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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtagacctttacctcaagttgtcaatctgtgcctcacaattctttaacgtgtgaaaagctaatgtgaaattctgcagAATGAAGTATCTGAAGGCTGCAAATGTCCACCAGGTTTCAAGGGTGATGGAATAAAAAGTTGTGAAG

Basic information

species Oryza sativa
transcript LOC_Os03g21720.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g21720.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G067546_T01 (Zea mays), 3'ss of exon 8
gtaagtagacctttacctcaagttgtcaatctgtgcctcacaattctttaacgt-gtgaaaagctaatgtgaaattctgcagAATGAAGTATCTGAAGGCTGCAAATGTCCACCAGGTTTCAAGGGTGATGGAATAAAAAGTTGTGAAG
||||||| |  ||    | |   | |   | | ||| |  || ||  || || | || ||||   ||| |||| |||||||||| ||| |||||||||| || |||||||||   ||||||||||||||||||  ||||||||||||||
gtaagta-atgttgttttgagactttagttttctgctttccagtttgtttacattgttaaaactaaatttgaagttctgcagAACGAAATATCTGAAGGTTGTAAATGTCCAATGGGTTTCAAGGGTGATGGAGAAAAAAGTTGTGAAG
















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|29627369|gb|CB632380.1|CB632380
EST:     GAGGATGCTGGAAAGAAACTAGAAATAGCAAGACAATATCTGCCTGCTCA                         AATGAAGTATCTGAAGGCTGCAAATGTCCACCAGGTTTCAAGGGTGATGGA
genomic: GAGGATGCTGGAAAGAAACTAGAAATGGCAAGACAATATCTGCCTGCTCAgtaagtagac ... aattctgcagAATGAAGTATCTGAAGGCTGCAAATGTCCACCAGGTTTCAAGGGTGATGGA
EST: gi|29665177|gb|CB661452.1|CB661452
EST:     GAAAGAAACTAGAAATGGCAAGACAATATCTGCCTGCTCA                         AATGAAGTATCTGAAGGCTGCAAATGTCCACCAGGTTTCAAGGGTGATGGA
genomic: GAAAGAAACTAGAAATGGCAAGACAATATCTGCCTGCTCAgtaagtagac ... aattctgcagAATGAAGTATCTGAAGGCTGCAAATGTCCACCAGGTTTCAAGGGTGATGGA
EST: gi|29663536|gb|CB659811.1|CB659811
EST:     AAAGAAACTAGAAATGGCAAGACAATATCTGCCTGCTCA                         AATGAAGTATCTGAAGGCTGCAAATGTCCACCAGGTTTCAAGGGTGATGGA
genomic: AAAGAAACTAGAAATGGCAAGACAATATCTGCCTGCTCAgtaagtagac ... aattctgcagAATGAAGTATCTGAAGGCTGCAAATGTCCACCAGGTTTCAAGGGTGATGGA
EST: gi|58687228|gb|CK075915.1|CK075915
EST:     GAGGATGCTGGAAAGAAACTAGAAATGGCAAGACAATATCTGCCTGCTCA                         AATGAAGTATCTGAAGGCTGCAAATGTCCACCAGGTTTCAAGGGTGATGGA
genomic: GAGGATGCTGGAAAGAAACTAGAAATGGCAAGACAATATCTGCCTGCTCAgtaagtagac ... aattctgcagAATGAAGTATCTGAAGGCTGCAAATGTCCACCAGGTTTCAAGGGTGATGGA
EST: gi|38479499|gb|CF963610.1|CF963610
EST:     CTGGAAAGAAACTAGAAATAGCAAGACAATATCTGCCTGCTCA                         AATGAAGTATCTGAAGGCTGCAAATGTCCGCCGGGTTTCAAGGGTGATGGA
genomic: CTGGAAAGAAACTAGAAATGGCAAGACAATATCTGCCTGCTCAgtaagtagac ... aattctgcagAATGAAGTATCTGAAGGCTGCAAATGTCCACCAGGTTTCAAGGGTGATGGA
EST: gi|29665176|gb|CB661451.1|CB661451
EST:     GAGGATGCTGGAAAGAAACTAGAAATGGCAAGACAATATCTGCCTGCTCA                         AATGAAGTATCTGAAGGCTGCAAATGTCCACCAGGTTTCAAGGGTGATGGA
genomic: GAGGATGCTGGAAAGAAACTAGAAATGGCAAGACAATATCTGCCTGCTCAgtaagtagac ... aattctgcagAATGAAGTATCTGAAGGCTGCAAATGTCCACCAGGTTTCAAGGGTGATGGA
EST: gi|218494604|gb|FG959186.1|FG959186
EST:     AGGATGCTGCGAAAGAAACTAGAAATAGCAAGACAATATCTGCCTGCTCA                         AATGAAGTATCTGAAGGCTGC-AATGTCCACCAGGTTTCAAGGGTGATGGA
genomic: AGGATGCTG-GAAAGAAACTAGAAATGGCAAGACAATATCTGCCTGCTCAgtaagtagac ... aattctgcagAATGAAGTATCTGAAGGCTGCAAATGTCCACCAGGTTTCAAGGGTGATGGA
EST: gi|300215578|gb|HO088204.1|HO088204
EST:     GAGGATGCTGGAAAGAAACTAGAAATAGCAAGACAATATCTGCCTGCTCA                         AATGAAGTATCTGAAGGCTGCAAATGTCCACCAGGTTTCAAGGGTGATGGA
genomic: GAGGATGCTGGAAAGAAACTAGAAATGGCAAGACAATATCTGCCTGCTCAgtaagtagac ... aattctgcagAATGAAGTATCTGAAGGCTGCAAATGTCCACCAGGTTTCAAGGGTGATGGA
EST: gi|14571249|gb|BI118617.1|BI118617
EST:     GAGGATGCTGGAAAGAAACTAGAAATAGCAAGACAATATCTGCCTGCTCA                         AATGAAGTATCTGAAGGCTGCAAATGTCCACCAGGTTTCAAGGGTGATGGA
genomic: GAGGATGCTGGAAAGAAACTAGAAATGGCAAGACAATATCTGCCTGCTCAgtaagtagac ... aattctgcagAATGAAGTATCTGAAGGCTGCAAATGTCCACCAGGTTTCAAGGGTGATGGA
EST: gi|58692052|gb|CK080739.1|CK080739
EST:     GAGGATGCTGGAAAGAAACTAGAAATGGCAAGACAATATCTGCCTGCTCA                         AATGAAGTATCTGAAGGCTGCAAATGTCCACCAGGTTTCAAGGGTGATGGA
genomic: GAGGATGCTGGAAAGAAACTAGAAATGGCAAGACAATATCTGCCTGCTCAgtaagtagac ... aattctgcagAATGAAGTATCTGAAGGCTGCAAATGTCCACCAGGTTTCAAGGGTGATGGA
EST: gi|58595298|gb|CF993606.1|CF993606
EST:     GAGGATGCTGGAAAGAAACTAGAAATGGCAAGACAATATCTGCCTGCTCG                         AATGAAGTATCTGAAGGCTGCAAATGTCCACCAGGTTTCAAGGGTGATGGA
genomic: GAGGATGCTGGAAAGAAACTAGAAATGGCAAGACAATATCTGCCTGCTCAgtaagtagac ... aattctgcagAATGAAGTATCTGAAGGCTGCAAATGTCCACCAGGTTTCAAGGGTGATGGA

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: 69 (upstream exon), 67 (downstream exon)
Score: 62

CTTCTGGCATTGGTAGGTGCGAAATTAAAAATGGAGGATGCTGGAAAGAAACTAGAAATGGCAAGACAATATCTGCCTGCTCAgtaagtagac ... aattctgcagAATGAAGTATCTGAAGGCTGCAAATGTCCACCAGGTTTCAAGGGTGATGGAATAAAAAGTTGTGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatctgtgcctcacaattctttaacgtgtgaaaagctaatgtgaaattctgcagAATGAAGTATCTGAAGGCTGCAAATGTCCACCAGGTTTCAAGGGTGATGGAATAAAAAGTTGTGAAG
                                  agctaat  putative branch site (score: 62)
               aattctttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtagacctttacctcaagttgtcaatctgtgcctcacaattctttaacgtgtgaaaagctaatgtgaaattctgcagAATGAAGTATCTGAAGGCTGCAAATGTCCACCAGGTTTCAAGGGTGATGGAATAAAAAGTTGTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA