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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATAAAGGCTTGGCTATATGATAATTTGGGATCCAGAGTTGACTATGATGCGCCAGGACATTGGTGCACAACAATGGCATATAGTGCAGATGGTTCAAGgttcataattatttctttgttagcatgattcatgtgggtaactgggtttttgtctttgttttcactgattctttttgcccttgtgagtag

Basic information

species Oryza sativa
transcript LOC_Os03g14980.1
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g14980.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G550865_T02 (Zea mays), 5'ss of exon 1
AGATAAAGGCTTGGCTATATGATAATTTGGGATCCAGAGTTGACTATGATGCGCCAGGACATTGGTGCACAACAATGGCATATAGTGCAGATGGTTCAAGgttcataattatttcttt--gttagcatgattc-----atgtgggtaactgggtttttgtctttgttttc-actgattctttttgcccttgtgagtag
                                                                         |||||||||||| |||||||||||||||||| |  || | | |||  |||      |||      ||||||||  |||  ||||  |    |  ||| ||| ||| ||||  || || ||  |||
-------------------------------------------------------------------------AATGGCATATAGCGCAGATGGTTCAAGgttcctgcttttctttttctgttcttgaaattaggagaatgtgggtgtctgtattttatttccagccttccactaatttttttatcctttatgcatag

upper sequence: LOC_Os03g14980.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G030422_T01 (Zea mays), 5'ss of exon 15
AGATAAAGGCTTGGCTATATGATAATTTGGGATCCAGAGTTGACTATGATGCGCCAGGACATTGGTGCACAACAATGGCATATAGTGCAGATGGTTCAAGgttcataattatttctttgttagcatgattcatgtgggtaactgg-gtttttgtctttg--ttttcactgattctttttgcccttgtgagtag
|||| ||||| ||||||||||||||||||||||| ||||||||||||||||| ||||| ||||||||||| ||||||||||||||||||||||||||||||||| |  ||   | ||| |   | |||     || |      || ||||||   |      || | || | | | | | |  || ||  |||
AGATCAAGGCATGGCTATATGATAATTTGGGATCTAGAGTTGACTATGATGCACCAGGTCATTGGTGCACTACAATGGCATATAGTGCAGATGGTTCAAGgttcctgctttcctttttctgttcttgaaggtagtagtatgtgggcgtttttaattccagccttccgctaaatttgtgt-cttttatgcatag

upper sequence: LOC_Os03g14980.1 (Oryza sativa), 5'ss of exon 15
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 5'ss of exon 14
AGATAAAGGCTTGGCTATATGATAATTTGGGATCCAGAGTTGACTATGATGCGCCAGGACATTGGTGCACAACAATGGCATATAGTGCAGATGGTTCAAGgttcata-attatttctttgttagcatgattcatgtgggtaactgggtttttgtctttgttttcactgattctttttgcc-cttgtgagtag--------
||||||| || ||||| ||||||  | | || || ||||||||||||||||| ||||| ||||||||||| |||||||| || ||||| |||||  | ||||   || |   ||  || |        |    |    ||   | |||||   ||  |   | | |    |    | |    |||||  |          
AGATAAAAGCCTGGCTCTATGATCTTCTTGGTTCTAGAGTTGACTATGATGCACCAGGGCATTGGTGCACTACAATGGCTTACAGTGCTGATGGCACTAGgtatgtagaaccttgattcgccttttatacgtgtcaaagttgtttggtttaattcactaaatgctccatctaaaatggatgtttgtggttgccatctgga

upper sequence: LOC_Os03g14980.1 (Oryza sativa), 5'ss of exon 15
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 5'ss of exon 14
AGATAAAGGCTTGGCTATATGATAATTTGGGATCCAGAGTTGACTATGATGCGCCAGGACATTGGTGCACAACAATGGCATATAGTGCAGATGGTTCAAGgt--tcataatt---atttctttgttagcat----gattcatgtgggtaactgggtttttgtctttgttttcactgattctttttgcccttgtgagtag--
||||||| |||||||| ||||||    | ||||| ||||||||||| ||||| || || ||||||||||| |||||||| || ||||| || ||  | ||||  ||  || |   || || ||  |  | |     | | || |||    |     |     || | |      | | | |   ||   || |  ||||  
AGATAAAAGCTTGGCTCTATGATCTCCTTGGATCTAGAGTTGACTACGATGCACCTGGTCATTGGTGCACTACAATGGCTTACAGTGCTGACGGCACTAGgtattccaaactttaatctcctttcttacgttttgaagttatttggtgtgcacaactaaacgctctatccaagatcaatgtgcgtggttttctt-gtagca

upper sequence: LOC_Os03g14980.1 (Oryza sativa), 5'ss of exon 15
lower sequence: EFJ37833 (Selaginella moellendorffii), 5'ss of exon 14
AGATAAAGGCTTGGCTATATGATAATTTGGGATCCAGAGTTGACTATGATGCGCCAGGACATTGGTGCACAACAATGGCATATAGTGCAGATGGTTCAAGgttcat---aattatttctttgttagcatgattcatgtgggtaactgggtttttgtctttgttttcactgattctttttgcccttgtgagtag
| || ||||| ||||| || |||    | || ||  | ||||||||||||||||| |||  |||||||||||||||||| || ||||| |||||  |||||||  |     |  | || ||  || | | |  || | |   |||  || | |    |||||                               
AAATCAAGGCGTGGCTGTACGATTGCCTTGGTTCACGGGTTGACTATGATGCGCCTGGAAGTTGGTGCACAACAATGGCCTACAGTGCTGATGGCACAAGgtttgtctcgttcgtctcgtttctatcgtaagacacgcgctaaacgaggctatgtgttttgtag-----------------------------

upper sequence: LOC_Os03g14980.1 (Oryza sativa), 5'ss of exon 15
lower sequence: EFJ32018 (Selaginella moellendorffii), 5'ss of exon 14
AGATAAAGGCTTGGCTATATGATAATTTGGGATCCAGAGTTGACTATGATGCGCCAGGACATTGGTGCACAACAATGGCATATAGTGCAGATGGTTCAAGgttcat---aattatttctttgttagcatgattcatgtgggtaactgggtttttgtctttgttttcactgattctttttgcccttgtgagtag
| || ||||| ||||| || |||    | || ||  | ||||||||||||||||| |||  |||||||||||||||||| || ||||| |||||  |||||||  |     || | || ||  || | | |  || | |   |||  || | |    |||||                               
AAATCAAGGCGTGGCTGTACGATTGCCTTGGTTCACGGGTTGACTATGATGCGCCTGGAAGTTGGTGCACAACAATGGCCTACAGTGCTGATGGCACAAGgtttgtctcgtttgtctcgtttctatcgtaagacacgcgctaaacgaggctatgtgttttgtag-----------------------------

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|29671653|gb|CB667928.1|CB667928
EST:     GCGCCAGGACATTGGTGCACAACAATGGCATATAGTGCAGATGGTTCAAG                         GTTATTTTCTTGTGGGACTATCAAGGATGGCGAATCACATCTAGTGGAATG
genomic: GCGCCAGGACATTGGTGCACAACAATGGCATATAGTGCAGATGGTTCAAGgttcataatt ... ttgtgagtagGTTATTTTCTTGTGGGACTAGCAAGGATGGCGAATCACATCTAGTGGAATG
EST: gi|58667991|gb|CK056677.1|CK056677
EST:     GCGCCAGGACATTGGTGCACAACAATGGCATATAGTGCAGATGGTTCAAG                         GTTATTTTCTTGTGGGACTAGCAAGGATGGCGAATCACATCTAGTGGAATG
genomic: GCGCCAGGACATTGGTGCACAACAATGGCATATAGTGCAGATGGTTCAAGgttcataatt ... ttgtgagtagGTTATTTTCTTGTGGGACTAGCAAGGATGGCGAATCACATCTAGTGGAATG
EST: gi|29631515|gb|CB636524.1|CB636524
EST:     GCGCCAGGACATTGGTGCACAACAATGGCATATAGTGCAGATGGTTCAAG                         GTTATTTTCTTGTGGGACTAGCAAGGATGGCGAATCACATCTAGTGGAATG
genomic: GCGCCAGGACATTGGTGCACAACAATGGCATATAGTGCAGATGGTTCAAGgttcataatt ... ttgtgagtagGTTATTTTCTTGTGGGACTAGCAAGGATGGCGAATCACATCTAGTGGAATG
EST: gi|44675806|gb|CR289240.1|CR289240
EST:     GGACATTGGTGCACAACAATGGCATATAGTGCAGATGGTTCAAT                         GTTATTTTCTTGTGGGACTAGCAATGATGGCGAATCACATCTAGTGGAATG
genomic: GGACATTGGTGCACAACAATGGCATATAGTGCAGATGGTTCAAGgttcataatt ... ttgtgagtagGTTATTTTCTTGTGGGACTAGCAAGGATGGCGAATCACATCTAGTGGAATG

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), 72 (downstream exon)
Score: 38

AGATAAAGGCTTGGCTATATGATAATTTGGGATCCAGAGTTGACTATGATGCGCCAGGACATTGGTGCACAACAATGGCATATAGTGCAGATGGTTCAAGgttcataatt ... ttgtgagtagGTTATTTTCTTGTGGGACTAGCAAGGATGGCGAATCACATCTAGTGGAATGGAATGAAAGTGAAGGAGCTGTCAAGAGAACTTACCAGGGATTTCGCAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATAAAGGCTTGGCTATATGATAATTTGGGATCCAGAGTTGACTATGATGCGCCAGGACATTGGTGCACAACAATGGCATATAGTGCAGATGGTTCAAGgttcataattatttctttgttagcatgattcatgtgggtaactgggtttttgtctttgttttcactgattctttttgcccttgtgagtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG