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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGAAATCCATGAAGCTGGGACTTTTACCTACCGAAGTGATGTTTACAGTTTTGGCGTGGTAATGCTAGAACTTCTCACTGGCCGTAAACCATATGACAGgtcagtgattcaccgtaatatgcatttcttaattttagtttcataattgtgttagatcaattgtctccaaatgttgtctgaactttctagtttgcttgcttattttccgttacaatatgcag

Basic information

species Oryza sativa
transcript LOC_Os02g07960.3
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07960.2 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G335638_T01 (Zea mays), 5'ss of exon 15
CTGAAATCCATGAAGCTGGGACTTTTACCTACCGAAGTGATGTTTACAGTTTTGGCGTGGTAATGCTAGAACTTCTCACTGGCCGTAAACCATATGACAGgtcagtgattcaccgtaatatgcatttcttaattttag--tttcataattgtgttagatcaattgtctccaaatgttgtctgaactttctagtttgcttgcttattttccgttacaatatgcag
|||||||||||||| ||| | |||||||    | ||| || || || ||||| || ||||| |||||||||||||| ||||| ||||| |||||||||||||||| ||| ||  | ||||||||| | | ||    ||  |||   |||| | ||  |||| || ||||| ||   |   |     || |||  | |||  ||||     |||  |||||||||
CTGAAATCCATGAATCTGAGCCTTTTACTCGTCAAAGCGACGTATATAGTTTGGGTGTGGTGATGCTAGAACTTCTTACTGGTCGTAAGCCATATGACAGgtcagagatccattgcaatatgcatgt-tgaacaagagccttttgcaattat-ttgaatcacttctctcctaaaaattcat-----ttttag--tacttctttat-----gttggaatatgcag

upper sequence: LOC_Os02g07960.2 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G124270_T01 (Zea mays), 5'ss of exon 1
CTGAAATCCATGAAGCTGGGACTTTTACCTACCGAAGTGATGTTTACAGTTTTGGCGTGGTAATGCTAGAACTTCTCACTGGCCGTAAACCATATGACAGgtcagtgattcaccgtaatatgcatttcttaattttagtttcat--aattgtgttagatcaattgtctccaaatgttgtctgaactttctagtttgcttgcttattttccgttacaatatgcag
|||||||||||||  ||| | |||||||  | || || || || || ||||| || ||||| |||||||||||||| ||||| ||||| |||||||||||||||| ||| ||  ||||||||||| | | ||    || ||  |  |||| | ||  |||| || ||||| ||         ||||   |      |||  ||||     |||  |||||||||
CTGAAATCCATGACTCTGAGCCTTTTACTCAGCGCAGCGACGTATATAGTTTCGGTGTGGTGATGCTAGAACTTCTTACTGGTCGTAAGCCATATGACAGgtcagagatccattgtaatatgcatgt-taaacaagagcttttttcaattat-ttgaatcacttctctcctaa--------aaactcatttcacaacttctttat-----gttggaatatgcag

upper sequence: LOC_Os02g07960.2 (Oryza sativa), 5'ss of exon 15
lower sequence: GLYMA15G07520.1 (Glycine max), 5'ss of exon 15
CTGAAATCCATGAAGCTGGGACTTTTACCTACCGAAGTGATGTTTACAGTTTTGGCGTGGTAATGCTAGAACTTCTCACTGGCCGTAAACCATATGACAGgtcagtgattcacc--gtaatatgcatttcttaatt--ttagtttcataattgtgt-tagatcaattgtctccaaatgttgtctgaactttctagtttgcttgcttattttccgttacaatatgcag
||  |     |||  |||| | || |||  | | ||||||||| | ||||||||| || ||||||||||||||||||||||| || ||| | ||||| | || ||| ||||     |||||    ||   |   ||  ||| |     |||  |   || | ||  |      |||   ||| | || | |  | |||   |||| |    || | |||  ||  ||
CTCCAGAATTTGAGTCTGGAAGTTATACGCAGCAAAGTGATGTCTTCAGTTTTGGTGTCGTAATGCTAGAACTTCTCACTGGACGAAAATCTTATGAAAAgtgagtaattccattagtaattaagatagttgtgttcattattccagcaatgatacctaaaccagcttaacagaaaccatgtttaaaatattgaattt---tgctaaaacaccat-acatgatttag

upper sequence: LOC_Os02g07960.2 (Oryza sativa), 5'ss of exon 15
lower sequence: GLYMA13G31780.1 (Glycine max), 5'ss of exon 14
CTGAAATCCATGAAGCTGGGACTTTTACCTACCGAAGTGATGTTTACAGTTTTGGCGTGGTAATGCTAGAACTTCTCACTGGCCGTAAACCATATGACAGgtcagtgattc----accg--taatatgcatttcttaattttagtttc--ataattgtgttagatcaattgtctccaaatgttgtctgaactttctagtttgcttgcttattttccgttacaatatgcag
||  |     |||  |||| | || |||  | | ||||||||| | ||||||||| || |||||||||||||| |||||||| || ||| | ||||||| || ||| ||||    ||    ||| ||   | | || ||| |  ||||  | |||  |   || | ||  |   |||     ||| | || | |  | ||||   ||  |    || |  ||   |  ||
CTCCAGAATTTGAGTCTGGAAGTTATACGCAGCAAAGTGATGTCTTCAGTTTTGGTGTCGTAATGCTAGAACTCCTCACTGGACGAAAATCCTATGACAAgtgagtaattccattactaactaagatagttgtgttcattatcttttccaacaatgataccagcttaacagaagcca-----tgtttaaaatattgaatttg---gcaaaaacaccat-gcatgttttag

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|58669825|gb|CK058511.1|CK058511
EST:     TTTGGCGTGGTAATGCTAGAACTTCTCACTGGCCGTAAACCATATGACAG                         TTCTCGTCCTCGTGCTGAAGAACATCTTGTTAGATGGGCTGATTCTCAATT
genomic: TTTGGCGTGGTAATGCTAGAACTTCTCACTGGCCGTAAACCATATGACAGgtcagtgatt ... caatatgcagTTCTCGTCCTCGTGCTGAACAACATCTTGTTAGATGGGCTGATTCTCAATT
EST: gi|29621906|gb|CB626917.1|CB626917
EST:     TTTGGCGTGGTAATGCTAGAACTTCTCACTGGCCGTAAACCATATGACAG                         TTCTCGTCCTCGTGCTGAACAACATCTTGTTAGATGGGCTGATTCTCAATT
genomic: TTTGGCGTGGTAATGCTAGAACTTCTCACTGGCCGTAAACCATATGACAGgtcagtgatt ... caatatgcagTTCTCGTCCTCGTGCTGAACAACATCTTGTTAGATGGGCTGATTCTCAATT
EST: gi|58687945|gb|CK076632.1|CK076632
EST:     TGGTAATGCTAGAACTTCTCACTGGCCGTAAACCATATGACAG                         TTCTCGTCCTCGTGCTGAACAACATCTTGTTAGATGGGCTGATTCTCAATT
genomic: TGGTAATGCTAGAACTTCTCACTGGCCGTAAACCATATGACAGgtcagtgatt ... caatatgcagTTCTCGTCCTCGTGCTGAACAACATCTTGTTAGATGGGCTGATTCTCAATT
EST: gi|29656568|gb|CB652843.1|CB652843
EST:     TTTGGCGTGGTAATGCTAGAACTTCTCACTGGCCGTAAACCATATGACAG                         TTCTCGTCCTCGTGCTGAACAACATCTTGTTAGATGGGCTGATTCTCAATT
genomic: TTTGGCGTGGTAATGCTAGAACTTCTCACTGGCCGTAAACCATATGACAGgtcagtgatt ... caatatgcagTTCTCGTCCTCGTGCTGAACAACATCTTGTTAGATGGGCTGATTCTCAATT
EST: gi|58611356|gb|CK039068.1|CK039068
EST:     TTTGGCGTGGTAATGCTAGAACTTCTCACTGGCCGTAAACCATATGACAG                         TTCTCGTCCTCGTGCTGAACAACATCTTGTTAGATGGGCTGATTCTCAATT
genomic: TTTGGCGTGGTAATGCTAGAACTTCTCACTGGCCGTAAACCATATGACAGgtcagtgatt ... caatatgcagTTCTCGTCCTCGTGCTGAACAACATCTTGTTAGATGGGCTGATTCTCAATT
EST: gi|29626065|gb|CB631076.1|CB631076
EST:     TTTGGCGTGGTAATGCTAGAACTTCTCACTGGCCGTAAACCATATGACAG                         TTCTCGTCCTCGTGCTGAACAACATCTTGTTAGATGGGCTGATTCTCAATT
genomic: TTTGGCGTGGTAATGCTAGAACTTCTCACTGGCCGTAAACCATATGACAGgtcagtgatt ... caatatgcagTTCTCGTCCTCGTGCTGAACAACATCTTGTTAGATGGGCTGATTCTCAATT
EST: gi|29626028|gb|CB631039.1|CB631039
EST:     TTTGGCGTGGTAATGCTAGAACTTCTCACTGGCCGTAAACCATATGACAG                         TTCTCGTCCTCGTGCTGAACAACATCTTGTTAGATGGGCTGATTCTCAATT
genomic: TTTGGCGTGGTAATGCTAGAACTTCTCACTGGCCGTAAACCATATGACAGgtcagtgatt ... caatatgcagTTCTCGTCCTCGTGCTGAACAACATCTTGTTAGATGGGCTGATTCTCAATT
EST: gi|29640907|gb|CB645914.1|CB645914
EST:     TTTGGCGTGGTAATGCTAGAACTTCTCACTGGCCGTAAACCATATGACAG                         TTCTCGTCCTCGTGCTGAACAACATCTTGTTAGATGGGCTGATTCTCAATT
genomic: TTTGGCGTGGTAATGCTAGAACTTCTCACTGGCCGTAAACCATATGACAGgtcagtgatt ... caatatgcagTTCTCGTCCTCGTGCTGAACAACATCTTGTTAGATGGGCTGATTCTCAATT
EST: gi|66927345|gb|CX114193.1|CX114193
EST:     TTTGGCGTGGTAATGCTAGAACTTCTCACTGGCCGTAAACCATATGACAG                         TTCTCGTCCTCGTGCTGAACAACATCTTGTTAGATGGGCTGATTCTCAATT
genomic: TTTGGCGTGGTAATGCTAGAACTTCTCACTGGCCGTAAACCATATGACAGgtcagtgatt ... caatatgcagTTCTCGTCCTCGTGCTGAACAACATCTTGTTAGATGGGCTGATTCTCAATT
EST: gi|29674397|gb|CB670672.1|CB670672
EST:     TTTGGTGTGGTAATGCTAGAACTTCTCACTGGCCGTAAACCATATGACAG                         TTCTCGTCCTCGTGCTGAACAACATCTTGTTAGATGGGCTGATTCTCAATT
genomic: TTTGGCGTGGTAATGCTAGAACTTCTCACTGGCCGTAAACCATATGACAGgtcagtgatt ... caatatgcagTTCTCGTCCTCGTGCTGAACAACATCTTGTTAGATGGGCTGATTCTCAATT
EST: gi|29671438|gb|CB667713.1|CB667713
EST:     TTTGGCGTGGTAATGCTAGAACTTCTCACTGGCCGTAAACCATATGACAG                         TTCTCGTCCTCGTGCTGAACAACATCTTGTTAGATGGGCTGATTCTCAATT
genomic: TTTGGCGTGGTAATGCTAGAACTTCTCACTGGCCGTAAACCATATGACAGgtcagtgatt ... caatatgcagTTCTCGTCCTCGTGCTGAACAACATCTTGTTAGATGGGCTGATTCTCAATT
EST: gi|29638004|gb|CB643013.1|CB643013
EST:     TTTGGCGTGGTAATGCTAGAACTTCTCACTGGCCGTAAACCATATGACAG                         TTCTCGTCCTCGTGCTGAACAACATCTTGTTAGATGGGCTGATTCTCAATT
genomic: TTTGGCGTGGTAATGCTAGAACTTCTCACTGGCCGTAAACCATATGACAGgtcagtgatt ... caatatgcagTTCTCGTCCTCGTGCTGAACAACATCTTGTTAGATGGGCTGATTCTCAATT
EST: gi|29631499|gb|CB636508.1|CB636508
EST:     GCCGTAAACCATATGACAG                         TTCTCGTCCTCGTGCTGAACAACATCTTGTTAGATGGGCTGATTCTCAATT
genomic: GCCGTAAACCATATGACAGgtcagtgatt ... caatatgcagTTCTCGTCCTCGTGCTGAACAACATCTTGTTAGATGGGCTGATTCTCAATT
EST: gi|58690978|gb|CK079665.1|CK079665
EST:     TTTGGCGTGGTAATGCTAGAACTTCTCACTGGCCGTAAACCATATGACAG                         TTCTCGTCCTCGTGCTGAACAACATCTTGTTAGATGGGCTGATTCTCAATT
genomic: TTTGGCGTGGTAATGCTAGAACTTCTCACTGGCCGTAAACCATATGACAGgtcagtgatt ... caatatgcagTTCTCGTCCTCGTGCTGAACAACATCTTGTTAGATGGGCTGATTCTCAATT

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: 61 (upstream exon), 62 (downstream exon)
Score: 34

CTGAAATCCATGAAGCTGGGACTTTTACCTACCGAAGTGATGTTTACAGTTTTGGCGTGGTAATGCTAGAACTTCTCACTGGCCGTAAACCATATGACAGgtcagtgatt ... caatatgcagTTCTCGTCCTCGTGCTGAACAACATCTTGTTAGATGGGCTGATTCTCAATTTCATGACATTGAGTCCATATCAAAGATGGTTGATCCTTCTATTCAAGGA




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