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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgaaacatatacccctcaacaatcttttctgttcagattgttacagccaaaaagggatgacagaaatttcttcattctgatcacttgaatgcagGGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG

Basic information

species Oryza sativa
transcript LOC_Os01g07090.1
intron # 9
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|55413992|gb|CV726368.1|CV726368
EST:     CAGTGGATGTCACCTTTGATTCACCCTACTCAATGGAGGCTCGGAGTCGG                         GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG
genomic: CAGTGGATGTCACCTTTGATTCACCCTACTCAATGGAGGCTCGGAGTCGGgtgcgaaaca ... ttgaatgcagGGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG
EST: gi|88470794|gb|CI408065.1|CI408065
EST:     CCTACTCAATGGAGGCTCGGAGTCGG                         GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG
genomic: CCTACTCAATGGAGGCTCGGAGTCGGgtgcgaaaca ... ttgaatgcagGGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG
EST: gi|24468854|gb|CA305803.1|CA305803
EST:     CGGTGGATGTCACCTTTGATTCACCCTACTCAATGGAGGCTCGGAGTCGG                         GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG
genomic: CAGTGGATGTCACCTTTGATTCACCCTACTCAATGGAGGCTCGGAGTCGGgtgcgaaaca ... ttgaatgcagGGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG
EST: gi|117230125|gb|CT846221.1|CT846221
EST:     CGGTGGATGTCACCTTTGATTCACCCTACTCAATGGAGGCTCGGAGTCGG                         GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG
genomic: CAGTGGATGTCACCTTTGATTCACCCTACTCAATGGAGGCTCGGAGTCGGgtgcgaaaca ... ttgaatgcagGGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG
EST: gi|88487810|gb|CI425081.1|CI425081
EST:     CCCTACTCAATGGAGGCTCGGAGTCGG                         GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG
genomic: CCCTACTCAATGGAGGCTCGGAGTCGGgtgcgaaaca ... ttgaatgcagGGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG
EST: gi|88487832|gb|CI425103.1|CI425103
EST:     CTCAATGGAGGCTCGGAGTCGG                         GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG
genomic: CTCAATGGAGGCTCGGAGTCGGgtgcgaaaca ... ttgaatgcagGGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG
EST: gi|29641054|gb|CB646061.1|CB646061
EST:     CAGTGGATGTCACCTTTGATTCACCCTACTCAATGGAGGCTCGGAGTCGG                         GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG
genomic: CAGTGGATGTCACCTTTGATTCACCCTACTCAATGGAGGCTCGGAGTCGGgtgcgaaaca ... ttgaatgcagGGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG
EST: gi|88844338|gb|CI005711.1|CI005711
EST:     CAGTGGATGTCACCTTTGATTCACCCTACTCAATGGAGGCTCGGAGTCGG                         GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG
genomic: CAGTGGATGTCACCTTTGATTCACCCTACTCAATGGAGGCTCGGAGTCGGgtgcgaaaca ... ttgaatgcagGGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG
EST: gi|29685959|gb|CB682234.1|CB682234
EST:     CAGTGGATGTCACCTTTGATTCACCCTACTCAATGGAGGCTCGGAGTCGG                         GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG
genomic: CAGTGGATGTCACCTTTGATTCACCCTACTCAATGGAGGCTCGGAGTCGGgtgcgaaaca ... ttgaatgcagGGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG
EST: gi|29685960|gb|CB682235.1|CB682235
EST:     CAGTGGATGTCACCTTTGATTCACCCTACTCAATGGAGGCTCGGAGTCGG                         GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG
genomic: CAGTGGATGTCACCTTTGATTCACCCTACTCAATGGAGGCTCGGAGTCGGgtgcgaaaca ... ttgaatgcagGGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG
EST: gi|86259009|gb|CI004553.1|CI004553
EST:     CAGTGGATGTCACCTTTGATTCACCCTACTCAATGGAGGCTCGGAGTCGG                         GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG
genomic: CAGTGGATGTCACCTTTGATTCACCCTACTCAATGGAGGCTCGGAGTCGGgtgcgaaaca ... ttgaatgcagGGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG
EST: gi|86903280|gb|CI313643.1|CI313643
EST:     CAGTGGATGTCACCTTTGATTCACCCTACTCAATGGAGCCTCGGAGTC-G                         GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAGTAG
genomic: CAGTGGATGTCACCTTTGATTCACCCTACTCAATGGAGGCTCGGAGTCGGgtgcgaaaca ... ttgaatgcagGGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG
EST: gi|88283322|gb|CI404768.1|CI404768
EST:     CAGTGGATGTCACCTTTGATTCACCCTACTCAATGGAGGCTCGGAGTCGG                         GGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG
genomic: CAGTGGATGTCACCTTTGATTCACCCTACTCAATGGAGGCTCGGAGTCGGgtgcgaaaca ... ttgaatgcagGGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG

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: 68 (upstream exon), 53 (downstream exon)
Score: 17

CAAAAGCACTAGCAGAGCTTGCAAGGAAGCATTCAGTGGATGTCACCTTTGATTCACCCTACTCAATGGAGGCTCGGAGTCGGgtgcgaaaca ... ttgaatgcagGGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttacagccaaaaagggatgacagaaatttcttcattctgatcacttgaatgcagGGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG
                                   ttctgat  putative branch site (score: 17)
                        aaatttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgaaacatatacccctcaacaatcttttctgttcagattgttacagccaaaaagggatgacagaaatttcttcattctgatcacttgaatgcagGGTTTTGATGTCCCCTCGTGGAAAAAGTTCATTGGAGGGAAACTAATAG

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