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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtggcaagttttttggttcctcatcacatcattattatatttgattcgcctaggtaggtcagataagctgaacataattgtttctctttcttcatcagATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCAT

Basic information

species Oryza sativa
transcript LOC_Os01g73880.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g73880.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G002616_T01 (Zea mays), 3'ss of exon 3
ttgtggcaagttttttggttcctcatca-catcattattat-atttgattcgcctaggtag--gtcagataagctgaacataattgt--ttctctttcttcatcagATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCAT
       ||||| |    |    | ||  || |||| || | ||||  | |   |  |||      |  ||  || |||||        || || | ||  ||||| ||||||| |||||||||||||| ||| ||||||| ||||||||||| ||||| ||||||||||||
------aaagttataaaatgttgcctcttcagcattgttgtcatttattccatatgtgtaataactaattagactaaacatgccgagcattttcctcctctatcagGTAAGCATCGGGAAGCAGTGGAAGGAACTTCTGGACTACAAGGACTCCATTGGATTCATTGTTCAT
















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|88551571|gb|CI481639.1|CI481639
EST:     AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAG                         ATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
genomic: AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAGgtactatttc ... tcttcatcagATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
EST: gi|86544785|gb|CI184991.1|CI184991
EST:     AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAG                         ATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
genomic: AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAGgtactatttc ... tcttcatcagATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
EST: gi|88990171|gb|CI107597.1|CI107597
EST:     AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAG                         ATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
genomic: AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAGgtactatttc ... tcttcatcagATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
EST: gi|88288752|gb|CI517883.1|CI517883
EST:     AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGGTCAG                         ATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
genomic: AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAGgtactatttc ... tcttcatcagATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
EST: gi|88529129|gb|CI456611.1|CI456611
EST:     AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAG                         ATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
genomic: AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAGgtactatttc ... tcttcatcagATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
EST: gi|86854076|gb|CI252067.1|CI252067
EST:     AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAG                         ATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
genomic: AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAGgtactatttc ... tcttcatcagATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
EST: gi|88560717|gb|CI491406.1|CI491406
EST:     AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAG                         ATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
genomic: AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAGgtactatttc ... tcttcatcagATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
EST: gi|88539299|gb|CI466400.1|CI466400
EST:     AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAG                         ATAAGCATTGGGAAGCAGTGGAAAGTATTTCTGGATTACAAGGACTCGATT
genomic: AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAGgtactatttc ... tcttcatcagATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
EST: gi|88424017|gb|CI689716.1|CI689716
EST:     AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAG                         ATAAGCATTGGGAAGCAGTGGAAAGTATTTCTGGATTACAAGGACTCGATT
genomic: AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAGgtactatttc ... tcttcatcagATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
EST: gi|14571254|gb|BI118622.1|BI118622
EST:     AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAG                         ATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
genomic: AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAGgtactatttc ... tcttcatcagATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
EST: gi|58680307|gb|CK068994.1|CK068994
EST:     AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAG                         ATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
genomic: AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAGgtactatttc ... tcttcatcagATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
EST: gi|58692941|gb|CK081628.1|CK081628
EST:     AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCCATGAAGCTGCTCAG                         ATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
genomic: AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAGgtactatttc ... tcttcatcagATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
EST: gi|8527831|gb|AU092646.1|AU092646
EST:     AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAG                         ATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
genomic: AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAGgtactatttc ... tcttcatcagATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
EST: gi|88540755|gb|CI468824.1|CI468824
EST:     AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAG                         ATAAGCATTGGGAAGCAGTGGAAAGTATTTCTGGATTACAAGGACTCGATT
genomic: AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAGgtactatttc ... tcttcatcagATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
EST: gi|14571263|gb|BI118631.1|BI118631
EST:     AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAG                         ATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
genomic: AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAGgtactatttc ... tcttcatcagATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
EST: gi|88213475|gb|CI213324.1|CI213324
EST:     AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAG                         ATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
genomic: AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAGgtactatttc ... tcttcatcagATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
EST: gi|86543932|gb|CI184138.1|CI184138
EST:     AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAG                         ATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
genomic: AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAGgtactatttc ... tcttcatcagATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
EST: gi|88524848|gb|CI453801.1|CI453801
EST:     AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAG                         ATAAGCATTGGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGAT
genomic: AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAGgtactatttc ... tcttcatcagATAAGCATT-GGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGAT
EST: gi|88578465|gb|CI687398.1|CI687398
EST:     AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAG                         ATAAGCATTGGGAAGCAGTGGAAAGTATTTCTGGATTACAAGGACTCGATT
genomic: AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAGgtactatttc ... tcttcatcagATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
EST: gi|58686020|gb|CK074707.1|CK074707
EST:     AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAG                         ATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
genomic: AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAGgtactatttc ... tcttcatcagATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
EST: gi|88548459|gb|CI476833.1|CI476833
EST:     AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAG                         ATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
genomic: AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAGgtactatttc ... tcttcatcagATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
EST: gi|87034065|gb|CI187427.1|CI187427
EST:     AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAG                         ATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
genomic: AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAGgtactatttc ... tcttcatcagATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
EST: gi|10794861|gb|AU108827.1|AU108827
EST:     AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAG                         ATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
genomic: AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAGgtactatttc ... tcttcatcagATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
EST: gi|88323665|gb|CI558686.1|CI558686
EST:     AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAG                         ATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
genomic: AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAGgtactatttc ... tcttcatcagATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
EST: gi|86529829|gb|CI170035.1|CI170035
EST:     AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAG                         ATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
genomic: AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAGgtactatttc ... tcttcatcagATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
EST: gi|8858103|gb|AU095421.1|AU095421
EST:     AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAG                         ATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
genomic: AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAGgtactatttc ... tcttcatcagATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
EST: gi|86527733|gb|CI167939.1|CI167939
EST:     AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAG                         ATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT
genomic: AGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAGgtactatttc ... tcttcatcagATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATT

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), 67 (downstream exon)
Score: 54

CGATTATGGGGATGAAATTTGTGGAGCAGTTGTTAGTGTGCGTGGCAAGCAGGAAAGAATAGCTATCTGGACTAAAAATGCTGCCAATGAAGCTGCTCAGgtactatttc ... tcttcatcagATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcgcctaggtaggtcagataagctgaacataattgtttctctttcttcatcagATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCAT
 atttgat  putative branch site (score: 54)
                                  ttgtttctctttcttc  putative PPT
                              ataattgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtggcaagttttttggttcctcatcacatcattattatatttgattcgcctaggtaggtcagataagctgaacataattgtttctctttcttcatcagATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- -tggcaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgaac