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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtatctgagattattcatatctgatcctgtcaagtgacaattcagttgataacagtcttaattgattttttaatgcagCGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACAGTACAATCTTCCCACTAATAAGCTTGAGAGGCT

Basic information

species Oryza sativa
transcript LOC_Os03g08550.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g08550.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G330907_T01 (Zea mays), 3'ss of exon 3
gtgagtatctgag-attattcatatctgatcctgtcaa--gtgacaattcagttgataacagtcttaattgattttttaatgcagCGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACAGTACAATCTTCCCACTAATAAGCTTGAGAGGCT
||||||  |  |  || | |   |    | | |||| |  ||||   ||||||| |||     | ||| | |  |||| |||||| ||  |||||||||| ||||||||||||||    || ||||||||||||||||||| |   ||||||||||  ||
gtgagtccccaattataaatttcactcaaacttgtccattgtgaggcttcagttaataggcaccctaaatcaacttttgatgcagTGACTTGAGCCAAAATAACCTTGGTGGTGGAGGCCAAATACAGTACAATCTTCCCAATGTGAAGCTTGAGAAACT

upper sequence: LOC_Os03g08550.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G153393_T01 (Zea mays), 3'ss of exon 3
gtgagtatctgag-attattcatatctgatcctgtcaa--gtgacaattcagttgataacagtcttaattgattttttaatgcagCGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACAGTACAATCTTCCCACTAATAAGCTTGAGAGGCT
||||||  | |   || | |     |  | | |||| |  ||||   || || |||||     | ||  | |  |||| |||||| || ||||||||||| |||||||| |||||    || ||||||||||||||||||| ||  ||||||||||  ||
gtgagtccccggttataaatttcgcccaaacttgtccattgtgaggctttagctgataggcaccctatatcaacttttgatgcagTGACATGAGCCAAAATAACCTTGGCGGTGGAGGTCAAATACAGTACAATCTTCCCAATATGAAGCTTGAGAAACT
















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|88362223|gb|CI608614.1|CI608614
EST:     TCCGGTAATTTGGCGTACAATATGAATACCATGGGTTCATTGATTGAGAT                         CGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACA
genomic: TCCGGTAATTTGGCGTACAATATGAATACCATGGGTTCATTGATTGAGATgtgagtatct ... tttaatgcagCGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACA
EST: gi|88299950|gb|CI580011.1|CI580011
EST:     TCCGGTAATTTGGCGTACAATATGAATACCATGGGTTCATTGATTGAGAT                         AGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACAGTACAATCT
genomic: TCCGGTAATTTGGCGTACAATATGAATACCATGGGTTCATTGATTGAGATgtgagtatct ... tttaatgcagCGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACAGTACAATCT
EST: gi|44665230|gb|CR278664.1|CR278664
EST:     TCCGGTAATTTGGCGTACAATATGAATACCATGGGTTCATTGATTGAGAT                         CGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACAGTACAATCT
genomic: TCCGGTAATTTGGCGTACAATATGAATACCATGGGTTCATTGATTGAGATgtgagtatct ... tttaatgcagCGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACAGTACAATCT
EST: gi|88421797|gb|CI621441.1|CI621441
EST:     TCCGGTAATTTGGCGTACAATATGAATACCATGGGTTCATTGATTGAGAT                         CGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACAGTACAATCT
genomic: TCCGGTAATTTGGCGTACAATATGAATACCATGGGTTCATTGATTGAGATgtgagtatct ... tttaatgcagCGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACAGTACAATCT
EST: gi|88299567|gb|CI574680.1|CI574680
EST:     TCCGGTAATTTGGCGTACAATATGAATACCATGGGTTCATTGATTGAGAT                         CGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAG
genomic: TCCGGTAATTTGGCGTACAATATGAATACCATGGGTTCATTGATTGAGATgtgagtatct ... tttaatgcagCGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAG
EST: gi|29644649|gb|CB649656.1|CB649656
EST:     TCCGGTAATTTGGCGTACAATATGAATACCATGGGTTCATTGATTGAGAT                         CGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACAGTACAATCT
genomic: TCCGGTAATTTGGCGTACAATATGAATACCATGGGTTCATTGATTGAGATgtgagtatct ... tttaatgcagCGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACAGTACAATCT
EST: gi|29624948|gb|CB629959.1|CB629959
EST:     TCCGGTAATTTGGCGTACAATATGAATACCATGGGTTCATTGATTGAGAT                         CGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACAGTACAATCT
genomic: TCCGGTAATTTGGCGTACAATATGAATACCATGGGTTCATTGATTGAGATgtgagtatct ... tttaatgcagCGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACAGTACAATCT
EST: gi|66914683|gb|CX101531.1|CX101531
EST:     TCCGGTAATTTGGCGTACAATATGAATACCATGGGTTCATTGATTGAGAT                         CGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACAGTACAATCT
genomic: TCCGGTAATTTGGCGTACAATATGAATACCATGGGTTCATTGATTGAGATgtgagtatct ... tttaatgcagCGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACAGTACAATCT
EST: gi|88726200|gb|CI749855.1|CI749855
EST:     TCCGGTAATTTGGCGTANAATATGAATACCATGGGTTCATCGATTGAGAT                         CGATATGAGCCAAAA
genomic: TCCGGTAATTTGGCGTACAATATGAATACCATGGGTTCATTGATTGAGATgtgagtatct ... tttaatgcagCGATATGAGCCAAAA
EST: gi|88386689|gb|CI682838.1|CI682838
EST:     TCCGGTAATTTGGCGTACAATATGAATACCATGGGTTCATTGATTGAGAT                         CGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACAGTACAATC-
genomic: TCCGGTAATTTGGCGTACAATATGAATACCATGGGTTCATTGATTGAGATgtgagtatct ... tttaatgcagCGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACAGTACAATCT
EST: gi|88432225|gb|CI565258.1|CI565258
EST:     TCCGGTAATTTGGCGTACAATATGAATACCATGGGTTCATTGATTGAGAT                         CGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACAGTACAATCT
genomic: TCCGGTAATTTGGCGTACAATATGAATACCATGGGTTCATTGATTGAGATgtgagtatct ... tttaatgcagCGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACAGTACAATCT
EST: gi|117225926|gb|CT846035.1|CT846035
EST:     TCCGGTAATTTGGCGTACAATATGAATACCATGGGTTCATTGATTGAGAT                         CGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACAGTACAATCT
genomic: TCCGGTAATTTGGCGTACAATATGAATACCATGGGTTCATTGATTGAGATgtgagtatct ... tttaatgcagCGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACAGTACAATCT
EST: gi|88301108|gb|CI594634.1|CI594634
EST:     TCCGGTAATTTGGCGTACAATATGAATACCATGGGTTCATTGATTGAGAT                         CGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACAGTACAATCT
genomic: TCCGGTAATTTGGCGTACAATATGAATACCATGGGTTCATTGATTGAGATgtgagtatct ... tttaatgcagCGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACAGTACAATCT
EST: gi|29681108|gb|CB677383.1|CB677383
EST:     TCCGGTAATTTGGCGTACAATATGAATACCATGGGTTCATTGATTGAGAT                         CGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACAGTACAATCT
genomic: TCCGGTAATTTGGCGTACAATATGAATACCATGGGTTCATTGATTGAGATgtgagtatct ... tttaatgcagCGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACAGTACAATCT
EST: gi|88399209|gb|CI618399.1|CI618399
EST:     TCCGGTAATTTGGCGTACAATATGAATACCATGGGTTCATTGATTGAGAT                         CGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACAGTACAATCT
genomic: TCCGGTAATTTGGCGTACAATATGAATACCATGGGTTCATTGATTGAGATgtgagtatct ... tttaatgcagCGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACAGTACAATCT
EST: gi|88358901|gb|CI619405.1|CI619405
EST:     TCCGGTAATTTGGCGTACAATATGAATACCATGGGTTCATTGATTGAGAT                         CGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACAGTACAATCT
genomic: TCCGGTAATTTGGCGTACAATATGAATACCATGGGTTCATTGATTGAGATgtgagtatct ... tttaatgcagCGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACAGTACAATCT

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: 72 (upstream exon), 67 (downstream exon)
Score: 20

CAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATACCATGGGTTCATTGATTGAGATgtgagtatct ... tttaatgcagCGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACAGTACAATCTTCCCACTAATAAGCTTGAGAGGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcctgtcaagtgacaattcagttgataacagtcttaattgattttttaatgcagCGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACAGTACAATCTTCCCACTAATAAGCTTGAGAGGCT
                                          tttttt  CT-rich tract
                              agtcttaattgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtatctgagattattcatatctgatcctgtcaagtgacaattcagttgataacagtcttaattgattttttaatgcagCGATATGAGCCAAAACAACCTTGGTGGTGGCCAACAGATACAGTACAATCTTCCCACTAATAAGCTTGAGAGGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG