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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAGAACTGGCACTCCTGTATCCAGGGCGTCGCTACACACTAGTTAGGATGCGCCTCAGgtattttggcttgaacttctgtctatgttttgaactcttgatgatttctcagtgcttctaatttgaaatttgtgcggacattttgtag

Basic information

species Oryza sativa
transcript LOC_Os04g35190.1
intron # 9
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|25806565|gb|CA762526.1|CA762526
EST:     GCACTCCTGTATCCAGGGCGTCGCTACACACTAGTTAGGATGCGCCTCAG                         GCTTAGAGGCACAACTCTGGGCGCAAACAACAGGTTGGATGTATTGAAGAT
genomic: GCACTCCTGTATCCAGGGCGTCGCTACACACTAGTTAGGATGCGCCTCAGgtattttggc ... cattttgtagGCTTAGAGGCACAACTCTGGGCGCAAACAACAGGTTGGATGTATTGAAGAT
EST: gi|86832622|gb|CI345056.1|CI345056
EST:     GTTAGGATGCGCCTCAG                         GCTTAGAGGCACAACTCTGGGCGCAAACAACAGGTTGGATGTATTGAAGAT
genomic: GTTAGGATGCGCCTCAGgtattttggc ... cattttgtagGCTTAGAGGCACAACTCTGGGCGCAAACAACAGGTTGGATGTATTGAAGAT
EST: gi|58691809|gb|CK080496.1|CK080496
EST:     GCACTCCTGTATCCAGTGCGTCGCTACACACTAGTTAGGATGCGCCTCAG                         GCTTAGAGGCACAACACTTGGGCGCAAACAACAGGTTGGATGTATTGAAGA
genomic: GCACTCCTGTATCCAGGGCGTCGCTACACACTAGTTAGGATGCGCCTCAGgtattttggc ... cattttgtagGCTTAGAGGCACAACTCT-GGGCGCAAACAACAGGTTGGATGTATTGAAGA
EST: gi|218488546|gb|FG955819.1|FG955819
EST:     GCACTCCTGTATCCAGGGCGTCGCTACACACTAGTTAGGATGCGCCTCAG                         GCTTAGAGGCACAACTCTGGGCGCCAAACAACAGGTTGGATGTATTGAAGA
genomic: GCACTCCTGTATCCAGGGCGTCGCTACACACTAGTTAGGATGCGCCTCAGgtattttggc ... cattttgtagGCTTAGAGGCACAACTCTGGGCGC-AAACAACAGGTTGGATGTATTGAAGA
EST: gi|29645691|gb|CB650698.1|CB650698
EST:     GCACTCCTGTATCCAGGGCGTCGCTACACACTAGTTAGGATGCGCCTCAG                         GCTTAGAGGCACAACTCTGGGCGCAAACAACAGGTTGGATGTATTGAAGAT
genomic: GCACTCCTGTATCCAGGGCGTCGCTACACACTAGTTAGGATGCGCCTCAGgtattttggc ... cattttgtagGCTTAGAGGCACAACTCTGGGCGCAAACAACAGGTTGGATGTATTGAAGAT
EST: gi|66924057|gb|CX110905.1|CX110905
EST:     GCACTCCTGTATCCAGGGCGTCGCTACACACTAGTTAGGATGCGCCTCAG                         GCTTAGAGGCACAACTCTGGGCGCAAACAACAGGTTGGATGTATTGAAGAT
genomic: GCACTCCTGTATCCAGGGCGTCGCTACACACTAGTTAGGATGCGCCTCAGgtattttggc ... cattttgtagGCTTAGAGGCACAACTCTGGGCGCAAACAACAGGTTGGATGTATTGAAGAT
EST: gi|29655902|gb|CB652177.1|CB652177
EST:     GCACTCCTGTATCCAGGGCGTCGCTACACACTAGTTAGGATGCGCCTCAG                         GCTTAGAGGCACAACTCTGGGCGCAAACAACAGGTTGGATGTATTGAAGAT
genomic: GCACTCCTGTATCCAGGGCGTCGCTACACACTAGTTAGGATGCGCCTCAGgtattttggc ... cattttgtagGCTTAGAGGCACAACTCTGGGCGCAAACAACAGGTTGGATGTATTGAAGAT
EST: gi|29623230|gb|CB628241.1|CB628241
EST:     GCACTCCTGTATCCAGGGCGTCGCTACACACTAGTTAGGATGCGCCTCAG                         GCTTAGAGGCACAACTCTGGGCGCAAACAACAGGTTGGATGTATTGAAGAT
genomic: GCACTCCTGTATCCAGGGCGTCGCTACACACTAGTTAGGATGCGCCTCAGgtattttggc ... cattttgtagGCTTAGAGGCACAACTCTGGGCGCAAACAACAGGTTGGATGTATTGAAGAT
EST: gi|86481675|gb|CI124308.1|CI124308
EST:     GCACTCCTGTATCCAGGGCGTCGCTACACACTAGTTAGGATGCGCCTCAG                         GCTTAGAGGCACAACTCTGGGCGCAAACAACAGGTTGGATGTATTGAAGAT
genomic: GCACTCCTGTATCCAGGGCGTCGCTACACACTAGTTAGGATGCGCCTCAGgtattttggc ... cattttgtagGCTTAGAGGCACAACTCTGGGCGCAAACAACAGGTTGGATGTATTGAAGAT

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: 75 (upstream exon), 72 (downstream exon)
Score: 31

ATAGAACTGGCACTCCTGTATCCAGGGCGTCGCTACACACTAGTTAGGATGCGCCTCAGgtattttggc ... cattttgtagGCTTAGAGGCACAACTCTGGGCGCAAACAACAGGTTGGATGTATTGAAGATCTTAACCACCGGGGTGAATGCAACCGAACTGAGAAACTGGAAAGGCAGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATAGAACTGGCACTCCTGTATCCAGGGCGTCGCTACACACTAGTTAGGATGCGCCTCAGgtattttggcttgaacttctgtctatgttttgaactcttgatgatttctcagtgcttctaatttgaaatttgtgcggacattttgtag

- - - - - - - - - - - - - - - - - - - - - -  AGGATG