTGAGGATGAG
genomic: ATTTATCCTCATTCTGTGGAAGgtatgacaaa ... catggtgcagGTTACTGGAGGAAACTGAGGATGAG
EST: gi|88271484|gb|CI387537.1|CI387537
EST:     AGCACGACCACACTCCAAAAATTTATCCTCATTCTGTGGAAG                         GTTACTGGAGGAAACTGAGGATGAG
genomic: AGCACGAGCACACTCCAAAAATTTATCCTCATTCTGTGGAAGgtatgacaaa ... catggtgcagGTTACTGGAGGAAACTGAGGATGAG
EST: gi|3767712|gb|AU031739.1|AU031739
EST:     ATTTATCCTCATTCTGTGGAAG                         GTTACTGGAGGAAACTGAGGATGAG
genomic: ATTTATCCTCATTCTGTGGAAGgtatgacaaa ... catggtgcagGTTACTGGAGGAAACTGAGGATGAG
EST: gi|86538953|gb|CI179159.1|CI179159
EST:     AAGGCCGCAGCACGAGCACACTCCGAAAATTTATCCTCATTCTGTGGAAG                         GTTACTGGGAGGAAACTGAGGATGAG
genomic: AAGGCCGCAGCACGAGCACACTCCAAAAATTTATCCTCATTCTGTGGAAGgtatgacaaa ... catggtgcagGTTACT-GGAGGAAACTGAGGATGAG
EST: gi|88836249|gb|CI371354.1|CI371354
EST:     AAGGCCGCAGCACGAGCACACTCCAAAAATTTATCCTCATTCTGTGGAAG                         GTTACTGGAGGGAAACTGAGGATGAG
genomic: AAGGCCGCAGCACGAGCACACTCCAAAAATTTATCCTCATTCTGTGGAAGgtatgacaaa ... catggtgcagGTTACTGGA-GGAAACTGAGGATGAG
EST: gi|33678092|gb|CF306331.1|CF306331
EST:     CAGCACGAGCACACTCCAAAAATTTATCCTCATTCTGTGGAAG                         GTTACTGGAGGAAACTGAGGATGAG
genomic: CAGCACGAGCACACTCCAAAAATTTATCCTCATTCTGTGGAAGgtatgacaaa ... catggtgcagGTTACTGGAGGAAACTGAGGATGAG
EST: gi|88525538|gb|CI452543.1|CI452543
EST:     TCCTCATTCTGTGGAAG                         GTTACTGGAGGAAACTGAGGATGAG
genomic: TCCTCATTCTGTGGAAGgtatgacaaa ... catggtgcagGTTACTGGAGGAAACTGAGGATGAG

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: 70 (upstream exon), 25 (downstream exon)
Score: 22

AAAAGAAGGCCGCAGCACGAGCACACTCCAAAAATTTATCCTCATTCTGTGGAAGgtatgacaaa ... catggtgcagGTTACTGGAGGAAACTGAGGATGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAAGAAGGCCGCAGCACGAGCACACTCCAAAAATTTATCCTCATTCTGTGGAAGgtatgacaaacaatatctatttcctccctaacccttcttgattttttatttgttttttggatttaaaagttgttttattgcatatctgacctcttattac

- - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcctcc