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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtcttctgtttattctgatctgtcatgtatctctaattcctaacatgcttacctccaaggcgaggaggacaaaaagaataaatgtcaacatgtattcctaatattattcatattattagcagAGTATCAAGACAGAGATGAATCCCATTTTGACACCAAGGTCAGCAGGTCCTGAGGGGTCATTTATTGGTGTCCAAG

Basic information

species Oryza sativa
transcript LOC_Os01g42260.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g42260.4 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G022383_T01 (Zea mays), 3'ss of exon 6
gttagtcttctgtttattctgatctgtcatgtatctctaattcctaacatgcttacctccaaggcgaggaggacaaaaagaataaatgtcaacatgtattcctaatattattcatattattagcagAGTATCAAGACAGAGATGAATCCCATTTTGACACCAAGGTCAGCAGGTCCTGAGGGGTCATTTATTGGTGTCCAAG
|||||||||||   ||  ||| | | || |||   | ||      | |||  |  ||||||            ||    | ||  | || |||   | || || ||  |||||||||||||| ||| |||||||||||||||| |||| | || |||| || ||    ||||| || || ||||||||||| ||||||||||
gttagtcttcttggtaccctggtttatcttgt---tttatcatacatcatagtgtcctcca------------cacttgggattgaagtgaactattgtttcttattgtattcatattattatcagGGTATCAAGACAGAGATTAATCACGTTCTGACTCCCAGAGGTGCAGGCCCAGAAGGGTCATTTATAGGTGTCCAAG
















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|88343088|gb|CI641614.1|CI641614
EST:     GTCTGCAACAAGTTCAGTCCAGGAGTCCACAGATTCGTGGGCCAGGTCAG                         AGTATCAAGACAGAGATGAATCCCATTTTGACACCAAGGTCAGCAGGTCCT
genomic: GTCTGCAACAAGTTCAGTCCAGGAGTCCACAGATTCCTGGGCCAGCTCAGgttagtcttc ... ttattagcagAGTATCAAGACAGAGATGAATCCCATTTTGACACCAAGGTCAGCAGGTCCT
EST: gi|88342451|gb|CI645973.1|CI645973
EST:     GTCTGCAACAAGTTCAGTCCAGGAGTCCACAGATTCCTGGGCCAGCTCAG                         AGTATCAAGACAGAGATGAATCCCATTTTGACACCAAGGTCAGCAGGTCCT
genomic: GTCTGCAACAAGTTCAGTCCAGGAGTCCACAGATTCCTGGGCCAGCTCAGgttagtcttc ... ttattagcagAGTATCAAGACAGAGATGAATCCCATTTTGACACCAAGGTCAGCAGGTCCT
EST: gi|87006683|gb|CI285717.1|CI285717
EST:     GTCTGCAACAAGTTCAGTCCAGGAGTCCACAGATTCCTGGGCCAGCTCAG                         AGTATCAAGACAGAGATGAATTCCCATTTTGACACCAAGGTCAGCAGGTCC
genomic: GTCTGCAACAAGTTCAGTCCAGGAGTCCACAGATTCCTGGGCCAGCTCAGgttagtcttc ... ttattagcagAGTATCAAGACAGAGATGAA-TCCCATTTTGACACCAAGGTCAGCAGGTCC
EST: gi|58608936|gb|CK036969.1|CK036969
EST:     GTCTGCAACAAGTTCAGTCCAGGAGTCCACAGATTCCTGGGCCAGCTCAG                         AGTATCAAGACAGAGATGAATCCCATTTTGACACCAAGGTCAGCAGGTCCT
genomic: GTCTGCAACAAGTTCAGTCCAGGAGTCCACAGATTCCTGGGCCAGCTCAGgttagtcttc ... ttattagcagAGTATCAAGACAGAGATGAATCCCATTTTGACACCAAGGTCAGCAGGTCCT
EST: gi|58676165|gb|CK064852.1|CK064852
EST:     GTCTGCAACAAGTTCAGTCCAGGAGTCCACAGATTCCTGGGCCAGCTCAG                         AGTATCAAGACAGAGATGAATCCCATTTTGACACCAAGGTCAGCAGGTCCT
genomic: GTCTGCAACAAGTTCAGTCCAGGAGTCCACAGATTCCTGGGCCAGCTCAGgttagtcttc ... ttattagcagAGTATCAAGACAGAGATGAATCCCATTTTGACACCAAGGTCAGCAGGTCCT
EST: gi|88290429|gb|CI665218.1|CI665218
EST:     GTCTGCAACAAGTTCAGTCCAGGAGTCCACAGATTCCTGGGCCAGCTCAG                         AGTATCAAGACAGAGATGAATCCCATTTTGACACCAAGGTCAGCAGGTCCT
genomic: GTCTGCAACAAGTTCAGTCCAGGAGTCCACAGATTCCTGGGCCAGCTCAGgttagtcttc ... ttattagcagAGTATCAAGACAGAGATGAATCCCATTTTGACACCAAGGTCAGCAGGTCCT

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: 68 (upstream exon), 66 (downstream exon)
Score: 38

GCAAATTTTGCATGGTACTGTTGGTGGTCTGTCAGGCAGTCTGCAACAAGTTCAGTCCAGGAGTCCACAGATTCCTGGGCCAGCTCAGgttagtcttc ... ttattagcagAGTATCAAGACAGAGATGAATCCCATTTTGACACCAAGGTCAGCAGGTCCTGAGGGGTCATTTATTGGTGTCCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacaaaaagaataaatgtcaacatgtattcctaatattattcatattattagcagAGTATCAAGACAGAGATGAATCCCATTTTGACACCAAGGTCAGCAGGTCCTGAGGGGTCATTTATTGGTGTCCAAG
                            tcctaat  putative branch site (score: 38)
                      atgtattcctaatatt  TA-rich tract