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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcctcttttttcagcgaacatcgtcgatgcaacaattttgagctttgcagtaacggttgttaacaaatccataaatatgcagGTGTTTTCTATTGTGGATCCCCTACACTCACGAAACAACTCAAGGATCTTTCAAAAGAATTCAGCCAGACAACCACAACTAGATTCCACTTCCACAAGGA

Basic information

species Oryza sativa
transcript LOC_Os01g61880.2
intron # 11
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|86481607|gb|CI124240.1|CI124240
EST:     GAGAAAGGTGTTCTCTGACTTGGCGAATGCCCACAAAAACTCACGCATAG                         GTGTTTTCTATTGTGGATCCCCTACACTCACGAAACAACTCAAGGATCTTT
genomic: GAGAAAGGTGTTCTCTGACTTGGCGAATGCCCACAAAAACTCACGCATAGgtgagcctct ... aaatatgcagGTGTTTTCTATTGTGGATCCCCTACACTCACGAAACAACTCAAGGATCTTT
EST: gi|88270393|gb|CI385651.1|CI385651
EST:     GAGAAAGGTGTTCTCTGACTTGGCGAATGCCCACAAAAACTCACGCATAG                         GTGTTTTCTATTGTGGATCCCCTACACTCACGAAACAACTCAAGGATCTTT
genomic: GAGAAAGGTGTTCTCTGACTTGGCGAATGCCCACAAAAACTCACGCATAGgtgagcctct ... aaatatgcagGTGTTTTCTATTGTGGATCCCCTACACTCACGAAACAACTCAAGGATCTTT
EST: gi|86865969|gb|CI335558.1|CI335558
EST:     GAGAAAGGTGTTCTCTGACTTGGCGAATGCCCACAAAAACTCACGCATAG                         GTGTTTTCTATTGTGGATCCCCTACACTCACGAAACAACTC-AGGATCTTT
genomic: GAGAAAGGTGTTCTCTGACTTGGCGAATGCCCACAAAAACTCACGCATAGgtgagcctct ... aaatatgcagGTGTTTTCTATTGTGGATCCCCTACACTCACGAAACAACTCAAGGATCTTT
EST: gi|86887101|gb|CI325916.1|CI325916
EST:     AGAAAGGTGTTCTCTGACTTGGCGAATGCCCACAAAAACTCACCCATAGG                         GTGTTTTCTATTGTGGATCCCCTACACTCACGAAACAACTCAAGGATCTT
genomic: AGAAAGGTGTTCTCTGACTTGGCGAATGCCCACAAAAACTCACGCATA-Ggtgagcctct ... aaatatgcagGTGTTTTCTATTGTGGATCCCCTACACTCACGAAACAACTCAAGGATCTT
EST: gi|87039381|gb|CI194003.1|CI194003
EST:     GAGAAAGGTGTTCTCTGACTTGGCGAATGCCCACAAAAACTCACGCATAG                         GTGTTTTCTATTGTGGATCCCCTACACTCACGAAACAACTCAAGGATCTTT
genomic: GAGAAAGGTGTTCTCTGACTTGGCGAATGCCCACAAAAACTCACGCATAGgtgagcctct ... aaatatgcagGTGTTTTCTATTGTGGATCCCCTACACTCACGAAACAACTCAAGGATCTTT
EST: gi|29688221|gb|CB684496.1|CB684496
EST:     GAGAAAGGTGTTCTCTGACTTGGCGAATGCCCACAAAAACTCACGCATAG                         GTGTTTTCTATTGTGGATCCCCTACACTCACGAAACAACTCAAGGATCTTT
genomic: GAGAAAGGTGTTCTCTGACTTGGCGAATGCCCACAAAAACTCACGCATAGgtgagcctct ... aaatatgcagGTGTTTTCTATTGTGGATCCCCTACACTCACGAAACAACTCAAGGATCTTT
EST: gi|86519889|gb|CI160095.1|CI160095
EST:     GAGAAAGGTGTTCTCTGACTTGGCGAATGCCCACAAAAACTCACGCATAG                         GTGTTTTCTATTGTGGATCCCCTACACTCACGAAACAACTCAAGGATCTTT
genomic: GAGAAAGGTGTTCTCTGACTTGGCGAATGCCCACAAAAACTCACGCATAGgtgagcctct ... aaatatgcagGTGTTTTCTATTGTGGATCCCCTACACTCACGAAACAACTCAAGGATCTTT
EST: gi|86484673|gb|CI127306.1|CI127306
EST:     GAGAAAGGTGTTCTCTGACTTGGCGAATGCCCACAAAAACTCACGCATAG                         GTGTTTTCTATTGTGGATCCCCTACACTCACGAAACAACTCAAGGATCTTT
genomic: GAGAAAGGTGTTCTCTGACTTGGCGAATGCCCACAAAAACTCACGCATAGgtgagcctct ... aaatatgcagGTGTTTTCTATTGTGGATCCCCTACACTCACGAAACAACTCAAGGATCTTT
EST: gi|86480722|gb|CI123355.1|CI123355
EST:     GAGAAAGGTGTTCTCTGACTTGGCGAATGCCCACAAAAACTCACGCATAG                         GTGTTTTCTATTGTGGATCCCCTACACTCACGAAACAACTCAAGGATCTTT
genomic: GAGAAAGGTGTTCTCTGACTTGGCGAATGCCCACAAAAACTCACGCATAGgtgagcctct ... aaatatgcagGTGTTTTCTATTGTGGATCCCCTACACTCACGAAACAACTCAAGGATCTTT
EST: gi|27728130|gb|CB035350.1|CB035350
EST:     GAGAAAGGTGTTCTCTGACTTGGCGAATGCCCACAAAAACTCACGCATAG                         GTGTTTTCTATTGTGGATCCCCTACACTCACGAAACAACTCAAGGATCTTT
genomic: GAGAAAGGTGTTCTCTGACTTGGCGAATGCCCACAAAAACTCACGCATAGgtgagcctct ... aaatatgcagGTGTTTTCTATTGTGGATCCCCTACACTCACGAAACAACTCAAGGATCTTT
EST: gi|86834297|gb|CI344057.1|CI344057
EST:     GAGAAAGGTGTTCTCTGACTTGGCGAATGCCCACAAAAACTCACGCATAG                         GTGGTTTTCTATTGTGGATCCCCTACACTCACCAAACAACTCAAGGATCTT
genomic: GAGAAAGGTGTTCTCTGACTTGGCGAATGCCCACAAAAACTCACGCATAGgtgagcctct ... aaatatgcagGT-GTTTTCTATTGTGGATCCCCTACACTCACGAAACAACTCAAGGATCTT
EST: gi|88962578|gb|CI097730.1|CI097730
EST:     GAGAAAGGTGTTCTCTGACTTGGCGAATGCCCACAAAAACTCACGCATAG                         GTGTTTTCTATTGTGGATCCCCTACACTCACGAAACAACTCAAGGATCTTT
genomic: GAGAAAGGTGTTCTCTGACTTGGCGAATGCCCACAAAAACTCACGCATAGgtgagcctct ... aaatatgcagGTGTTTTCTATTGTGGATCCCCTACACTCACGAAACAACTCAAGGATCTTT
EST: gi|86478047|gb|CI120680.1|CI120680
EST:     GAGAAAGGTGTTCTCTGACTTGGCGAATGCCCACAAAAACTCACGCATAG                         GTGTTTTCTATTGTGGATCCCCTACACTCACGAAACAACTCAAGGATCTTT
genomic: GAGAAAGGTGTTCTCTGACTTGGCGAATGCCCACAAAAACTCACGCATAGgtgagcctct ... aaatatgcagGTGTTTTCTATTGTGGATCCCCTACACTCACGAAACAACTCAAGGATCTTT
EST: gi|87028963|gb|CI351266.1|CI351266
EST:     AGAAAGGTGTTCTCTGACTTGGCGAATGCCCACAAAAACTCACGGCATAG                         GTGTTTTCTATTGTTGATCCCCTACACTCACGAAACAACTCAAGGATCTT
genomic: AGAAAGGTGTTCTCTGACTTGGCGAATGCCCACAAAAACTCAC-GCATAGgtgagcctct ... aaatatgcagGTGTTTTCTATTGTGGATCCCCTACACTCACGAAACAACTCAAGGATCTT
EST: gi|86881864|gb|CI324129.1|CI324129
EST:     GAGAAAGGTGTTCTCTGACTTGGCGAATGCCCACAAAAACTCACGCATAG                         GTGTTTTCTATTGTGGATCCCCTACACTCACGAAACAACTCAAGGATCTTT
genomic: GAGAAAGGTGTTCTCTGACTTGGCGAATGCCCACAAAAACTCACGCATAGgtgagcctct ... aaatatgcagGTGTTTTCTATTGTGGATCCCCTACACTCACGAAACAACTCAAGGATCTTT
EST: gi|88259648|gb|CI363941.1|CI363941
EST:     GAGAAAGGTGTTCTCTGACTTGCCGAATGCCCACAAAAACTCACGCATAG                         GTGTTTTCTATTGTGGATCCCCTACACTCACGAAACAACTCAAGGATCTTT
genomic: GAGAAAGGTGTTCTCTGACTTGGCGAATGCCCACAAAAACTCACGCATAGgtgagcctct ... aaatatgcagGTGTTTTCTATTGTGGATCCCCTACACTCACGAAACAACTCAAGGATCTTT

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: 74 (upstream exon), 74 (downstream exon)
Score: 39

ATTCGCACACATTTTGCGAGGCCTAACTGGAGAAAGGTGTTCTCTGACTTGGCGAATGCCCACAAAAACTCACGCATAGgtgagcctct ... aaatatgcagGTGTTTTCTATTGTGGATCCCCTACACTCACGAAACAACTCAAGGATCTTTCAAAAGAATTCAGCCAGACAACCACAACTAGATTCCACTTCCACAAGGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaacaattttgagctttgcagtaacggttgttaacaaatccataaatatgcagGTGTTTTCTATTGTGGATCCCCTACACTCACGAAACAACTCAAGGATCTTTCAAAAGAATTCAGCCAGACAACCACAACTAGATTCCACTTCCACAAGGA
                              tgttaac  putative branch site (score: 39)
                                     aaatccataaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcctcttttttcagcgaacatcgtcgatgcaacaattttgagctttgcagtaacggttgttaacaaatccataaatatgcagGTGTTTTCTATTGTGGATCCCCTACACTCACGAAACAACTCAAGGATCTTTCAAAAGAATTCAGCCAGACAACCACAACTAGATTCCACTTCCACAAGGA

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