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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtacatgtgcatcaagaaggcttcctttcatgttttggatggtcagaatttaatattgaattactaactttgtcagGTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGTTATCGTGCATTTCCGATCGACCTTGTTCGGGAATTTGCCAGACAAATAT

Basic information

species Oryza sativa
transcript LOC_Os01g62080.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g62080.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G386991_T01 (Zea mays), 3'ss of exon 5
gtaagtacatgtgcatcaagaaggcttcctttca--tgttttggatggtcagaatttaatattgaattactaactttgtcagGTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGTTATCGTGCATTTCCGATCGACCTTGTTCGGGAATTTGCCAGACAAATAT
|||||| || ||| ||||||||||| || | |||||| |||| |||| | | |||||||||| | | | |||||||||||||| ||| || |||||| |||||||||| || ||||||||||| || ||| ||||||| || |||||||| || |||||||||||||||||||
gtaagtgaatatgcgtcaagaaggctatactttacttgtttttgatgatcaggttatgatattgaattgatgatctcttcagGTATTTGAGAAGCTTGGGCCAAGCCTATATGACTTTCTGCGAAAGAATAGCTACCGTTCATTTCCTATTGACCTTGTCCGAGAATTTGCCAGACAAATAT

upper sequence: LOC_Os01g62080.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA19G35800.1 (Glycine max), 3'ss of exon 3
--------------gtaagtacatgtgcatcaag---aaggcttcctttcatgttttggatggtcagaatttaatattgaattac-taactttgtcagGTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGTTATCGTGCATTTCCGATCGACCTTGTTCGGGAATTTGCCAGACAAATAT
|| | | | || || | | | | || | | | | | | || || || ||| | || ||||||||||||| ||| |||||||||||||| || || ||||| || || | ||||||| | || | || || ||||||||||| |||| ||||||| | |
gtaagtatttattgatatttgtaatttgattaaatgaaggaatgtgcattatcatgcgagttgaaaaacttgtggatggatttaaatggtttcaacagGTATTTGAGAAGCTTGGACCAAGCTTATACGATTTTCTCCGCAAAAACAATTATCGTTCTTTATCAATTGATCTTGTTCGGGAGTTTGGCAGACAACTTT

upper sequence: LOC_Os01g62080.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA03G33100.1 (Glycine max), 3'ss of exon 5
-----------------------------gtaagt-acatgtgcatcaaga-aggcttcctttcatgttttggatggtcagaa-tttaatattgaatt--actaactttgtcagGTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGTTATCGTGCATTTCCGATCGACCTTGTTCGGGAATTTGCCAGACAAATAT
||| | ||| | || | | | | ||| || || || | | | || || || ||| | | || ||||||||||||| ||| ||||||||||||||||| || ||||| || || || |||||| | ||||| || || ||||||||||| |||| ||||||| | |
gtaagtatttattgatatttgtaatttaattaaatgacaggaatgtctattcaatcatgcttaaatattctgtgagttaaaaaacttgcggatggatttaaatggtttcaacagGTATTTGAGAAGCTTGGACCAAGCTTATATGATTTTCTCCGCAAAAACAGCTATCGTTCTTTTCCTATTGATCTTGTTCGGGAGTTTGGCAGACAACTTT

upper sequence: LOC_Os01g62080.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT3G53570.4 (Arabidopsis thaliana), 3'ss of exon 7
-----------------------gtaagtacatgtgcatcaagaaggcttcct---ttcatgttttggatggtc----agaatttaatattgaatt--actaactttgtcagGTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGTTATCGTGCATTTCCGATCGACCTTGTTCGGGAATTTGCCAGACAAATAT
|||| | | | | | | | || | || || |||| || || || | | || ||||||||||||| ||| ||||||||||||||||| || ||||| || || || || ||| ||||||| || || ||||||||||| ||| ||||||| | |
gtaagtgctgttacctttatttgacaagtttgaggggaaaatgcaatttcttcacgcccaaatgttatgtgagttaaaagaacttgcgcatgggtttaaatggtttcaacagGTATTTGAGAAGCTTGGACCAAGCTTATATGATTTTCTCCGCAAAAACAGCTACCGTTCATTTCCCATTGATCTTGTTCGGGAGCTTGGCAGACAACTTT

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|117243444|gb|CT848361.1|CT848361
EST:     CTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATA                         GTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGT
genomic: CTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATAgtaagtacat ... actttgtcagGTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGT
EST: gi|58654607|gb|CK043287.1|CK043287
EST:     CTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATA                         GTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGT
genomic: CTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATAgtaagtacat ... actttgtcagGTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGT
EST: gi|29665089|gb|CB661364.1|CB661364
EST:     CTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATA                         GTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGT
genomic: CTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATAgtaagtacat ... actttgtcagGTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGT
EST: gi|29679261|gb|CB675536.1|CB675536
EST:     CTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATA                         GTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGT
genomic: CTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATAgtaagtacat ... actttgtcagGTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGT

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), 72 (downstream exon)
Score: 42

CTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATAgtaagtacat ... actttgtcagGTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGTTATCGTGCATTTCCGATCGACCTTGTTCGGGAATTTGCCAGACAAATAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcctttcatgttttggatggtcagaatttaatattgaattactaactttgtcagGTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGTTATCGTGCATTTCCGATCGACCTTGTTCGGGAATTTGCCAGACAAATAT
                                        tactaac  putative branch site (score: 42)
 ctttgtc  CT-rich tract
 agaatttaatattgaa  TA-rich tract