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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTAGCTGTATCTGGCTCCATGCTGGCCTAATCCATTTGGTTGTGAACATGCTGAGTTTACTGTTTATTGGAATCCGCCTTGAACAGCAATTTGGGTTCGgtaagtttcttactatgctgattcagtgtcatttttaactatgagaatacgttcttagtgttaacatatatctttgaatacatgccatctcatagaattt...

Basic information

species Oryza sativa
transcript LOC_Os09g35730.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g35730.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G033937_T01 (Zea mays), 5'ss of exon 2
ATTAGCTGTATCTGGCTCCATGCTGGCCTAATCCATTTGGTTGTGAACATGCTGAGTTTACTGTTTATTGGAATCCGCCTTGAACAGCAATTTGGGTTCGgtaagtttcttactatgctgattcagtgt-catttttaactatgaga--atacgttcttagtgttaacat----atatctttgaatacatg-ccatctcataga-attt---------------
|||||||| ||||||||||||||||||||||| |||||||||||||||||||| ||||| ||||||||||||||||| ||||| ||||||||||| || |||||| || | |  |      ||||   | ||     | ||||   |  || | || | ||| | ||  |    || | | |   | ||||  ||| |||  || | ||               
ATTAGCTGCATCTGGCTCCATGCTGGCCTAATTCATTTGGTTGTGAACATGCTAAGTTTGCTGTTTATTGGAATCCGTCTTGAGCAGCAATTTGGATTTGgtaagcttttaaaaaaatattttcatcttacaccaacatctatccaaccattcattttcagt-taaatgttccaatctttcttccttcatggtcatttcactgacactttttcctgcctgcaag

upper sequence: LOC_Os09g35730.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G116514_T01 (Zea mays), 5'ss of exon 2
ATTAGCTGTATCTGGCTCCATGCTGGCCTAATCCATTTGGTTGTGAACATGCTGAGTTTACTGTTTATTGGAATCCGCCTTGAACAGCAATTTGGGTTCGgtaagtttctta--ctatgctgattcagtgtcatttttaactatgagaatacgttc----ttagtgtt---aacatatatctttgaata-catgccatctcatagaattt--------------
|||||||| |||||||||||||||||||||||||||||||||||||||||||| ||||| ||||||||||||||||||||||| ||||||||||| || |||||| || | |    ||  | ||     |  | | |  |     |  || | ||     | ||||||   | |||    | || |    |||  || || | |   |||              
ATTAGCTGCATCTGGCTCCATGCTGGCCTAATCCATTTGGTTGTGAACATGCTAAGTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTGgtaagcttttaaaatcattttcatcgtacgcgaatatcgatc-caaccattcatttcagttaagtgttccaaccattcgcccttcatggtcatttca-ctgacactgtttttcctgcttgcaag

upper sequence: LOC_Os09g35730.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA09G26610.1 (Glycine max), 5'ss of exon 2
ATTAGCTGTATCTGGCTCCATGCTGGCCTAATCCATTTGGTTGTGAACATGCTGAGTTTACTGTTTATTGGAATCCGCCTTGAACAGCAATTTGGGTTCGgtaagtttcttac-tatgctgattcagtgtcatttttaactatgagaatacgttcttagtgttaacatatatctttgaatacatgccatctcatagaattt------
 | |  || || ||| | ||||||||  |  | ||||| | ||  |||||| ||||| |  | || ||||| || ||||||||||| ||||||||||| |||| |||||||   | |||| |||    || ||||  | | ||     | | ||  |||||| ||  ||||     |||   | |  ||   | | | |        
GTCACTTGCATTTGGTTGCATGCTGGAGTTGTTCATTTAGCTGCCAACATGTTGAGTCTGGTCTTCATTGGCATTCGCCTTGAACAACAATTTGGGTTTGgtatgtttcttttatctgcttatttcaggttatttgaagcaat-----tccatt--tagtgtgaatttatacacccgaagttaggaaataaaaaacattcaagtttt

upper sequence: LOC_Os09g35730.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT1G63120.1 (Arabidopsis thaliana), 5'ss of exon 2
ATTAGCTGTATCTGGCTCCATGCTGGCCTAATCCATTTGGTTGTGAACATGCTGAGTTTACTGTTTATTGGAATCCGCCTTGAACAGCAATTTGGGTTCGgtaagtttcttactatgctgattcagtgtcatttttaactatgagaatacgttcttagtgttaacatatatctttgaatacatg--ccatctcatagaattt-----------
 |    ||||| ||||| || |||||  | || ||| |  ||   |||||| |||||||  | || ||||| ||||||||||| ||||||||||| ||| |||||| |     |    ||    ||  | ||| || | |       ||   |||   |||| |         |  || |  ||  |  | ||   | | |            
CTCTCTTGTATGTGGCTTCACGCTGGTATCATTCATCTTCTTACAAACATGTTGAGTTTGATCTTCATTGGTATCCGCCTTGAGCAGCAATTTGGCTTCAgtaagtcttacctttacgtgtacaagaattattgttcagtcaagttttagactctctttgtttaatcgccaagtgaaacatttgatctttatcgcgggaatgttactgtgcag

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|38478939|gb|CF963072.1|CF963072
EST:     GCTGAGTTTACTGTTTATTGGAATCCGCCTTGAACAGCAATTTGGGTTCG                         TTCGCATTGGTGCCATATACCTGCTATCTGGTTTTGGCGGGAGTGTGTTGT
genomic: GCTGAGTTTACTGTTTATTGGAATCCGCCTTGAACAGCAATTTGGGTTCGgtaagtttct ... tacctactagTTCGCATTGGTGCCATATACCTGCTATCTGGTTTTGGCGGGAGTGTGTTGT
EST: gi|27578050|gb|CB000745.1|CB000745
EST:     GCTGAGTTTACTGTTTATTGGAATCCGCCTTGAACAGCAATTTGGGTTCG                         TTCGCATTGGTGCCATATACCTGCTATCTGGTTTTGGCGGGAGTGTGTTGT
genomic: GCTGAGTTTACTGTTTATTGGAATCCGCCTTGAACAGCAATTTGGGTTCGgtaagtttct ... tacctactagTTCGCATTGGTGCCATATACCTGCTATCTGGTTTTGGCGGGAGTGTGTTGT
EST: gi|58598617|gb|CK009145.1|CK009145
EST:     GCTGAGTTTACTGTTTATTGGAATCCGCCTTGAACAGCAATTTGGGTTCG                         TTCGCATTGGTGCCATATACCTGCTATCTGGTTTTGGCGGGAGTGTGTTGT
genomic: GCTGAGTTTACTGTTTATTGGAATCCGCCTTGAACAGCAATTTGGGTTCGgtaagtttct ... tacctactagTTCGCATTGGTGCCATATACCTGCTATCTGGTTTTGGCGGGAGTGTGTTGT
EST: gi|11442952|gb|BF430849.1|BF430849
EST:     GCTGAGTTTACTGTTTATTGGAATCCGCCTTGAACAGCAATTTGGGTTCG                         TTCGCATTGGTGCCATATACCTGCTATCTGGTTTTGGCGGGAGTGTGTTGT
genomic: GCTGAGTTTACTGTTTATTGGAATCCGCCTTGAACAGCAATTTGGGTTCGgtaagtttct ... tacctactagTTCGCATTGGTGCCATATACCTGCTATCTGGTTTTGGCGGGAGTGTGTTGT
EST: gi|218497364|gb|FG953028.1|FG953028
EST:     GCTGAGTTTACTGTTTATTGGAATCCGCCTTGAACAGCAATTTGGGTTCG                         TTCGCATTGGTGCCATATACCTGCTATCTGGTTTTGGCGGGAGTGTGTTGT
genomic: GCTGAGTTTACTGTTTATTGGAATCCGCCTTGAACAGCAATTTGGGTTCGgtaagtttct ... tacctactagTTCGCATTGGTGCCATATACCTGCTATCTGGTTTTGGCGGGAGTGTGTTGT
EST: gi|218485738|gb|FG958746.1|FG958746
EST:     GCTGAGTTTACTGTTTATTGGAATCCGCCTTGAACAGCAATTTGGGTTCG                         TTCGCATTGGTGCCATATACCTGCTATCTGGTTTTGGCGGGAGTGTGTTGT
genomic: GCTGAGTTTACTGTTTATTGGAATCCGCCTTGAACAGCAATTTGGGTTCGgtaagtttct ... tacctactagTTCGCATTGGTGCCATATACCTGCTATCTGGTTTTGGCGGGAGTGTGTTGT
EST: gi|29659848|gb|CB656123.1|CB656123
EST:     AGTTTACTGTTTATTGGAATCCGCCTTGAACAGCAATTTGGGTTCG                         TTCGCATTGGTGCCATATACCTGCTATCTGGTTTTGGCGGGAGTGTGTTGT
genomic: AGTTTACTGTTTATTGGAATCCGCCTTGAACAGCAATTTGGGTTCGgtaagtttct ... tacctactagTTCGCATTGGTGCCATATACCTGCTATCTGGTTTTGGCGGGAGTGTGTTGT
EST: gi|163928838|gb|EG711925.1|EG711925
EST:     GCTGAGTTTACTGTTTATTGGAATCCGCCTTGAACAGCAATTTGGGTTCG                         TTCGCATTGGTGCCATATACCTGCTATCTGGTTTTGGCGGGAGTGTGTTGT
genomic: GCTGAGTTTACTGTTTATTGGAATCCGCCTTGAACAGCAATTTGGGTTCGgtaagtttct ... tacctactagTTCGCATTGGTGCCATATACCTGCTATCTGGTTTTGGCGGGAGTGTGTTGT

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: 69 (upstream exon), 74 (downstream exon)
Score: 46

ATTAGCTGTATCTGGCTCCATGCTGGCCTAATCCATTTGGTTGTGAACATGCTGAGTTTACTGTTTATTGGAATCCGCCTTGAACAGCAATTTGGGTTCGgtaagtttct ... tacctactagTTCGCATTGGTGCCATATACCTGCTATCTGGTTTTGGCGGGAGTGTGTTGTCTGCGCTTTTCCTTCGTAATAACTACATCTCTGTTGGAGCCTCTGGAGC




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