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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGCATTACTGGATAAGCATTTGGCGACAGGCACTTTTGATGAGGAGATTAGACCAATTGGCCGCCCAGTAAAATCATTGCTGgtaaaatctcaataccggagcattttacttaattgcataaaagatagtctctaggttagaacctagggctaatggcagtgtgcagacataccagtacggt...

Basic information

species Oryza sativa
transcript LOC_Os11g41900.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g41900.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G037104_T01 (Zea mays), 5'ss of exon 10
GATGCATTACTGGATAAGCATTTGGCGACAGGCACTTTTGATGAGGAGATTAGACCAATTGGCCGCCCAGTAAAATCATTGCTGgtaaaatctcaataccggagcattttacttaattgcataaaagata-gtctctaggttagaacctagggc-taatggcagtgtgcagacataccagtacggt-
||||| |||||||| ||||||||||| ||||||||||| ||||||||||||||||| |||||||| ||||| |||||||||||||||||| | || ||| |  |||| |||  || |    | || |  | ||| ||   | |   ||   |||  |    ||   |  | | ||  |  |  | | 
GATGCCTTACTGGACAAGCATTTGGCAACAGGCACTTTCGATGAGGAGATTAGACCTATTGGCCGTCCAGTGAAATCATTGCTGgtaaaaccccactacagttgcatgttatatagtc---tgaatggcatgtcactgcctcactgccagtggcacacccacacaatctatagatggctatcggctt

upper sequence: LOC_Os11g41900.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM5G878139_T02 (Zea mays), 5'ss of exon 8
GATGCATTACTGGATAAGCATTTGGCGACAGGCACTTTTGATGAGGAGATTAGACCAATTGGCCGCCCAGTAAAATCATTGCTGgtaaaatctcaa-taccggagcattttacttaattgcataaaagatagtctctaggttagaacctagg-gctaatggcagtgtgcagacataccagtacggt-
||||| |||||||| || |||||||| ||||||||||| ||||||||||||||||| || ||||||||||| |||||||||||||||||| | | | ||| |  |||| |||  || |  |  ||  |   ||| || | | |   ||| |  || | |||||   |    |  |      | ||| 
GATGCCTTACTGGACAAACATTTGGCAACAGGCACTTTCGATGAGGAGATTAGACCTATCGGCCGCCCAGTGAAATCATTGCTGgtaaaacccccactacagttgcatgttatatagtc-cgcaatggcatgtcactggctcactgcctcgctgccagtggcaacctcacaatctgt--agatggtc
















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|29686574|gb|CB682849.1|CB682849
EST:     CTTTTGATGAGGAGATTAGACCAATTGGCCGCCCAGTAAAATCATTGCTG                         GTGACTTTGTTTTGGTCATGTCTCCTTTTATATGGCGCCGTCAAGCTCTTC
genomic: CTTTTGATGAGGAGATTAGACCAATTGGCCGCCCAGTAAAATCATTGCTGgtaaaatctc ... tatgtaacagGTGACTTTGTTTTGGTCATGTCTCCTTTTATATGGCGCCGTCAAGCTCTTC
EST: gi|86435824|gb|CI107057.1|CI107057
EST:     CGCCCAGTAAAATCATTGCTG                         GTGACTTTGTTTTGGTCATGTCTCCTTTTATATGGCGCCGTCAAGCTCTTC
genomic: CGCCCAGTAAAATCATTGCTGgtaaaatctc ... tatgtaacagGTGACTTTGTTTTGGTCATGTCTCCTTTTATATGGCGCCGTCAAGCTCTTC
EST: gi|29639123|gb|CB644132.1|CB644132
EST:     CTTTTGATGAGGAGATTAGACCAATTGGCCGCCCAGTAAAATCATTGCTG                         GTGACTTTGTTTTGGTCATGTCTCCTTTTATATGGCGCCGTCAAGCTCTTC
genomic: CTTTTGATGAGGAGATTAGACCAATTGGCCGCCCAGTAAAATCATTGCTGgtaaaatctc ... tatgtaacagGTGACTTTGTTTTGGTCATGTCTCCTTTTATATGGCGCCGTCAAGCTCTTC
EST: gi|29615790|gb|CB620802.1|CB620802
EST:     CTTTTGATGAGGAGATTAGACCAATTGGCCGCCCAGTAAAATCATTGCTG                         GTGACTTTGTTTTGGTCATGTCTCCTTTTATATGGCGCCGTCAAGCTCTTC
genomic: CTTTTGATGAGGAGATTAGACCAATTGGCCGCCCAGTAAAATCATTGCTGgtaaaatctc ... tatgtaacagGTGACTTTGTTTTGGTCATGTCTCCTTTTATATGGCGCCGTCAAGCTCTTC
EST: gi|117217204|gb|CT845404.1|CT845404
EST:     CTTTTGATGAGGAGATTAGACCAATTGGCCGCCCAGTAAAATCATTGCTG                         GTGACTTTGTTTTGGTCATGTCTCCTTTTATATGGCGCCGTCAAGCTCTTC
genomic: CTTTTGATGAGGAGATTAGACCAATTGGCCGCCCAGTAAAATCATTGCTGgtaaaatctc ... tatgtaacagGTGACTTTGTTTTGGTCATGTCTCCTTTTATATGGCGCCGTCAAGCTCTTC
EST: gi|86494086|gb|CI136719.1|CI136719
EST:     CTTTTGATGAGGAGATTAGACCAATTGGCCGCCCAGTAAAATCATTGCTG                         GTGACTTTGTTTTGGTCATGTCTCCTTTTATATGGCGCCGTCAAGCTCTTC
genomic: CTTTTGATGAGGAGATTAGACCAATTGGCCGCCCAGTAAAATCATTGCTGgtaaaatctc ... tatgtaacagGTGACTTTGTTTTGGTCATGTCTCCTTTTATATGGCGCCGTCAAGCTCTTC
EST: gi|86512250|gb|CI154883.1|CI154883
EST:     AGGAGATTAGACCAATTGNCCGCCCAGTAAAATCATTGCTG                         GTGACTTTGTTTTGGTCATGTCTCCTTTTATATGGCGCCGTCAAGCTCTTC
genomic: AGGAGATTAGACCAATTGGCCGCCCAGTAAAATCATTGCTGgtaaaatctc ... tatgtaacagGTGACTTTGTTTTGGTCATGTCTCCTTTTATATGGCGCCGTCAAGCTCTTC
EST: gi|29639077|gb|CB644086.1|CB644086
EST:     CTTTTGATGAGGAGATTAGACCAATTGGCCGCCCAGTAAAATCATTGCTG                         GTGACTTTGTTTTGGTCATGTCTCCTTTTATATGGCGCCGTCAAGCTCTTC
genomic: CTTTTGATGAGGAGATTAGACCAATTGGCCGCCCAGTAAAATCATTGCTGgtaaaatctc ... tatgtaacagGTGACTTTGTTTTGGTCATGTCTCCTTTTATATGGCGCCGTCAAGCTCTTC
EST: gi|88967516|gb|CI002607.1|CI002607
EST:     CTTTTGATGAGGAGATTAGACCAATTGGCCGCCCAGTAAAATCATTGCTG                         GTGACTTTGTTTTGGTCATGTCTCCTTTTATATGGCGCCGTCAAGCTCTTC
genomic: CTTTTGATGAGGAGATTAGACCAATTGGCCGCCCAGTAAAATCATTGCTGgtaaaatctc ... tatgtaacagGTGACTTTGTTTTGGTCATGTCTCCTTTTATATGGCGCCGTCAAGCTCTTC
EST: gi|112785295|gb|EE590405.1|EE590405
EST:     CTTTTGATGAGGAGATTAGACCAATTGGCCGCCCAGTAAAATCATTGCTG                         GTGACTTTGTTTTGGTCATGTCTCCTTTTATATGGCGCCGTCAAGCTCTTC
genomic: CTTTTGATGAGGAGATTAGACCAATTGGCCGCCCAGTAAAATCATTGCTGgtaaaatctc ... tatgtaacagGTGACTTTGTTTTGGTCATGTCTCCTTTTATATGGCGCCGTCAAGCTCTTC
EST: gi|86594010|gb|CI260239.1|CI260239
EST:     CTTTTGATGAGGAGATTAGACCAATTGGCCGCCCAGTAAAATCATTGCTG                         GTGACTTTGTTTTGGTCATGTCTCCTTTTATATGGCGCCGTCAAGCTCTTC
genomic: CTTTTGATGAGGAGATTAGACCAATTGGCCGCCCAGTAAAATCATTGCTGgtaaaatctc ... tatgtaacagGTGACTTTGTTTTGGTCATGTCTCCTTTTATATGGCGCCGTCAAGCTCTTC
EST: gi|86828111|gb|CI274978.1|CI274978
EST:     CTTTTGATGAGGAGATTAGACCAATTGGCCGCCCAGTAAAATCATTGCTG                         GTGACTTTGTTTTGGTCATGTCTCCTTTTATATGGCGCCGTCAAGCTCTTC
genomic: CTTTTGATGAGGAGATTAGACCAATTGGCCGCCCAGTAAAATCATTGCTGgtaaaatctc ... tatgtaacagGTGACTTTGTTTTGGTCATGTCTCCTTTTATATGGCGCCGTCAAGCTCTTC
EST: gi|86434685|gb|CI105918.1|CI105918
EST:     CCAATTGGCCGCCCAGTAAAATCATTGCTG                         GTGACTTTGTTTTGGTCATGTCTCCTTTTATATGGCGCCGTCAAGCTCTTC
genomic: CCAATTGGCCGCCCAGTAAAATCATTGCTGgtaaaatctc ... tatgtaacagGTGACTTTGTTTTGGTCATGTCTCCTTTTATATGGCGCCGTCAAGCTCTTC

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: 50

GATGCATTACTGGATAAGCATTTGGCGACAGGCACTTTTGATGAGGAGATTAGACCAATTGGCCGCCCAGTAAAATCATTGCTGgtaaaatctc ... tatgtaacagGTGACTTTGTTTTGGTCATGTCTCCTTTTATATGGCGCCGTCAAGCTCTTCCTATGGACTCAACTCCTGTCGACATGGAAAGGAGTCGGGTTTACGGGCC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGCATTACTGGATAAGCATTTGGCGACAGGCACTTTTGATGAGGAGATTAGACCAATTGGCCGCCCAGTAAAATCATTGCTGgtaaaatctcaataccggagcattttacttaattgcataaaagatagtctctaggttagaacctagggctaatggcagtgtgcagacataccagtacggt

- - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - GGAGAT