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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATTGATAATGATGCAACAATTTGCTCTCCGCGAATCAAGAGAAGCACAAGACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAGgtagaagagctggtttttgcttacatgcctcccaccctggaaacttgaaaatctattttcttaactctatcatttgctgtcaacag

Basic information

species Oryza sativa
transcript LOC_Os01g06590.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g06590.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G165044_T01 (Zea mays), 5'ss of exon 5
CAATTGATAATGATGCAACAATTTGCTCTCCGCGAATCAAGAGAAGCACAAG---ACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAGgtagaaga----gctg-gtttttgct----tacatgcctcccaccctggaaacttgaaaatctattttcttaact----ctatcatttgctgtcaacag
     | | |||||| | || || |   ||  |||||| |||| ||||   |   |||||||||||| ||||||||||||||||||||| ||||| || ||||||   |      ||| ||||| |||        ||  ||     | ||||| ||  |||  | | ||  |||||     | |  |   | ||| | ||
---CGGTTCATGATGGACCACTTGGTCTTCTACGAATCGAGAGCAGCAGCTGCTGACCCCCACAGGGACATGAGACTGGACATTGACAACATGAGCTACGAGgtaagcggcggtactgcgttttcgctgttccgactgtgtcttgttccggaaattttgaaagatttcttagtaactaatgtttttgtcgtccgtccatag

upper sequence: LOC_Os01g06590.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G305901_T01 (Zea mays), 5'ss of exon 5
CAATTGATAATGATGCAACAATTTGCTCTCCGCGAATCAAGAGAAGCACAAG---ACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAGgta-gaagagctggtttttgcttacatgcctcccaccctggaaacttgaaaatctattttc--ttaactctatcatttgctgtcaacag
     | | |||||| | || || |   |   ||||||||||| ||||   |   |||||||||||| ||||||||||||||| ||||| ||||| || |||||| | || ||||  | |||||  ||     |   | | |||||  |||| || |  || |   |||  | ||  || | ||||  |||
---CGGTTCATGATGGACCAGTTGGTCTTTTACGAATCAAGAGCAGCAGCCGCTGACCCCCACAGGGACATGAGACTGGACATCGACAACATGAGCTACGAGgtaaggagtgctgcatcttgctc-caactgccttgctccggaaatctgaagattttcttccaactaatacaatatttcgttgtcctcag
















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|29684935|gb|CB681210.1|CB681210
EST:     AAGACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAG                         GACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTG
genomic: AAGACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAGgtagaagagc ... ctgtcaacagGACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTG
EST: gi|88993479|gb|CI110300.1|CI110300
EST:     AAGACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAG                         GACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTG
genomic: AAGACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAGgtagaagagc ... ctgtcaacagGACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTG
EST: gi|3760896|gb|C98150.1|C98150
EST:     AAGACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAG                         GACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTG
genomic: AAGACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAGgtagaagagc ... ctgtcaacagGACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTG
EST: gi|29684936|gb|CB681211.1|CB681211
EST:     AAGACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAG                         GACCTGCTGGCTTTGGGAGAATTTATTGGTAATGTCTGCACAGGCTTGGTG
genomic: AAGACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAGgtagaagagc ... ctgtcaacagGACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTG
EST: gi|396941343|gb|HO188552.1|HO188552
EST:     AAGACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAG                         GACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTG
genomic: AAGACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAGgtagaagagc ... ctgtcaacagGACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTG
EST: gi|88530273|gb|CI458653.1|CI458653
EST:     TTGACAATATGANTTATGAG                         GACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTG
genomic: TTGACAATATGAGTTATGAGgtagaagagc ... ctgtcaacagGACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTG

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), 50 (downstream exon)
Score: 14

CAATTGATAATGATGCAACAATTTGCTCTCCGCGAATCAAGAGAAGCACAAGACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAGgtagaagagc ... ctgtcaacagGACCTGCTGGCTTTGGGAGAATCTATTGGTAATGTCTGCACAGGCTTGGTGGACGAGAAAATCTCAGGTTGTGTGAGAGAAGTGATCTATTGCAGTTCTG




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