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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGCAAATGGTGAAAATGCTTGGGTTGGCATTGATGGAAGCAGTGGTGATATTGTGGATATGAAAGAGCGGAAGgtctctctccccccctcgtgcttgtgcttttgcgtgtttgcattcatcttgaaacctcattatctatccttttcag

Basic information

species Oryza sativa
transcript LOC_Os02g14929.1
intron # 13
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|88538071|gb|CI467069.1|CI467069
EST:     TTGGCATTGATGGAAGCAGTGGTGATATTGTGAATATGAAAGAGCGGAAG                         ATCTGGGACTCGTACANTGTCAAGGCGCAGACATTCAAGACAGCTATTGAG
genomic: TTGGCATTGATGGAAGCAGTGGTGATATTGTGGATATGAAAGAGCGGAAGgtctctctcc ... tccttttcagATCTGGGACTCGTACAGTGTCAAGGCGCAGACATTCAAGACAGCTATTGAG
EST: gi|88484521|gb|CI421792.1|CI421792
EST:     AGCAGTGGTGATATTGTGGATATGAAAGAGCGGAAG                         ATCTGGGACTCGTACAGTGTCAAGGCNCAGACATTCAAGACAGCTATTGAG
genomic: AGCAGTGGTGATATTGTGGATATGAAAGAGCGGAAGgtctctctcc ... tccttttcagATCTGGGACTCGTACAGTGTCAAGGCGCAGACATTCAAGACAGCTATTGAG
EST: gi|88478301|gb|CI415572.1|CI415572
EST:     TTGTGGATATGAAAGAGCGGAAG                         ATCTGGGACTCGTACAGTGTCAAGGCGCAGACATTCAAGACAGCTATTGAG
genomic: TTGTGGATATGAAAGAGCGGAAGgtctctctcc ... tccttttcagATCTGGGACTCGTACAGTGTCAAGGCGCAGACATTCAAGACAGCTATTGAG
EST: gi|426945|gb|D23021.1|D23021
EST:     TTGGCATTGATGGAAGCAGTNGTGATATTGTGGATATGAAAGAGCGGAAG                         ATCTGGGACTCGTACAGTGTCAAGGCGCAGACATTCAAGACAGCTATTGAG
genomic: TTGGCATTGATGGAAGCAGTGGTGATATTGTGGATATGAAAGAGCGGAAGgtctctctcc ... tccttttcagATCTGGGACTCGTACAGTGTCAAGGCGCAGACATTCAAGACAGCTATTGAG
EST: gi|89180165|gb|CI044444.1|CI044444
EST:     TTGGCATTGATGGAAGCAGTGGTGATATTGTGGATATGAAAGAGCGGAAG                         ATCTGGGACTCGTACAGTGTCAAGGCGCAGACATTCAAGACAGCTATTGAG
genomic: TTGGCATTGATGGAAGCAGTGGTGATATTGTGGATATGAAAGAGCGGAAGgtctctctcc ... tccttttcagATCTGGGACTCGTACAGTGTCAAGGCGCAGACATTCAAGACAGCTATTGAG
EST: gi|86492124|gb|CI134757.1|CI134757
EST:     CAGTGGTGATATTGTGGATATGAAAGAGCGGAAG                         ATCTGGGACTCGTACAGTGTCAAGGCGCAGACATTCAAGACAGCTATTGAG
genomic: CAGTGGTGATATTGTGGATATGAAAGAGCGGAAGgtctctctcc ... tccttttcagATCTGGGACTCGTACAGTGTCAAGGCGCAGACATTCAAGACAGCTATTGAG
EST: gi|88268309|gb|CI378244.1|CI378244
EST:     TTGGCATTGATGGAAGCACTGGTGATATTGTGGATATGAAAGAGCGGAAG                         ATCT-GGACTCGTACAGTGTCAAGGCGCAGACATTCAAGACAGCTATTGAG
genomic: TTGGCATTGATGGAAGCAGTGGTGATATTGTGGATATGAAAGAGCGGAAGgtctctctcc ... tccttttcagATCTGGGACTCGTACAGTGTCAAGGCGCAGACATTCAAGACAGCTATTGAG
EST: gi|88455551|gb|CI521771.1|CI521771
EST:     CATTGATGGAAGCAGTGGTGATATTGTGGATATGAAAGAGCGGAAG                         ATCTGGGACTCGTACAGTGTCAAGGCGCAGACATTCAAGACAGCTATTGAG
genomic: CATTGATGGAAGCAGTGGTGATATTGTGGATATGAAAGAGCGGAAGgtctctctcc ... tccttttcagATCTGGGACTCGTACAGTGTCAAGGCGCAGACATTCAAGACAGCTATTGAG
EST: gi|89178997|gb|CI043502.1|CI043502
EST:     TTGGCATTGATGGAAGCAGTGGTGATATTGTGGATATGAAAGAGCGGAAG                         ATCTGGGACTCGTACAGTGTCAAGGCGCAGACATTCAAGACAGCTATTGAG
genomic: TTGGCATTGATGGAAGCAGTGGTGATATTGTGGATATGAAAGAGCGGAAGgtctctctcc ... tccttttcagATCTGGGACTCGTACAGTGTCAAGGCGCAGACATTCAAGACAGCTATTGAG
EST: gi|88446737|gb|CI526570.1|CI526570
EST:     GTGGATATGAAAGAGCGGAAG                         ATCTGGGACTCGTACAGTGTCAAGGCGCAGACATTCAAGACAGCTATTGAG
genomic: GTGGATATGAAAGAGCGGAAGgtctctctcc ... tccttttcagATCTGGGACTCGTACAGTGTCAAGGCGCAGACATTCAAGACAGCTATTGAG
EST: gi|88548722|gb|CI478541.1|CI478541
EST:     TGATATTGTGGATATGAAAGAGCGGAAG                         ATCTGGAACTCGTACANTGTCAAGGCGCAGACATTCAAGACAGCTATTGAG
genomic: TGATATTGTGGATATGAAAGAGCGGAAGgtctctctcc ... tccttttcagATCTGGGACTCGTACAGTGTCAAGGCGCAGACATTCAAGACAGCTATTGAG
EST: gi|88971190|gb|CI387163.1|CI387163
EST:     TTGGCATTGATGGAAGCAGTGGTGATATTGTGGATATGAAAGAGCGGAAG                         ATCTGGGACTCGTACAGTGTCAAGGCGCAGACATTCAAGACAGCTATTGAG
genomic: TTGGCATTGATGGAAGCAGTGGTGATATTGTGGATATGAAAGAGCGGAAGgtctctctcc ... tccttttcagATCTGGGACTCGTACAGTGTCAAGGCGCAGACATTCAAGACAGCTATTGAG
EST: gi|88262365|gb|CI366139.1|CI366139
EST:     -TGGCATTGATGGAAACAGTGGTGATATT-TGGATAT-AAAGAGC-GAAG                         ATCTGGGACTCGTACAGTTTCAAGGCGCAGACATTCAAGACAGCTATTGAG
genomic: TTGGCATTGATGGAAGCAGTGGTGATATTGTGGATATGAAAGAGCGGAAGgtctctctcc ... tccttttcagATCTGGGACTCGTACAGTGTCAAGGCGCAGACATTCAAGACAGCTATTGAG

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: 62 (upstream exon), 48 (downstream exon)
Score: 3

CATGCAAATGGTGAAAATGCTTGGGTTGGCATTGATGGAAGCAGTGGTGATATTGTGGATATGAAAGAGCGGAAGgtctctctcc ... tccttttcagATCTGGGACTCGTACAGTGTCAAGGCGCAGACATTCAAGACAGCTATTGAGGCTGCCTGCATGCTCCTGAGGATCGATGATATTGTCAGTGGCATCAAGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATGCAAATGGTGAAAATGCTTGGGTTGGCATTGATGGAAGCAGTGGTGATATTGTGGATATGAAAGAGCGGAAGgtctctctccccccctcgtgcttgtgcttttgcgtgtttgcattcatcttgaaacctcattatctatccttttcag

- - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - -  TGGAAG