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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCAGGCGATGAAGTGGATTGTGGCAATGCCAGTTATCATTCTCGGCTCCAGTCTTTAAAACCACAGATGCCAAAATCATTGGGCAGCAGTTGTGCCACGgtaagtgctcaatgaaatgttcttttggcatcttcttcctgaaattgcttgctaaccgaattatttacag

Basic information

species Oryza sativa
transcript LOC_Os01g48060.1
intron # 10
splice site 5'
intron type U2

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|86432440|gb|CI086051.1|CI086051
EST:     AGTCTTTAAAACCACAGATGCCAAAATCATTGGGCAGCAGTTGTGCCACG                         GTCCATGAACAAAGGCCTGTTGTTGGCAGGGTCGTTGATATTTCAGCAGTG
genomic: AGTCTTTAAAACCACAGATGCCAAAATCATTGGGCAGCAGTTGTGCCACGgtaagtgctc ... ttatttacagGTCCATGAACAAAGGCCTGTTGTTGGCAGGGTCGTTGATATTTCAGCAGTG
EST: gi|29678648|gb|CB674923.1|CB674923
EST:     AGTCTTTAAAACCACAGATGCCAAAATCATTGGGCAGCAGTTGTGCCACG                         GTCCATGAACAAAGGCCTGTTGTTGGCAGGGTCGTTGATATTTCAGCAGTG
genomic: AGTCTTTAAAACCACAGATGCCAAAATCATTGGGCAGCAGTTGTGCCACGgtaagtgctc ... ttatttacagGTCCATGAACAAAGGCCTGTTGTTGGCAGGGTCGTTGATATTTCAGCAGTG
EST: gi|163925863|gb|EG709635.1|EG709635
EST:     AGTCTTTAAAACCACAGATGCCAAAATCATTGGGCAGCAGTTGTGCCACG                         GTCCATGAACAAAGGCCTGTTGTTGGCAGGGTCGTTGATATTTCAGCAGTG
genomic: AGTCTTTAAAACCACAGATGCCAAAATCATTGGGCAGCAGTTGTGCCACGgtaagtgctc ... ttatttacagGTCCATGAACAAAGGCCTGTTGTTGGCAGGGTCGTTGATATTTCAGCAGTG
EST: gi|86869521|gb|CI346381.1|CI346381
EST:     GTCTTTAAAACCACAGATGCCAAAATCATTGGGCAGGCGGTTGTGCCACG                         GTCCATGAACAAAGGCCTGGTTGTTGGCAGGGTCGTTGATATTTCAGCAGT
genomic: GTCTTTAAAACCACAGATGCCAAAATCATTGGGCA-GCAGTTGTGCCACGgtaagtgctc ... ttatttacagGTCCATGAACAAAGGCCT-GTTGTTGGCAGGGTCGTTGATATTTCAGCAGT
EST: gi|86851859|gb|CI316428.1|CI316428
EST:     CAGCAGTTGTGCCACG                         GTCCATGAACAAAGGCCTGTTGTTGGCAGGGTCCTTGATATTTCAGCAGTG
genomic: CAGCAGTTGTGCCACGgtaagtgctc ... ttatttacagGTCCATGAACAAAGGCCTGTTGTTGGCAGGGTCGTTGATATTTCAGCAGTG
EST: gi|86537351|gb|CI177557.1|CI177557
EST:     CAGCAGTTGTGCCACG                         GTCCATGAACAAAGGCCTGTTGTTGGCAGGGTCGTTGATATTTCAGCAGTG
genomic: CAGCAGTTGTGCCACGgtaagtgctc ... ttatttacagGTCCATGAACAAAGGCCTGTTGTTGGCAGGGTCGTTGATATTTCAGCAGTG
EST: gi|88477575|gb|CI414846.1|CI414846
EST:     ACCACAGATGCCGAAATCATTGGGCGGCGGTTGTGCCACG                         GTCCATGAACAAAGGCCTGTTGTTGGCAGGGTCGTTGATATTTCAGCAGTG
genomic: ACCACAGATGCCAAAATCATTGGGCAGCAGTTGTGCCACGgtaagtgctc ... ttatttacagGTCCATGAACAAAGGCCTGTTGTTGGCAGGGTCGTTGATATTTCAGCAGTG
EST: gi|86538454|gb|CI178660.1|CI178660
EST:     AGTCTTTAAAACCACAGATGCCAAAATCATTGGGCAGCAGTTGTGCCACG                         GTCCATGAACAAAGGCCTGTTGTTGGCAGGGTCGTTGATATTTCAGCAGTG
genomic: AGTCTTTAAAACCACAGATGCCAAAATCATTGGGCAGCAGTTGTGCCACGgtaagtgctc ... ttatttacagGTCCATGAACAAAGGCCTGTTGTTGGCAGGGTCGTTGATATTTCAGCAGTG
EST: gi|88513849|gb|CI441355.1|CI441355
EST:     AGTCTTTAAAACCACAGATGCCCAAATCATTGGGCACCAATTGTNCCACG                         GTCCATGAACAAAGGCCTGTTGTTGGCAGGGTCGTTGATATTTCAGCAGTG
genomic: AGTCTTTAAAACCACAGATGCCAAAATCATTGGGCAGCAGTTGTGCCACGgtaagtgctc ... ttatttacagGTCCATGAACAAAGGCCTGTTGTTGGCAGGGTCGTTGATATTTCAGCAGTG
EST: gi|325493604|gb|JG458128.1|JG458128
EST:     GGGCAGCAGTTGTGCCACG                         GTCCATGAACAAAGGCCTGTTGTTGGCAGGGTCGTTGATATTTCAGCAGTG
genomic: GGGCAGCAGTTGTGCCACGgtaagtgctc ... ttatttacagGTCCATGAACAAAGGCCTGTTGTTGGCAGGGTCGTTGATATTTCAGCAGTG
EST: gi|88509476|gb|CI436982.1|CI436982
EST:     AGTCTTTAAAACCACAGATGCCAAAATCATTGGGCAGCAGTTGTGCCACG                         GTCCATGAACAAAGGCCTGTTGTTGGCAGGGTCGTTGATATTTCAGCAGTG
genomic: AGTCTTTAAAACCACAGATGCCAAAATCATTGGGCAGCAGTTGTGCCACGgtaagtgctc ... ttatttacagGTCCATGAACAAAGGCCTGTTGTTGGCAGGGTCGTTGATATTTCAGCAGTG
EST: gi|88469954|gb|CI407225.1|CI407225
EST:     AGTCTTTAAAACCACAGATGCCAAAATCATTGGGCAGCAGTTGTGCCACG                         GTCCATGAACGAAGGCCTGTTGGTGGCAGGGTCGTTGATATTTCAGCAGTG
genomic: AGTCTTTAAAACCACAGATGCCAAAATCATTGGGCAGCAGTTGTGCCACGgtaagtgctc ... ttatttacagGTCCATGAACAAAGGCCTGTTGTTGGCAGGGTCGTTGATATTTCAGCAGTG
EST: gi|3766812|gb|AU030922.1|AU030922
EST:     AGTCTTTAAAACCACAGATGCCAAAATCATTGGGCAGCNGTTGTGCCACG                         GTCCATGAACAAAGGCCTGTTGTTGGCAGGGTCGTTGATATTTCAGCNGTG
genomic: AGTCTTTAAAACCACAGATGCCAAAATCATTGGGCAGCAGTTGTGCCACGgtaagtgctc ... ttatttacagGTCCATGAACAAAGGCCTGTTGTTGGCAGGGTCGTTGATATTTCAGCAGTG
EST: gi|88472677|gb|CI409948.1|CI409948
EST:     AGTCTTTAAAACCACAGATGCCAAAATCATTGGGCAGCAGTTGTGCCACG                         GTCCATGAACAAAGGCCTGTTGTTGGCAGGGTCGTTGATATTTCAGCAGTG
genomic: AGTCTTTAAAACCACAGATGCCAAAATCATTGGGCAGCAGTTGTGCCACGgtaagtgctc ... ttatttacagGTCCATGAACAAAGGCCTGTTGTTGGCAGGGTCGTTGATATTTCAGCAGTG

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: 57 (upstream exon), 9 (downstream exon)
Score: 1

AGCAGGCGATGAAGTGGATTGTGGCAATGCCAGTTATCATTCTCGGCTCCAGTCTTTAAAACCACAGATGCCAAAATCATTGGGCAGCAGTTGTGCCACGgtaagtgctc ... ttatttacagGTCCATGAACAAAGGCCTGTTGTTGGCAGGGTCGTTGATATTTCAGCAGTGAATACGATGATCTGATACATTTACTGTATCCAGGGAGTATGCTTGCAGA




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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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCAGGCGATGAAGTGGATTGTGGCAATGCCAGTTATCATTCTCGGCTCCAGTCTTTAAAACCACAGATGCCAAAATCATTGGGCAGCAGTTGTGCCACGgtaagtgctcaatgaaatgttcttttggcatcttcttcctgaaattgcttgctaaccgaattatttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG