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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAAGGAAATAATAAAATACAAGGGGTTCCAAGTACCTCCTGCGGAACTTGAAGCTCTTCTCATCACACACCCTGATATCAAGGATGCTGCCGTTGTACCgtaagttgatccatgcttagatgaacagaaggtcagcatgttccatcacatcagaggactaaattcttattgaattcttgcag

Basic information

species Oryza sativa
transcript LOC_Os06g44620.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g44620.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G055320_T01 (Zea mays), 5'ss of exon 4
TCAAGGAAATAATAAAATACAAGGGGTTCCAAGTACCTCCTGCGGAACTTGAAGCTCTTCTCATCACACACCCTGATATCAAGGATGCTGCCGTTGTACCgtaagttgatccatgcttagatgaacagaaggt------cagcatgttcca--tcacatcag-----aggactaaattcttattgaattcttgcag
| ||||| ||||| ||||||||||| |||||||||||||||||||| |||||||| |||||||||||||| ||||| ||||||||||| || |||||  |||||||||||||   || | ||    ||| ||       | ||||| ||||  || | |  |     |||| | ||| ||| | ||    ||||||
TGAAGGAGATAATCAAATACAAGGGCTTCCAAGTACCTCCTGCGGAGCTTGAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTCgtaagttgatccgcactgaaatcctgagatggcattaagccgcatggtccacatcgctttggtgtcgaggaattaatacttttggatcaattgcag
















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|29659176|gb|CB655451.1|CB655451
EST:     GAAGCTCTTCTCATCACACACCCTGATATCAAGGATGCTGCCGTTGTACC                         GATGATAGACGAAATTGCGGGTGAAGTGCTGGTTGCATTCATTGTACGGAT
genomic: GAAGCTCTTCTCATCACACACCCTGATATCAAGGATGCTGCCGTTGTACCgtaagttgat ... attcttgcagGATGATAGACGAAATTGCGGGTGAAGTGCCGGTTGCATTCATTGTACGGAT
EST: gi|29664259|gb|CB660534.1|CB660534
EST:     GAAGCTCTTCTCATCACACACCCTGATATCAAGGATGCTGCCGTTGTACC                         GATGATAGACGAAATTGCGGGTGAAGTGCCGGTTGCATTCATTGTACGGAT
genomic: GAAGCTCTTCTCATCACACACCCTGATATCAAGGATGCTGCCGTTGTACCgtaagttgat ... attcttgcagGATGATAGACGAAATTGCGGGTGAAGTGCCGGTTGCATTCATTGTACGGAT
EST: gi|29664258|gb|CB660533.1|CB660533
EST:     GAAGCTCTTCTCATCACACACCCTGATATCAAGGATGCTGCCGTTGTACC                         GATGATAGACGAAATTGCGGGTGAAGTGCCGGTTGCATTCATTGTACGGAT
genomic: GAAGCTCTTCTCATCACACACCCTGATATCAAGGATGCTGCCGTTGTACCgtaagttgat ... attcttgcagGATGATAGACGAAATTGCGGGTGAAGTGCCGGTTGCATTCATTGTACGGAT
EST: gi|58666259|gb|CK054945.1|CK054945
EST:     GAAGCTCTTCTCATCACACACCCTGATATCAAGGATGCTGCCGTTGTACC                         GATGATAGACGAAATTGCGGGTGAAGTGCCGGTTGCATTCATTGTACGGAT
genomic: GAAGCTCTTCTCATCACACACCCTGATATCAAGGATGCTGCCGTTGTACCgtaagttgat ... attcttgcagGATGATAGACGAAATTGCGGGTGAAGTGCCGGTTGCATTCATTGTACGGAT
EST: gi|89161555|gb|CI099527.1|CI099527
EST:     GAAGCTCTTCTCATCACACACCCTGATATCAAGGATGCTGCCGTTGTACC                         GATGATAGACGAAATTGCGGGTGAAGTGCCGGTTGCATTCATTGTACGGAT
genomic: GAAGCTCTTCTCATCACACACCCTGATATCAAGGATGCTGCCGTTGTACCgtaagttgat ... attcttgcagGATGATAGACGAAATTGCGGGTGAAGTGCCGGTTGCATTCATTGTACGGAT
EST: gi|38482262|gb|CF966310.1|CF966310
EST:     ATCACACACCCTGATATCAAGGATGCTGCCGTTGTACC                         GATGATAGACGAAATTGCGGGTGAAGTGCCGGTTGCATTCATTGTACGGAT
genomic: ATCACACACCCTGATATCAAGGATGCTGCCGTTGTACCgtaagttgat ... attcttgcagGATGATAGACGAAATTGCGGGTGAAGTGCCGGTTGCATTCATTGTACGGAT
EST: gi|29676730|gb|CB673005.1|CB673005
EST:     GAAGCTCTTCTCATCACACACCCTGATATCAAGGATGCTGCCGTTGTACC                         GATGATAGACGAAATTGCGGGTGAAGTGCCGGTTGCATTCATTGTACGGAT
genomic: GAAGCTCTTCTCATCACACACCCTGATATCAAGGATGCTGCCGTTGTACCgtaagttgat ... attcttgcagGATGATAGACGAAATTGCGGGTGAAGTGCCGGTTGCATTCATTGTACGGAT
EST: gi|58611802|gb|CK039514.1|CK039514
EST:     GAAGCTCTTCTCATCACACACCCTGATATCAAGGATGCTGCCGTTGTACC                         GATGATAGACGAAATTGCGGGTGAAGTGCCG
genomic: GAAGCTCTTCTCATCACACACCCTGATATCAAGGATGCTGCCGTTGTACCgtaagttgat ... attcttgcagGATGATAGACGAAATTGCGGGTGAAGTGCCG
EST: gi|29623324|gb|CB628335.1|CB628335
EST:     GAAGCTCTTCTCATCACACACCCTGATATCAAGGATGCTGCCGTTGTACC                         GATGATAGACGAAATTGCAGGTGAAGTGCCGGTTGCATTCATTGTACGGAT
genomic: GAAGCTCTTCTCATCACACACCCTGATATCAAGGATGCTGCCGTTGTACCgtaagttgat ... attcttgcagGATGATAGACGAAATTGCGGGTGAAGTGCCGGTTGCATTCATTGTACGGAT
EST: gi|29673469|gb|CB669744.1|CB669744
EST:     GAAGCTCTTCTCATCACACACCCTGATATCAAGGATGCTGCCGTTGTACC                         GATGATAGACGAAATTGCGGGTGAAGTGCCGGTTGCATTCATTGTACGGAT
genomic: GAAGCTCTTCTCATCACACACCCTGATATCAAGGATGCTGCCGTTGTACCgtaagttgat ... attcttgcagGATGATAGACGAAATTGCGGGTGAAGTGCCGGTTGCATTCATTGTACGGAT

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: 73 (upstream exon), 70 (downstream exon)
Score: 11

TCAAGGAAATAATAAAATACAAGGGGTTCCAAGTACCTCCTGCGGAACTTGAAGCTCTTCTCATCACACACCCTGATATCAAGGATGCTGCCGTTGTACCgtaagttgat ... attcttgcagGATGATAGACGAAATTGCGGGTGAAGTGCCGGTTGCATTCATTGTACGGATTGAAGGATCTGCAATCAGCGAGAATGAGATCAAGCAATTTGTGGCAAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAAGGAAATAATAAAATACAAGGGGTTCCAAGTACCTCCTGCGGAACTTGAAGCTCTTCTCATCACACACCCTGATATCAAGGATGCTGCCGTTGTACCgtaagttgatccatgcttagatgaacagaaggtcagcatgttccatcacatcagaggactaaattcttattgaattcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC