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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaaaaacggttttttgttgcttcttatcatgcaccactagtcgtagcttaatttggtgctcctatacctccttgcagGCGGGTGTTAGTTTTTCCAACTGGAAACAGTGTACAGTCCCTTTCGATGTACCTAGATATTGCTGACGCAAATGAACAGCCTCATGGATGGAGTAAATAT

Basic information

species Oryza sativa
transcript LOC_Os01g56490.1
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|88390787|gb|CI611013.1|CI611013
EST:     AATCACAGAAAGCTGTACTCTGATGTTTTTGTGGTTGGGGGGCACAAATG                         GCGGGTGTTAGTTTTTCCAACTGGAAACAGTGTACA
genomic: AATCACAGAAAGCTGTACTCTGATGTTTTTGTGGTTGGGGGGCACAAATGgtgagtaaaa ... ctccttgcagGCGGGTGTTAGTTTTTCCAACTGGAAACAGTGTACA
EST: gi|88402176|gb|CI615019.1|CI615019
EST:     AATCACAGAAAGGTGTACTCTGATGTTTGTGTGGTTGGGGGGCACAA-TG                         GCGGGTGTTAGTTTTTCCAACTGGAAACAGTGTACAGTCC-TTTCGATGTA
genomic: AATCACAGAAAGCTGTACTCTGATGTTTTTGTGGTTGGGGGGCACAAATGgtgagtaaaa ... ctccttgcagGCGGGTGTTAGTTTTTCCAACTGGAAACAGTGTACAGTCCCTTTCGATGTA
EST: gi|86904504|gb|CI308714.1|CI308714
EST:     AATCACAGAAAGCTGTACTCTGATGTTTTTGTGGTTGGGGGGCACAAATG                         GCGGGTGTTAGTTTTTCCAACTGGAAACAGTGTACAGTCCCTTTCGATGTA
genomic: AATCACAGAAAGCTGTACTCTGATGTTTTTGTGGTTGGGGGGCACAAATGgtgagtaaaa ... ctccttgcagGCGGGTGTTAGTTTTTCCAACTGGAAACAGTGTACAGTCCCTTTCGATGTA
EST: gi|88311790|gb|CI577396.1|CI577396
EST:     AATCACAGAAAGCTGTACTCTGATGTTTTTGTGGTTGGGGGGCACAAATG                         GCGGGTGTTAGTTTT
genomic: AATCACAGAAAGCTGTACTCTGATGTTTTTGTGGTTGGGGGGCACAAATGgtgagtaaaa ... ctccttgcagGCGGGTGTTAGTTTT
EST: gi|88453182|gb|CI563422.1|CI563422
EST:     AATCACAGAAAGCTGTACTCTGATGTTTTTGTGGTTGGGGGGCACAAATG                         GCGGGTGTTAGTTTTTCCAACTGGAAACAGTGTACAGTCCCTTTCGATGTA
genomic: AATCACAGAAAGCTGTACTCTGATGTTTTTGTGGTTGGGGGGCACAAATGgtgagtaaaa ... ctccttgcagGCGGGTGTTAGTTTTTCCAACTGGAAACAGTGTACAGTCCCTTTCGATGTA
EST: gi|88315847|gb|CI617320.1|CI617320
EST:     ATCACAGAAAGCTGTACTCTGATGTTTTTTGTGGTTGGGGGGCACAAATG                         GTGGGTGTTAGTTTTTTCCAACTGGAAACAGTGTACAGTCCCTTTCGATGT
genomic: ATCACAGAAAGCTGTACTCTGATGTTTTT-GTGGTTGGGGGGCACAAATGgtgagtaaaa ... ctccttgcagGCGGGTGTTAGTTTTT-CCAACTGGAAACAGTGTACAGTCCCTTTCGATGT
EST: gi|88371255|gb|CI597732.1|CI597732
EST:     AATCACAGAAAGCTGTACTCTGATGTTTTTGTGGTTGGGGGGCACAAATG                         GCGGGTGTTAGTTTTTCCAACTGGAAACAGTGTACAG
genomic: AATCACAGAAAGCTGTACTCTGATGTTTTTGTGGTTGGGGGGCACAAATGgtgagtaaaa ... ctccttgcagGCGGGTGTTAGTTTTTCCAACTGGAAACAGTGTACAG
EST: gi|88298888|gb|CI567891.1|CI567891
EST:     AATCACAGAAAGCTGTACTCTGATGTTTTTGTGGTTGGGGGGCACAAATG                         GCGGGTGTTAGTTTTTCCAACTGGAAACAGTGTACAGTCCCTTTCGATGTA
genomic: AATCACAGAAAGCTGTACTCTGATGTTTTTGTGGTTGGGGGGCACAAATGgtgagtaaaa ... ctccttgcagGCGGGTGTTAGTTTTTCCAACTGGAAACAGTGTACAGTCCCTTTCGATGTA
EST: gi|88372041|gb|CI609949.1|CI609949
EST:     AATCACAGAAAGCTGTACTCTGATGTTTTTGTGGTTGGGGGGCACAAATG                         GCGGGTGTTAG
genomic: AATCACAGAAAGCTGTACTCTGATGTTTTTGTGGTTGGGGGGCACAAATGgtgagtaaaa ... ctccttgcagGCGGGTGTTAG

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: 71 (upstream exon), 65 (downstream exon)
Score: 25

TACCAGAAACCTCTACGTCCAGATTTACGTGGACCATTGAAGATTTTTCGAATCACAGAAAGCTGTACTCTGATGTTTTTGTGGTTGGGGGGCACAAATGgtgagtaaaa ... ctccttgcagGCGGGTGTTAGTTTTTCCAACTGGAAACAGTGTACAGTCCCTTTCGATGTACCTAGATATTGCTGACGCAAATGAACAGCCTCATGGATGGAGTAAATAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttatcatgcaccactagtcgtagcttaatttggtgctcctatacctccttgcagGCGGGTGTTAGTTTTTCCAACTGGAAACAGTGTACAGTCCCTTTCGATGTACCTAGATATTGCTGACGCAAATGAACAGCCTCATGGATGGAGTAAATAT
                       gcttaat  putative branch site (score: 25)
                                    ctcctatacctcctt  putative PPT
                         ttaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtaaaaacggttttttgttgcttcttatcatgcaccactagtcgtagcttaatttggtgctcctatacctccttgcagGCGGGTGTTAGTTTTTCCAACTGGAAACAGTGTACAGTCCCTTTCGATGTACCTAGATATTGCTGACGCAAATGAACAGCCTCATGGATGGAGTAAATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA