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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatttcactatttttttggccgtcattttaatgtgcatttacctttgctgatgttatgatttatgttgctgacattttcagGTCATGCACATAGCAGCAGCCACAGAGATCAATTCAAGGTTTGTCCCAAGCTTGCAACAGTTGCATAAGTCACTTGATTCAAAG

Basic information

species Oryza sativa
transcript LOC_Os03g21950.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 4
gtaagatttcactatttttttggccgtcattttaatgt-gcatttacctttgctgatgtt-atgatttatgttgctgacattttcagGTCATGCACATAGCAGCAGCCACAGAGATCAATTCAAGGTTTGTCCCAAGCTTGCAACAGTTGCATAAGTCACTTGATTCAAAG
|||||  || |||||||||         |||| | | |  |  ||||   ||| |||||| || ||| |||    |||| ||| ||||| ||||| |||||  | |||   |||||  |||| |||||| ||||||| ||||||||||||||| | |||||| |||| || 
gtaagccttaactattttt---------atttcagtattactattactgctgcagatgtttattattcatggcattgacgtttccagGTAATGCATATAGCGACGGCCGTTGAGATACATTCGAGGTTTATCCCAAGTTTGCAACAGTTGCATGATTCACTTCATTCGAAA
















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|58692734|gb|CK081421.1|CK081421
EST:     CTAATGATCATGTGAACAGATCACAGTCCTCAAATGATACATTTCCCACT                         GTCATGCACATAGCAGCAGCCACAGAGATCAATTCAAGGTTGGTCCCAAGC
genomic: CTAATGATCATGTGAACAGATCACAGTCCTCAAATGATACATTTCCCACTgtaagatttc ... acattttcagGTCATGCACATAGCAGCAGCCACAGAGATCAATTCAAGGTTTGTCCCAAGC
EST: gi|42592105|gb|CK738591.1|CK738591
EST:     CTAATGATCATGTGAACAGATCACAGTCCTCAAATGATACATTTCCCACT                         GTCATGTTCATAGCAGCAGCCACAGAGATCAATTCAAGGTTTGTCCCAAGC
genomic: CTAATGATCATGTGAACAGATCACAGTCCTCAAATGATACATTTCCCACTgtaagatttc ... acattttcagGTCATGCACATAGCAGCAGCCACAGAGATCAATTCAAGGTTTGTCCCAAGC
EST: gi|33795747|gb|CF323743.1|CF323743
EST:     CTAATGATCATGTGAACAGATCACAGTCCTCAAATGATACATTTCCCACT                         GTCATGCACATAGCAGCAGCCACAGAGATCAATTCAAGGTTTGTCCCAAGC
genomic: CTAATGATCATGTGAACAGATCACAGTCCTCAAATGATACATTTCCCACTgtaagatttc ... acattttcagGTCATGCACATAGCAGCAGCCACAGAGATCAATTCAAGGTTTGTCCCAAGC
EST: gi|33676561|gb|CF304800.1|CF304800
EST:     CTAATGATCATGTGAACAGATCACAGTCCTCAAATGATACATTTCCCACT                         GTCATGCACATAGCAGCAGCCACAGAGATCAATTCAAGGTTTGTCCCAAGC
genomic: CTAATGATCATGTGAACAGATCACAGTCCTCAAATGATACATTTCCCACTgtaagatttc ... acattttcagGTCATGCACATAGCAGCAGCCACAGAGATCAATTCAAGGTTTGTCCCAAGC
EST: gi|33674910|gb|CF303149.1|CF303149
EST:     CTAATGATCATGTGAACAGATCACAGTCCTCAAATGATACATTTCCCACT                         GTCATGCACATAGCAGCAGCCACAGAGATCAATTCAAGGTTTGTCCCAAGC
genomic: CTAATGATCATGTGAACAGATCACAGTCCTCAAATGATACATTTCCCACTgtaagatttc ... acattttcagGTCATGCACATAGCAGCAGCCACAGAGATCAATTCAAGGTTTGTCCCAAGC
EST: gi|58681064|gb|CK069751.1|CK069751
EST:     CTAATGATCATGTGAACAGATCACAGTCCTCAAATGATACATTTCCCACT                         GTCATGCACATAGCAGCAGCCACAGAGATCAATTCAAGGTTTGTCCCAAGC
genomic: CTAATGATCATGTGAACAGATCACAGTCCTCAAATGATACATTTCCCACTgtaagatttc ... acattttcagGTCATGCACATAGCAGCAGCCACAGAGATCAATTCAAGGTTTGTCCCAAGC
EST: gi|33676642|gb|CF304881.1|CF304881
EST:     CTAATGATCATGTGAACAGATCACAGTCCTCAAATGATACATTTCCCACT                         GTCATGCACATAGCAGCAGCCACAGAGATCAATTCAAGGTTTGTCCCAAGC
genomic: CTAATGATCATGTGAACAGATCACAGTCCTCAAATGATACATTTCCCACTgtaagatttc ... acattttcagGTCATGCACATAGCAGCAGCCACAGAGATCAATTCAAGGTTTGTCCCAAGC

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: 75 (upstream exon), 75 (downstream exon)
Score: 39

TAGGGCCGCTGAGATTCTTGGACATAAGCGTGGCGAGAAGTTTGTACACCCTAATGATCATGTGAACAGATCACAGTCCTCAAATGATACATTTCCCACTgtaagatttc ... acattttcagGTCATGCACATAGCAGCAGCCACAGAGATCAATTCAAGGTTTGTCCCAAGCTTGCAACAGTTGCATAAGTCACTTGATTCAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaatgtgcatttacctttgctgatgttatgatttatgttgctgacattttcagGTCATGCACATAGCAGCAGCCACAGAGATCAATTCAAGGTTTGTCCCAAGCTTGCAACAGTTGCATAAGTCACTTGATTCAAAG
                                        tgctgac  putative branch site (score: 39)
                                              cattttc  CT-rich tract
                        atgttatgatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatttcactatttttttggccgtcattttaatgtgcatttacctttgctgatgttatgatttatgttgctgacattttcagGTCATGCACATAGCAGCAGCCACAGAGATCAATTCAAGGTTTGTCCCAAGCTTGCAACAGTTGCATAAGTCACTTGATTCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT