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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGTCTCTTTTTGATGCAATACTGATTGTTCCAATGTTTCAGATTGCTTGGACCTTTTTTTCTATTTGCACAGGATTTGTGTACTTTCAAGAATATCAAgtgagtttctgtttgtaaatattatcgtaagcatgagaatcttgtgttgctcatgataaactaagggttttggattgccttcattag

Basic information

species Oryza sativa
transcript LOC_Os02g31874.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g31874.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G477146_T01 (Zea mays), 5'ss of exon 10
CCTGTCTCTTTTTGATGCAATACTGATTGTTCCAATGTTTCAGATTGCTTGGACCTTTTTTTCTATTTGCACAGGATTTGTGTACTTTCAAGAATATCAAgtgagtttctgtttgtaaatattatcgtaagcatgagaatcttgtgttgc-tcatgataaactaagggttttggattgccttcattag
 |||||  | |||||||||||||||||||||||||||||||| |||||||||||||| || |||||||| ||||||||||| |||||||||||||||||||| |||| |||||||| | || |    |||  | | ||||| ||  || | |||| ||||||  | | || ||  || |     | ||
GCTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGCTTGGACCTTCTTCTCTATTTGTACAGGATTTGTTTACTTTCAAGAATATCAAgtaagttcctgtttgtga-taatcggataatgaagtgaatcatgcatttcctcattataaaccgatgattctgtttttctgctgtcag

upper sequence: LOC_Os02g31874.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G144254_T03 (Zea mays), 5'ss of exon 7
CCTGTCTCTTTTTGATGCAATACTGATTGTTCCAATGTTTCAGATTGCTTGGACCTTTTTTTCTATTTGCACAGGATTTGTGTACTTTCAAGAATATCAAgtgagtttctgtttgtaaatattatcgtaagcatgag--aatcttgtgttgctca-tgataaactaagggttttggattgccttcattag
  ||||  | |||||||||||||||||||||||||||||||| |||||||||||||| || ||||| || ||||||||||| ||||||||||||||||||||  ||| ||||||| | ||| |    |||  |  ||  |||| ||  ||||| | | | |||||  |  || ||  || |||   | ||
GTTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGCTTGGACCTTCTTCTCTATCTGTACAGGATTTGTTTACTTTCAAGAATATCAAgtaggttcctgtttg-agataatgggataatgaaaagtgaatcatgcattgcttaattagaaactgggtattctgtttttcctctgtcag

upper sequence: LOC_Os02g31874.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA02G07510.2 (Glycine max), 5'ss of exon 11
CCTGTCTCTTTTTGATGCAATACTGATTGTTCCAATGTTTCAGATTGCTTGGACCTTTTTTTCTATTTGCACAGGATTTGTGTACTTTCAAGAATATCAAgtgagtttctgtttgtaaatattatcgtaagcatgagaatcttgtgttgctcatga-taaactaagggttttggattgccttcattag-------------------
 |||||  | ||||||||||| || |||||||| ||||||||||| || ||||| || || || || || ||||||||| | || |||||||||||||| || | || || |||      |   |  ||  ||   | | | | ||    |||||   |  |||||    ||  ||    ||  | |                    
ACTGTCATTGTTTGATGCAATTCTTATTGTTCCCATGTTTCAGATAGCATGGACTTTGTTCTCAATATGTACAGGATTTATATATTTTCAAGAATATCAGgt-acttcctcttt------aacttgatacacacaggtagcctttgcctttcatgggcactctaagaagatttaatcatattattgaagaaaactaattaaatatca

upper sequence: LOC_Os02g31874.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA16G26550.1 (Glycine max), 5'ss of exon 11
CCTGTCTCTTTTTGATGCAATACTGATTGTTCCAATGTTTCAGATTGCTTGGACCTTTTTTTCTATTTGCACAGGATTTGTGTACTTTCAAGAATATCAAgtgagtttctgtttgtaaatattatcgtaagcatgagaatcttgtgttgctcatga-taaactaagggttttggattgcctt-cattag------------------
 |||||  | ||||||||||| || |||||||| |||||||||||  | ||||| || || || || || ||||||||| | || |||||||||||||| || | ||||| | |  |  || |||     |||   | | | | || |   ||||   |  |||||    ||  ||    |   |||                    
ACTGTCATTGTTTGATGCAATTCTTATTGTTCCCATGTTTCAGATAACATGGACTTTCTTCTCAATCTGTACAGGATTTATCTATTTTCAAGAATATCAGgt-actttctctct-cacttaatat-----gcacaggtagcctttgctttgcatgggcactctaagaagatttaatcatataatattgaagaaaactaattaaatac

upper sequence: LOC_Os02g31874.2 (Oryza sativa), 5'ss of exon 10
lower sequence: AT3G26670.1 (Arabidopsis thaliana), 5'ss of exon 10
CCTGTCTCTTTTTGATGCAATACTGATTGTTCCAATGTTTCAGATTGCTTGGACCTTTTTTTCTATTTGCACAGGATTTGTGTACTTTCAAGAATATCAAgtgagtttctgtttgtaaatattatcgtaagcatgagaatcttgtgttgctcatgataaactaagggttttg--gattgccttcattag----------------------------------------------------------------
  ||||||| | ||||||||| || || |||||||||||||||||||||||||| || || || || || |||||||   | ||||||||||| | ||| ||   | | |   ||   | ||| |  |     |       ||   ||      |    | || || | | |  ||||   || || |                                                                 
ATTGTCTCTATATGATGCAATTCTCATAGTTCCAATGTTTCAGATTGCTTGGACTTTCTTCTCCATCTGTACAGGATGCATTTACTTTCAAGAGTTTCAGgttcatctat---tgactacattgtgatgcttttcctctcttttctttatcttcgggctaatacggatctagatgattagtttgatcattttgtcacagaatggtgtgggtttagggatagtcgcttagataattttcttcttccttaaacag

upper sequence: LOC_Os02g31874.2 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv14s0068g00780.t01 (Vitis vinifera), 5'ss of exon 10
CCTGTCTCTTTTTGATGCAATACTGATTGTTCCAATGTTTCAGATTGCTTGGACCTTTTTTTCTATTTGCACAGGATTTGTGTACTTTCAAGAATATCAAgtgagtttctgtttgtaaatattatcgtaagcatgagaatcttgtgttgctcatgataaactaagg-gttttggattgccttcattag---------------
  ||||  | ||||||||||| || |||||||| |||||||| ||||||||||| || || |||||||| ||||||||||| |||||||| |||||||| |||  | ||| | | |   |  | ||      || |||| || |||      |   |||  || |    ||||| |    || | | |               
GTTGTCATTGTTTGATGCAATTCTTATTGTTCCCATGTTTCAAATTGCTTGGACTTTCTTCTCTATTTGTACAGGATTTGTATACTTTCAGGAATATCAGgtgc-tctctctctctctct-ctctctctcttat-agaacctagtgactgaaaatttaacttaggtcaatttggctccattttacttgtgctgctcactggga

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|86593918|gb|CI260147.1|CI260147
EST:     TACTTTCAAGAATATCAA                         GTATTTGATACCCTGAGGATAGTGATGTTTGTACTGGGCATGACATCTGTC
genomic: TACTTTCAAGAATATCAAgtgagtttct ... ccttcattagGTATTTGATACCCTGAGGATAGTGATGTTTGTATTGGGCATGACATCTGTC




















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), 62 (downstream exon)
Score: 4

CCTGTCTCTTTTTGATGCAATACTGATTGTTCCAATGTTTCAGATTGCTTGGACCTTTTTTTCTATTTGCACAGGATTTGTGTACTTTCAAGAATATCAAgtgagtttct ... ccttcattagGTATTTGATACCCTGAGGATAGTGATGTTTGTATTGGGCATGACATCTGTCTTTATAGGCATCTCCTTACTGGCACCCGACGACAGTAAAG




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