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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATAATGTAAAGCTTGCTGACTTTGGTTTGAGTAACGTCATGCATGATGGCCATTTTTTGAAGACAAGCTGTGGGAGTCCAAACTATGCTGCTCCAGAGgtttttttttttttttttgtatcactgtgggactatatcttcttgctcctttgcatgcaatattttttcttattatagtattatggttcctttgcag

Basic information

species Oryza sativa
transcript LOC_Os03g17980.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g17980.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G107867_T04 (Zea mays), 5'ss of exon 3
GTATAATGTAAAGCTTGCTGACTTTGGTTTGAGTAACGTCATGCATGATGGCCATTTTTTGAAGACAAGCTGTGGGAGTCCAAACTATGCTGCTCCAGAGgttttttttttttttt-ttgtatcactgtgggactatatcttcttgctcctttgcatgcaatattttttcttattatagtattatggttcctttgcag
|||||||||||| ||||| || |||||| |||| || ||||||||||||||||||||| ||||||| |||||||||||||| |||||||||||||||||||| |||| || || ||  |||     ||  |  |||| | || || ||  || | |  | || ||| ||  ||  |||||   |  |||| |||||||
GTATAATGTAAAACTTGCGGATTTTGGTCTGAGCAATGTCATGCATGATGGCCATTTTCTGAAGACTAGCTGTGGGAGTCCGAACTATGCTGCTCCAGAGgtattttattcttattgctgtgagtttgctgatctatttttttttcctttttagaacaccatgtttcttgatac-atagtg--agtgttcttttgcag

upper sequence: LOC_Os03g17980.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA13G05700.1 (Glycine max), 5'ss of exon 4
GTATAATGTAAAGCTTGCTGACTTTGGTTTGAGTAACGTCATGCATGATGGCCATTTTTTGAAGACAAGCTGTGGGAGTCCAAACTATGCTGCTCCAGAGgttttttttttttttt-ttgtatcactgtgggactatatcttc----ttgctcctttgcatgcaatattttttcttattatagtattatggttcctttgcag--------------------------------------
 | |||  | ||| ||||||| ||||| ||||| ||| |||||| |||||| || ||| | |||||||| ||||| || || || ||||| ||||||||||||| |   |  ||   ||||| |    | |||   |||  |     ||  |  | |   |   ||||   | ||| | | | | |||   || | |    |                                      
ATTTAACATCAAGATTGCTGATTTTGGGTTGAGCAACATCATGCGTGATGGTCACTTTCTTAAGACAAGTTGTGGAAGCCCTAATTATGCGGCTCCAGAGgtttgtaaataattaaattgtaacggaataggatattattattaatgttattattattattattatatcactacttctgagact-ttacatttacctccttgtgattaataaatcaaggataaactgttgtttttcacag

upper sequence: LOC_Os03g17980.2 (Oryza sativa), 5'ss of exon 4
lower sequence: AT3G01090.2 (Arabidopsis thaliana), 5'ss of exon 4
GTATAATGTAAAGCTTGCTGACTTTGGTTTGAGTAACGTCATGCATGATGGCCATTTTTTGAAGACAAGCTGTGGGAGTCCAAACTATGCTGCTCCAGAGgtttttttttttttttttgtatcactgtgggactatatcttcttgctcctttgcatgcaatattttttcttattatagtattatggttcctttgcag
 |  ||||||||| ||||||| |||||  |||| ||| | ||||  ||||| ||||||||||||||||| ||||| |||||||| ||||| |||||||||||   |  ||      |    |  ||| || |   |||  |   |||  ||| ||    |||  || |   | |  ||   |||   |  ||| |||
ATGCAATGTAAAGATTGCTGATTTTGGCCTGAGCAACATAATGCGAGATGGTCATTTTTTGAAGACAAGTTGTGGAAGTCCAAATTATGCCGCTCCAGAGgtaagtgcttcagccctcaggtatctgaggaatactataattaggcttgttt-caaatgataggttat---agtcgagatctataaattgttt-cag

upper sequence: LOC_Os03g17980.2 (Oryza sativa), 5'ss of exon 4
lower sequence: AT5G39440.1 (Arabidopsis thaliana), 5'ss of exon 3
GTATAATGTAAAGCTTGCTGACTTTGGTTTGAGTAACGTCATGCATGATGGCCATTTTTTGAAGACAAGCTGTGGGAGTCCAAACTATGCTGCTCCAGAGgttttt----ttttttttttttgtatcactgtgggactatatcttcttgctcctttgcatgcaatattttttcttattatagtattatggttcctttgcag
 |  ||  ||||| ||| ||||||||| |||||||| |||||||||||||| |||||||| ||||| || ||||| || || || ||||||||||||||||| |      ||    | || |  ||   | |   | |  || |   |     |||| | | |  | ||  ||  |    |   ||||  ||   | |   
ATGCAACATAAAGATTGTTGACTTTGGATTGAGTAATGTCATGCATGATGGTCATTTTTTAAAGACTAGTTGTGGAAGCCCTAATTATGCTGCTCCAGAGgtataagagattaacatattcttcatttttatttca-tgaatttggatatatatttg-aagtatcaattactcacacctgaaacttat--ttatatag---

upper sequence: LOC_Os03g17980.2 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv14s0108g01230.t01 (Vitis vinifera), 5'ss of exon 4
GTATAATGTAAAGCTTGCTGACTTTGGTTTGAGTAACGTCATGCATGATGGCCATTTTTTGAAGACAAGCTGTGGGAGTCCAAACTATGCTGCTCCAGAGgtttttttttttttttttgtatcactgtgggactatatcttcttgctcctttgca-------tgcaatattttttcttattatagtattatggttcc--tttgcag---------------------------
 |  ||||| ||| ||||||| |||||||| |||||  |||||   ||||| ||||||||||||||||| ||||| || ||||| |||||||| ||||||||      |||      | ||| | | |  ||| ||  ||  ||  |  ||   |       | ||||| ||| |  |||   |  || ||||||    |||  |                            
ATGCAATGTGAAGATTGCTGATTTTGGTTTAAGTAATATCATGAGAGATGGTCATTTTTTGAAGACAAGTTGTGGAAGCCCAAATTATGCTGCCCCAGAGgtaaggagtttgcagcat-tat-aatataagacaattcctaatttttggttgagagatgagttacaatactttctaatatatgatgataatggttgaaatttctaaggttctaattagtgtcccattttatag

upper sequence: LOC_Os03g17980.2 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv08s0040g00720.t01 (Vitis vinifera), 5'ss of exon 5
GTATAATGTAAAGCTTGCTGACTTTGGTTTGAGTAACGTCATGCATGATGGCCATTTTTTGAAGACAAGCTGTGGGAGTCCAAACTATGCTGCTCCAGAGgttt---ttttttttttttttgtatcactgtgggactatatcttcttgctcctttgcatgcaat-attttttcttattatagtattatggttcctttgcag
    ||||| ||  |||| ||||||||  | || || || |||| |||||| |||||| | || ||||||||||| |||||||| ||||||||||| ||||| |   |    || || | |   |  |    | |||      |  |  | || ||  | |||| |  |  |  |  |  ||                   
ACGCAATGTCAAAGTTGCAGACTTTGGACTCAGCAATGTGATGCGTGATGGTCATTTTCTCAAAACAAGCTGTGGAAGTCCAAATTATGCTGCTCCTGAGgtatgggtcaacttgttatataagttgccaatgaacttgtgaataattatgctctgtgtacaatgaaatactgcttgtgcag-------------------

upper sequence: LOC_Os03g17980.2 (Oryza sativa), 5'ss of exon 4
lower sequence: PP1S28_12V6.1 (Physcomitrella patens), 5'ss of exon 3
GTATAATGTAAAGCTTGCTGACTTTGGTTTGAGTAACGTCATGCATGATGGCCATTTTTTGAAGACAAGCTGTGGGAGTCCAAACTATGCTGCTCCAGAGgtttttttttttttttttgtatcactgtgggactatatcttcttgc-tcctttgcatgcaatattttttcttattata-gtattatggttcctttgcag------------------------------------------------------------------
|| ||| || ||| ||||||| ||||| ||    || || |||   || || |||||  | || || |||||||| |||||||| ||||||||||||||||||||  | | |   |   |  |  |||  |||  | | ||  | | || | ||  ||    |  | ||  | || |  || ||  ||| |||   |                                                                    
GTCTAACGTCAAGATTGCTGATTTTGGGTTATCCAATGTTATGAGGGACGGTCATTTCCTCAAAACTAGCTGTGGAAGTCCAAATTATGCTGCTCCAGAGgttttgctctatgcctgattgcc-ttgtttgacactgttttaattcgtcatgtgattgtgtcacatgtttctgttttctgtgttg-ggtgcctgaaccaagttgtaggttttctgtgcccggacacactcctgcttgttgactgttgatattgttgaacatgcag

upper sequence: LOC_Os03g17980.2 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ35371 (Selaginella moellendorffii), 5'ss of exon 3
GTATAATGTAAAGCTTGCTGACTTTGGTTTGAGTAACGTCATGCATGATGGCCATTTTTTGAAGACAAGCTGTGGGAGTCCAAACTATGCTGCTCCAGAGgtttttttttttttttttgtatcactgtgggactatatcttcttgctcctttgcatgcaatattttttcttattatagtattatggttcctttgcag
||  ||||| ||| |||| |||||||| ||||||||  ||||||  ||||| || ||| |||| || |||||||| |||||||||||||| |||||||||||    ||    ||| || | || || | | |     | | ||| |                                                   
GTGCAATGTGAAGATTGCGGACTTTGGCTTGAGTAATATCATGCGAGATGGACACTTTCTGAAAACGAGCTGTGGAAGTCCAAACTATGCCGCTCCAGAGgtaagcttcgactttcttttttc-ctctagaaagccttttcctttcag-------------------------------------------------

upper sequence: LOC_Os03g17980.2 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ16445 (Selaginella moellendorffii), 5'ss of exon 3
GTATAATGTAAAGCTTGCTGACTTTGGTTTGAGTAACGTCATGCATGATGGCCATTTTTTGAAGACAAGCTGTGGGAGTCCAAACTATGCTGCTCCAGAGgtttttttttttttttttgtatcactgtgggactatatcttcttgctcctttgcatgcaatattttttcttattatagtattatggttcctttgcag
 |  | ||| ||| | || || |||||  |||| ||| | ||||  || || || ||| |||| ||||||||||| ||||| ||||||||||||||||||||   | | |   | |  || |   | | ||          || |    | |   |    | | |||    || | ||                   
ATGCAGTGTCAAGATAGCGGATTTTGGCCTGAGCAACATTATGCGAGACGGACACTTTCTGAAAACAAGCTGTGGAAGTCCGAACTATGCTGCTCCAGAGgtcagtatatcagtataagttttgttatagg----------ctcgtcattctaagt----tgtctttctcaatcacag-------------------

upper sequence: LOC_Os03g17980.2 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ10631 (Selaginella moellendorffii), 5'ss of exon 4
GTATAATGTAAAGCTTGCTGACTTTGGTTTGAGTAACGTCATGCATGATGGCCATTTTTTGAAGACAAGCTGTGGGAGTCCAAACTATGCTGCTCCAGAGgtttttttttttttttttgtatcactgtgggactatatcttcttgctcctttgcatgcaatattttttcttattatagtattatggttcctttgcag
||  ||||| ||| |||| |||||||| || |||||  ||||||  ||||| || ||| |||| || |||||||| |||||||||||||| |||||||||||    ||     || || | || || | | |     | | ||| |                                                   
GTGCAATGTGAAGATTGCGGACTTTGGCTTAAGTAATATCATGCGAGATGGACACTTTCTGAAAACGAGCTGTGGAAGTCCAAACTATGCCGCTCCAGAGgtaagcttcgacattcttttttc-ctctagaaagccttttcctttcag-------------------------------------------------

upper sequence: LOC_Os03g17980.2 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ17922 (Selaginella moellendorffii), 5'ss of exon 3
GTATAATGTAAAGCTTGCTGACTTTGGTTTGAGTAACGTCATGCATGATGGCCATTTTTTGAAGACAAGCTGTGGGAGTCCAAACTATGCTGCTCCAGAGgtttttttttttttttttgtatcactgtgggactatatcttcttgctcctttgcatgcaatattttttcttattatagtattatggttcctttgcag
 |  | ||| ||| | || || |||||  |||| ||| | ||||  || || || ||| |||| ||||||||||| ||||| ||||||||||||||||||||   | | |     |  || |     | ||          || |    | |   |    | | |||    || | ||                   
ATGCAGTGTCAAGATCGCGGATTTTGGCCTGAGCAACATTATGCGAGACGGTCACTTTCTGAAAACAAGCTGTGGAAGTCCGAACTATGCTGCTCCAGAGgtcagtatatcaggataagttttgtcatagg----------ctcgtcattctaagt----tgtctttctcaatcacag-------------------

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|58667418|gb|CK056104.1|CK056104
EST:     AGACAAGCTGTGGGAGTCCAAACTATGCTGCTCCAGAG                         GTGATCTCTGGTAAATTATATGCTGGACCTGAGGTTGATGTATGGAGCTGT
genomic: AGACAAGCTGTGGGAGTCCAAACTATGCTGCTCCAGAGgttttttttt ... tcctttgcagGTGATCTCTGGTAAATTATATGCTGGACCTGAGGTTGATGTATGGAGCTGT
EST: gi|29663426|gb|CB659701.1|CB659701
EST:     GCCATTTTTTGAAGACAAGCTGTGGGAGTCCAAACTATGCTGCTCCAGAG                         GTGATCTCTGGTAAATTATATGCTGGACCTGAGGTTGATGTATGGAGCTGT
genomic: GCCATTTTTTGAAGACAAGCTGTGGGAGTCCAAACTATGCTGCTCCAGAGgttttttttt ... tcctttgcagGTGATCTCTGGTAAATTATATGCTGGACCTGAGGTTGATGTATGGAGCTGT
EST: gi|58679972|gb|CK068659.1|CK068659
EST:     GCCATTTTTTGAAGACAAGCTGTGGGAGTCCAAACTATGCTGCTCCAGAG                         GTGATCTCTGGTAAATTATATGCTGGACCTGAGGTTGATGTATGGAGCTGT
genomic: GCCATTTTTTGAAGACAAGCTGTGGGAGTCCAAACTATGCTGCTCCAGAGgttttttttt ... tcctttgcagGTGATCTCTGGTAAATTATATGCTGGACCTGAGGTTGATGTATGGAGCTGT
EST: gi|58674982|gb|CK063669.1|CK063669
EST:     GCCATTTTTTGAAGACAAGCTGTGGGAGTCCAAACTATGCTGCTCCAGAG                         GTGATCTCTGGTAAATTATATGCTGGACCTGAGGTTGATGTATGGAGCTGT
genomic: GCCATTTTTTGAAGACAAGCTGTGGGAGTCCAAACTATGCTGCTCCAGAGgttttttttt ... tcctttgcagGTGATCTCTGGTAAATTATATGCTGGACCTGAGGTTGATGTATGGAGCTGT
EST: gi|33678911|gb|CF307150.1|CF307150
EST:     GCCATTTTTTGAAGACAAGCTGTGGGAGTCCAAACTATGCTGCTCCAGAG                         GTGATCTCTGGTAAATTATATGCTGGACCTGAGGTTGATGTATGGAGCTGT
genomic: GCCATTTTTTGAAGACAAGCTGTGGGAGTCCAAACTATGCTGCTCCAGAGgttttttttt ... tcctttgcagGTGATCTCTGGTAAATTATATGCTGGACCTGAGGTTGATGTATGGAGCTGT
EST: gi|218482816|gb|FG952976.1|FG952976
EST:     GCCATTTTTTGAAGACAAGCTGTGGGAGTCCAAACTATGCTGCTCCAGAG                         GTGATCTCTGGTAAATTATATGCTGGACCTGAGGTTGATGTATGGAGCTGT
genomic: GCCATTTTTTGAAGACAAGCTGTGGGAGTCCAAACTATGCTGCTCCAGAGgttttttttt ... tcctttgcagGTGATCTCTGGTAAATTATATGCTGGACCTGAGGTTGATGTATGGAGCTGT
EST: gi|218482252|gb|FG960526.1|FG960526
EST:     GCCATTTTTTGAAGACAAGCTGTGGGAGTCCAAACTATGCTGCTCCAGAG                         GTGATCTCTGGTAAATTATATGCTGGACCTGAGGTTGATGTATGGAGCTGT
genomic: GCCATTTTTTGAAGACAAGCTGTGGGAGTCCAAACTATGCTGCTCCAGAGgttttttttt ... tcctttgcagGTGATCTCTGGTAAATTATATGCTGGACCTGAGGTTGATGTATGGAGCTGT
EST: gi|29614995|gb|CB620008.1|CB620008
EST:     GCCATTTTTTGAAGACAAGCTGTGGGAGTCCAAACTATGCTGCTCCAGAG                         GTGATCTCTGGTAAATTATATGCTGGACCTGAGGTTGATGTATGGAGCTGT
genomic: GCCATTTTTTGAAGACAAGCTGTGGGAGTCCAAACTATGCTGCTCCAGAGgttttttttt ... tcctttgcagGTGATCTCTGGTAAATTATATGCTGGACCTGAGGTTGATGTATGGAGCTGT
EST: gi|33381730|gb|CF197073.1|CF197073
EST:     GCCATTTTTTGAAGACAAGCTGTGGGAGTCCAAACTATGCTGCTCCAGAG                         GTGATCTCTGGTAAATTATATGCTGGACCTGAGGTTGATGTATGGAGCTGT
genomic: GCCATTTTTTGAAGACAAGCTGTGGGAGTCCAAACTATGCTGCTCCAGAGgttttttttt ... tcctttgcagGTGATCTCTGGTAAATTATATGCTGGACCTGAGGTTGATGTATGGAGCTGT
EST: gi|218488644|gb|FG955529.1|FG955529
EST:     GCCATTTTTTGAAGACAAGCTGTGGGAGTCCAAACTATGCTGCTCCAGAG                         GTGATCTCTGGTAAATTATACNCTGGACCTGAGGTTGATGTATGGAGCTGT
genomic: GCCATTTTTTGAAGACAAGCTGTGGGAGTCCAAACTATGCTGCTCCAGAGgttttttttt ... tcctttgcagGTGATCTCTGGTAAATTATATGCTGGACCTGAGGTTGATGTATGGAGCTGT

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: 119

GTATAATGTAAAGCTTGCTGACTTTGGTTTGAGTAACGTCATGCATGATGGCCATTTTTTGAAGACAAGCTGTGGGAGTCCAAACTATGCTGCTCCAGAGgttttttttt ... tcctttgcagGTGATCTCTGGTAAATTATATGCTGGACCTGAGGTTGATGTATGGAGCTGTGGAGTGATCCTTTATGCTCTCCTTTGTGGTACTCTTCCATTTGATGATG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATAATGTAAAGCTTGCTGACTTTGGTTTGAGTAACGTCATGCATGATGGCCATTTTTTGAAGACAAGCTGTGGGAGTCCAAACTATGCTGCTCCAGAGgtttttttttttttttttgtatcactgtgggactatatcttcttgctcctttgcatgcaatattttttcttattatagtattatggttcctttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT