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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggggctctactaatggatgaatcaaataacttttgtacttattttattatagggatcaatttgaaaattttcttattcattggctctgtgcagATTATTGAGGCCCCTCTACCTAAAGCTCCTCTTGATACAGCAGTTGTAGCTCACTGGCTAGCCATTGAGGGAGTCCAGCCTGCAATTCCAGAGAATCCTC

Basic information

species Oryza sativa
transcript LOC_Os01g32750.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g32750.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G013908_T01 (Zea mays), 3'ss of exon 3
gtaggggctctactaatggatgaatcaaataacttttgtacttattttattatagggatcaatttgaaaattttcttattcattggctctgtgcagATTATTGAGGCCCCTCTACCTAAAGCTCCTCTTGATACAGCAGTTGTAGCTCACTGGCTAGCCATTGAGGGAGTCCAGCCTGCAATTCCAGAGAATCCTC
|||| |||  || |||||  |  || ||||   ||| ||||   || | | | |   ||  ||||||||  ||||||  |  || |     |||||||||||||    ||||| |||||||| || || || ||| |||||||||| || |||||||| |||||||| || ||||||||||| || ||||||||| 
gtagtggcattattaatgatt--attaaat---tttcgtaccacttatttcaaaaccattcatttgaaatgtttcttcctggttcgtgtcatgcagATTATTGACTGTCCTCTGCCTAAAGCCCCACTGGACACATCAGTTGTAGCCCATTGGCTAGCGATTGAGGGGGTACAGCCTGCAATACCGGAGAATCCTG
















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|88378515|gb|CI636462.1|CI636462
EST:     GACACAAGGATCTCTTCTATATTGATGACAGGGAGGTAGACTTCAAAGAG                         ATTATTGAGGCCCCTCTACCTAAAGCTCCTCTTGATACAGCAGTTGTAGCT
genomic: GACACAAGGATCTCTTCTATATTGATGACAGGGAGGTAGACTTCAAAGAGgtaggggctc ... ctctgtgcagATTATTGAGGCCCCTCTACCTAAAGCTCCTCTTGATACAGCAGTTGTAGCT
EST: gi|29614712|gb|CB619725.1|CB619725
EST:     GACACAAGGATCTCTTCTATATTGATGACAGGGAGGTAGACTTCAAAGAG                         ATTATTGAGGCCCCTCTACCTAAAGCTCCTCTTGATACAGCAGTTGTAGCT
genomic: GACACAAGGATCTCTTCTATATTGATGACAGGGAGGTAGACTTCAAAGAGgtaggggctc ... ctctgtgcagATTATTGAGGCCCCTCTACCTAAAGCTCCTCTTGATACAGCAGTTGTAGCT
EST: gi|88352072|gb|CI626072.1|CI626072
EST:     GACACAAGGATCTCTTCTATATTGATGACAGGGAGGTAGAATTCAAACAG                         ATTATTGAGGCCCCTCTACCTAAAGCTCCTCTTGATACAGCAGTTGTACCT
genomic: GACACAAGGATCTCTTCTATATTGATGACAGGGAGGTAGACTTCAAAGAGgtaggggctc ... ctctgtgcagATTATTGAGGCCCCTCTACCTAAAGCTCCTCTTGATACAGCAGTTGTAGCT
EST: gi|88334913|gb|CI648688.1|CI648688
EST:     GACACAAGGATCTCTTCTATATTGATGACAGGGAGGTAGACTTCAAAGAG                         ATTATTGAGGCCCCTCTACCTAAAGCTCCTCTTGATACAGCAGTTGTAGCT
genomic: GACACAAGGATCTCTTCTATATTGATGACAGGGAGGTAGACTTCAAAGAGgtaggggctc ... ctctgtgcagATTATTGAGGCCCCTCTACCTAAAGCTCCTCTTGATACAGCAGTTGTAGCT
EST: gi|88325722|gb|CI648166.1|CI648166
EST:     GACACAAGGATCTCTTCTATATTGATGACAGGGAGGTAGACTTCAAAGAG                         ATTATTGAGGCCCCTCTACCTAAAGCTCCTCTTGATACAGCAGTTGTAGCT
genomic: GACACAAGGATCTCTTCTATATTGATGACAGGGAGGTAGACTTCAAAGAGgtaggggctc ... ctctgtgcagATTATTGAGGCCCCTCTACCTAAAGCTCCTCTTGATACAGCAGTTGTAGCT
EST: gi|29681488|gb|CB677763.1|CB677763
EST:     GACACAAGGATCTCTTCTATATTGATGACAGGGAGGTAGACTTCAAAGAG                         ATTATTGAGGCCCCTCTACCTAAAGCTCCTCTTGATACAGCAGTTGTAGCT
genomic: GACACAAGGATCTCTTCTATATTGATGACAGGGAGGTAGACTTCAAAGAGgtaggggctc ... ctctgtgcagATTATTGAGGCCCCTCTACCTAAAGCTCCTCTTGATACAGCAGTTGTAGCT
EST: gi|88372867|gb|CI640318.1|CI640318
EST:     GACACAAGGATCTCTTCTATATTGATGACAGGGAGGTAGACTTCAAAGAG                         ATTATTGAGGCCCCTCTACCTAAAGCTCCTCTTGATACAGCAGTTGTAGCT
genomic: GACACAAGGATCTCTTCTATATTGATGACAGGGAGGTAGACTTCAAAGAGgtaggggctc ... ctctgtgcagATTATTGAGGCCCCTCTACCTAAAGCTCCTCTTGATACAGCAGTTGTAGCT

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), 49 (downstream exon)
Score: 20

TGTATATGGATTTGCTTCCGGTGACCCCTTGCGGTTTAAGAGAGCTGTGGGACACAAGGATCTCTTCTATATTGATGACAGGGAGGTAGACTTCAAAGAGgtaggggctc ... ctctgtgcagATTATTGAGGCCCCTCTACCTAAAGCTCCTCTTGATACAGCAGTTGTAGCTCACTGGCTAGCCATTGAGGGAGTCCAGCCTGCAATTCCAGAGAATCCTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattttattatagggatcaatttgaaaattttcttattcattggctctgtgcagATTATTGAGGCCCCTCTACCTAAAGCTCCTCTTGATACAGCAGTTGTAGCTCACTGGCTAGCCATTGAGGGAGTCCAGCCTGCAATTCCAGAGAATCCTC
                atcaatttgaaaattt  TA-rich tract