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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTTATTATCTGGTTGCTTGCTATTATCTACTTCATATCTGGTGTACCTGGTGCTTATGTGTTATGGTACCGCCCTCTTTATAATGCAATGAGgttggatatattaaatgagcattgttggctacacaactttttcaccttttaaaatatctaatacgctagtgtcttgttcttttttcaatgcctgttacag

Basic information

species Oryza sativa
transcript LOC_Os05g42330.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g42330.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G174730_T01 (Zea mays), 5'ss of exon 7
GTGTTATTATCTGGTTGCTTGCTATTATCTACTTCATATCTGGTGTACCTGGTGCTTATGTGTTATGGTACCGCCCTCTTTATAATGCAATGAGgttggatatattaaatgagcattgttggctacacaactttttcacc-ttttaaaatatctaatacgctagtgtcttgttcttttttcaatgcctgttacag
||||||| |||||| ||||||| ||||||||||||||||||||||  ||||| ||||||||||||||||| || ||||||||||||||||||||||||  |||||  |   | |  |     |   |||  ||||||||| ||| ||  |   | |||  |   | ||||||| |  ||| |||  ||| | |||
GTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGCGCCTGGGGCTTATGTGTTATGGTATCGACCTCTTTATAATGCAATGAGgttgtttatatgcatccatcccttaacacagtacatttttttcaccatttcaatgttcattataatcatatatcttgtt-tcgtttgaatatctgcttcag

upper sequence: LOC_Os05g42330.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G100809_T01 (Zea mays), 5'ss of exon 7
GTGTTATTATCTGGTTGCTTGCTATTATCTACTTCATATCTGGTGTACCTGGTGCTTATGTGTTATGGTACCGCCCTCTTTATAATGCAATGAGgttggatatattaaatgagcattgttggctacacaactttttcacc-ttttaaaatatctaatacgctagtgtcttgttcttttttcaatgcctgttacag
||||||| |||||| ||||||| ||||||||||||||||||||||| || || ||||||||||||||||| || ||||||||||||||||||||||||  |||||  |     |||   |   || |  ||||||||| | ||| ||  |  ||  |   |   | ||||||| || ||| |||| ||| |  ||
GTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGTGCCCGGGGCTTATGTGTTATGGTATCGGCCTCTTTATAATGCAATGAGgttgtttatatggatc---catctcttaatatattactttttcaacgtttcaatgttccttgtgatcatatatcttgtt-ttatttgaatgtctgctttag

upper sequence: LOC_Os05g42330.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA06G45160.1 (Glycine max), 5'ss of exon 8
GTGTTATTATCTGGTTGCTTGCTATTATCTACTTCATATCTGGTGTACCTGGTGCTTATGTGTTATGGTACCGCCCTCTTTATAATGCAATGAGgttggatatattaaatgagcattgttggctacacaactttttcaccttttaa----aatatctaatacgctagtgtcttgttcttttttcaatgcctgttacag-------
||   |  |||||||| |||||||||||||| || || |||||||  || ||  | |||||||| ||||| ||||||||||||  ||| ||||||| |    | ||  || ||  ||  ||      ||| |||| ||  ||  ||     ||||||  | |   ||| |      |  |||   |  |     | |        
GTCCAACCATCTGGTTTCTTGCTATTATCTATTTTATTTCTGGTGCTCCAGGATCCTATGTGTTGTGGTATCGCCCTCTTTATCGTGCTATGAGgtag----tgttcgatcagatttaatg------caatttttgcaatttagaatagggatatctg-ttcaagagttttacagccgatttgttaaactgaaaagaaaagaaaa

upper sequence: LOC_Os05g42330.1 (Oryza sativa), 5'ss of exon 7
lower sequence: AT2G20840.1 (Arabidopsis thaliana), 5'ss of exon 7
GTGTTATTATCTGGTTGCTTGCTATTATCTACTTCATATCTGGTGTACCTGGTGCTTATGTGTTATGGTACCGCCCTCTTTATAATGCAATGAGgttggatatattaaatgagcattgttggctacacaactttttcaccttttaaaatatctaatacgctagtgtcttgttcttttttcaat-gcctgttacag--------------------------------------------------------------
||   |  || ||||| || ||||||||||| |||||||| || || ||||| || |||||  | ||||| ||||||||||||  ||| |||||||     ||   |  | ||  || |    ||   || | | | | ||  ||     ||   |   |   | | | |          ||  |  | || |||                                                              
GTCCAACAATATGGTTTCTAGCTATTATCTATTTCATATCAGGGGTTCCTGGAGCGTATGTTATGTGGTATCGCCCTCTTTATCGTGCCATGAGgt-attcatgccacttaagatttttccttta---aaatatcttatctgctactgcgtcgtgtgttcctttatttagagggaaaacaaaaagagtattccagatagcatcgtagttaagagtcaaaactttcattgagatgtgtgttgatttggttgtgtgcag

upper sequence: LOC_Os05g42330.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv00s0301g00030.t01 (Vitis vinifera), 5'ss of exon 8
GTGTTATTATCTGGTTGCTTGCTATTATCTACTTCATATCTGGTGTACCTGGTGCTTATGTGTTATGGTACCGCCCTCTTTATAATGCAATGAGgt---tggatatattaaatgagcattgttggctacacaactttttcaccttttaaaatatctaatacgctagtgtcttgttcttttttcaat--gcctgttacag
| || |  |||||||| ||||||||||||||||||||| | || || || || ||||||||||| |||||||| || ||||||  |||  | ||||   |   | |  |   || |  | | || ||  |   |||||  ||     ||| |    ||| | | | |  | ||||  ||| | ||   |  ||||    
GGGTAAAAATCTGGTTTCTTGCTATTATCTACTTCATAGCCGGGGTCCCAGGAGCTTATGTGTTGTGGTACCGTCCACTTTATCGTGCTTTTAGgtatttccttctccttcctgggtgtggctgtctgtat--cttttggactcagcaaagtcctcaattc-caattcacatgtttatttgttaaaaagaatgttgt--

upper sequence: LOC_Os05g42330.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv12s0059g01930.t01 (Vitis vinifera), 5'ss of exon 7
GTGTTATTATCTGGTTGCTTGCTATTATCTACTTCATATCTGGTGTACCTGGTGCTTATGTGTTATGGTACCGCCCTCTTTATAATGCAATGAGgttggatatattaaatgagcattgttggctacacaactttttcaccttttaaaatatctaatacgctagtgtcttgttcttttttcaatg--cctgttacag----
||   |  || ||||| ||||| || ||||||||| |||| || || || || ||||||||||| ||||| || |||||||||  ||| |||||||   || ||     ||   |||     |   ||  |  ||  | | |  | | ||   | ||    ||  |     |  |     |  |  ||||| ||      
GTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAGGAGCTTATGTGTTGTGGTATCGTCCTCTTTATCGTGCCATGAGgtactattta-----tggttattccaaacatgactcccattatatcatccacactagaca-tatatcagacttccaattgtaggggatgggtcctgtcacgccatt

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|428525|gb|D24677.1|D24677
EST:     GTACCTGGTGCTTATGTGTTATGGTACCGCCCTCTTTATAATGCAATGAG                         AACTGAGAGTNCTTTGAAGTTTGGGTGGTTTTTTCTGTTTTACCTG
genomic: GTACCTGGTGCTTATGTGTTATGGTACCGCCCTCTTTATAATGCAATGAGgttggatata ... cctgttacagAACTGAGAGTGCTTTGAAGTTTGGGTGGTTTTTTCTGTTTTACCTG
EST: gi|33803682|gb|CF327716.1|CF327716
EST:     GTACCTGGTGCTTATGTGTTATGGTACCGCCCTCTTTATAATGCAATGAG                         AACTGAGAGTGCTTTGAAGTTTGGGTGGTTTTTTCTGTTTTACCTG
genomic: GTACCTGGTGCTTATGTGTTATGGTACCGCCCTCTTTATAATGCAATGAGgttggatata ... cctgttacagAACTGAGAGTGCTTTGAAGTTTGGGTGGTTTTTTCTGTTTTACCTG
EST: gi|4881016|gb|AU065315.1|AU065315
EST:     GTACCTGGTGCTTATGTGTTATGGTACCGCCCTCTTTATAATGCAATGAG                         AACTGAGAGTGCTTTGAAGTTTGGGTGGTTTTTTCTGTTTTACCTG
genomic: GTACCTGGTGCTTATGTGTTATGGTACCGCCCTCTTTATAATGCAATGAGgttggatata ... cctgttacagAACTGAGAGTGCTTTGAAGTTTGGGTGGTTTTTTCTGTTTTACCTG

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: 63 (upstream exon), 69 (downstream exon)
Score: 26

GTGTTATTATCTGGTTGCTTGCTATTATCTACTTCATATCTGGTGTACCTGGTGCTTATGTGTTATGGTACCGCCCTCTTTATAATGCAATGAGgttggatata ... cctgttacagAACTGAGAGTGCTTTGAAGTTTGGGTGGTTTTTTCTGTTTTACCTG




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