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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATACTACACACTCTTGCATTCTTAGCAGGTGTCATGATTTGGTCACAGgtatagaataattacttgtacctgccaagcatcttatatgtttattgcacatatatttttaccttcattgcattcaaaattaaattagcttccagttgtc...

Basic information

species Oryza sativa
transcript LOC_Os02g45650.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g45650.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM5G813909_T01 (Zea mays), 5'ss of exon 4
AAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATACTACACACTCTTGCATTCTTAGCAGGTGTCATGATTTGGTCACAGgtatagaataattacttgtacctgccaagcatcttatatgtttattgcacatatatttttaccttcattgcattcaaaattaaattagcttccagttgtc------------
|||||||||||| |||  |||| || ||| || | |||||| ||||||||| ||||||| ||||| |||||||| |||  |||| ||||||| ||||||   ||||||| ||  |   | |  | |||  ||||||||        | ||  ||||| | | |   |||  | |||  || |  ||  |   |||             
AAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAGgtact-aataatt-ctcctcattac--accataatatatgtt--------aaattcttttatccttagcccatctataatataactgactggcttctgtagcttttgacact

upper sequence: LOC_Os02g45650.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G702159_T01 (Zea mays), 5'ss of exon 4
AAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATACTACACACTCTTGCATTCTTAGCAGGTGTCATGATTTGGTCACAGgtatagaataattacttgtacctgccaagcatcttatatgtttattgcacatatatttttaccttcattgcattcaaaa--ttaaattagcttccagttgtc
|||||||||||| |||  ||||||| ||| || |||||||| ||||||||| ||||||| |||||||||||||| |||| |||| |||||||| |||||   ||||||  |    |      |   || ||| || |   |||    | |||    | ||  | |  ||   ||   ||    ||||||   |   | 
AAATCTGGAGAGTTAGTTACCAATGTTGGGCTGAATGCTGAGAATGAGATAATACACACCCTTGCATTCTTAGCTGGTGCCATGGTTTGGTCAAAGgtact-aataatctccctaaatcataatagatgttaaat-tcatttgtcattttatacccatctgtaatatatctgaatgctttttatagcttttggcactt

upper sequence: LOC_Os02g45650.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA18G47190.1 (Glycine max), 5'ss of exon 4
AAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATACTACACACTCTTGCATTCTTAGCAGGTGTCATGATTTGGTCACAGgtatagaataattacttgtacctgcca--------agcatcttatatgtttattgcacatatatttttaccttca-ttgcattcaaaattaaattagcttccagttgtc
| ||| |||||  |    || |  ||  | || |||||||| ||||| ||||| || || ||||| || ||||| || || ||||||||||||||||| |    |    |||| |   | | |        || |  || |  || ||||   |||| |||   |||  || ||  ||| |        | | ||||        
ATATCAGGAGATTTTATGACAATAGCCAGTCTCAATGCTGAGAATGAAATACTGCATACCCTTGCCTTTTTAGCTGGGGTGATGATTTGGTCACAGGtgtgtttttgacactttttattactagagaatatagtaatttttgggtgtattatgcata-attgagaccaccagttttatttactccatgttcaacttca-------

upper sequence: LOC_Os02g45650.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA09G39150.1 (Glycine max), 5'ss of exon 4
AAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATACTACACACTCTTGCATTCTTAGCAGGTGTCATGATTTGGTCACAGgtata-----gaataattacttgtacctgccaagcatcttatatgtttattgcacatatatttttaccttcatt---gcattcaaaattaa-attagcttccagttgtc---------------------------------------------------------------------------------
||||| |||||  |    || |  |||||  | |||||||| ||||| ||||| || || ||||| |||||||||||  | |||||||||||||||||||      ||   | || |  |        |   | |   || ||| || |   | ||||  |   |   ||   |||   ||   ||    ||||||   | ||                                                                                   
AAATCAGGAGATTTTATGACAATAGCTGGTTTCAATGCTGAGAATGAAATACTGCATACCCTTGCCTTCTTAGCAGGGCTGATGATTTGGTCACAGgtatgcttctgacatagtaatgctgaagttttattttttggaatatttttttcttttttattactttttgggttttggcagataatgatagtgctagctttttggtgcttctgataactgtgcatttgaattatcaatctaatatctacattttaataaactttattgtgcatgactacctattgtgcag

upper sequence: LOC_Os02g45650.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv15s0046g02040.t01 (Vitis vinifera), 5'ss of exon 4
AAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATACTACACACTCTTGCATTCTTAGCAGGTGTCATGATTTGGTCACAGgtatagaataattacttgtacctgccaagcatcttatatgtttattgcacatatatttttaccttcattgcattcaaaattaaattagcttccagt--tgtc---
||||| |||||  |   |      | |||| ||||||| || ||||||||||| || || ||||| |||||||| ||||| |||||||||||||||||  |||    ||   | ||      ||| || | |   |||| ||    ||    |   |  |  | || | |    |||   |  |||||   |   ||    
AAATCAGGAGACTTTCTAGTGGTAGTTGGCTTAAATGCAGAGAATGAGATACTGCATACCCTTGCGTTCTTAGCTGGTGTTATGATTTGGTCACAGgtgcagatctcttgtgtttattc-tgaaggatatgacccgtttttt---tattggctgaaaaatctagtggagtgtctattgtgt-ggcttctgatatcgttatt

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|88578235|gb|CI687155.1|CI687155
EST:     ACTCTTGCATTCTTAGCAGGTGTCATGATTTGGTCACAG                         ATCACAGACTTACCATTCTCTCTTTATTCAACATTTGTTATTGAAGCTAAA
genomic: ACTCTTGCATTCTTAGCAGGTGTCATGATTTGGTCACAGgtatagaata ... tgcaatgcagATCACAGACTTACCATTCTCTCTTTATTCAACATTTGTTATTGAAGCTAAA
EST: gi|88392342|gb|CI612816.1|CI612816
EST:     AGATACTACACACTCTTGCATTCTTAGCAGGTGTCATGATTTGGTCACAG                         ATCACAGACTTACCATTCTCTCTTTATTCAACATTTGTTATTGAAGCTAAA
genomic: AGATACTACACACTCTTGCATTCTTAGCAGGTGTCATGATTTGGTCACAGgtatagaata ... tgcaatgcagATCACAGACTTACCATTCTCTCTTTATTCAACATTTGTTATTGAAGCTAAA
EST: gi|58671695|gb|CK060381.1|CK060381
EST:     AGATACTACACACTCTTGCATTCTTAGCAGGTGTCATGATTTGGTCACAG                         ATCACAGACTTACCATTCTCT
genomic: AGATACTACACACTCTTGCATTCTTAGCAGGTGTCATGATTTGGTCACAGgtatagaata ... tgcaatgcagATCACAGACTTACCATTCTCT
EST: gi|58678385|gb|CK067072.1|CK067072
EST:     AGATACTACACACTCTTGCATTCTTAGCAGGTGTCATGATTTGGTCACAG                         ATCACAGACTTACCATTCTCTCTTTATTCAACATTTGTTATTGAAGCTAAA
genomic: AGATACTACACACTCTTGCATTCTTAGCAGGTGTCATGATTTGGTCACAGgtatagaata ... tgcaatgcagATCACAGACTTACCATTCTCTCTTTATTCAACATTTGTTATTGAAGCTAAA
EST: gi|58678409|gb|CK067096.1|CK067096
EST:     AGATACTACACACTCTTGCATTCTTAGCAGGTGTCATGATTTGGTCACAG                         ATCACAGACTTACCATTCTCTCTTTATTCAACATTTGTTATTGAAGCTAAA
genomic: AGATACTACACACTCTTGCATTCTTAGCAGGTGTCATGATTTGGTCACAGgtatagaata ... tgcaatgcagATCACAGACTTACCATTCTCTCTTTATTCAACATTTGTTATTGAAGCTAAA
EST: gi|58686372|gb|CK075059.1|CK075059
EST:     AGATACTACACACTCTTGCATTCTTAGCAGGTGTCATGATTTGGTCACAG                         ATCACAGACTTACCATTCTCTCTTTATTCAACATTTGTTATTGAAGCTAAA
genomic: AGATACTACACACTCTTGCATTCTTAGCAGGTGTCATGATTTGGTCACAGgtatagaata ... tgcaatgcagATCACAGACTTACCATTCTCTCTTTATTCAACATTTGTTATTGAAGCTAAA
EST: gi|58683468|gb|CK072155.1|CK072155
EST:     AGATACTACACACTCTTGCATTCTTAGCAGGTGTCATGATTTGGTCACAG                         ATCACAGACTTACCATTCTCTCTTTATTCAACATTTGTTATTGAAGCTAAA
genomic: AGATACTACACACTCTTGCATTCTTAGCAGGTGTCATGATTTGGTCACAGgtatagaata ... tgcaatgcagATCACAGACTTACCATTCTCTCTTTATTCAACATTTGTTATTGAAGCTAAA
EST: gi|58664452|gb|CK053138.1|CK053138
EST:     AGATACTACACACTCTTGCATTCTTAGCAGGTGTCATGATTTGGTCACAG                         ATCACAGACTTACCATTCTCTCTTTATTCAACATTTGTTATTGAAGCTAAA
genomic: AGATACTACACACTCTTGCATTCTTAGCAGGTGTCATGATTTGGTCACAGgtatagaata ... tgcaatgcagATCACAGACTTACCATTCTCTCTTTATTCAACATTTGTTATTGAAGCTAAA
EST: gi|58589625|gb|CF987933.1|CF987933
EST:     AGATACTACACACTCTTGCATTCTTAGCAGGTGTCATGATTTGGTCACAG                         ATCACAGACTTACCATTCTCTCTTTATTCAACATTTGTTATTGAAGCTAAA
genomic: AGATACTACACACTCTTGCATTCTTAGCAGGTGTCATGATTTGGTCACAGgtatagaata ... tgcaatgcagATCACAGACTTACCATTCTCTCTTTATTCAACATTTGTTATTGAAGCTAAA
EST: gi|58657010|gb|CK045690.1|CK045690
EST:     AGATACTACACACTCTTGCATTCTTAGCAGGTGTCATGATTTGGTCACAG                         ATCACAGACTTACCATTCTCTCTTTATTCAACATTTGTTATTGAAGCTAAA
genomic: AGATACTACACACTCTTGCATTCTTAGCAGGTGTCATGATTTGGTCACAGgtatagaata ... tgcaatgcagATCACAGACTTACCATTCTCTCTTTATTCAACATTTGTTATTGAAGCTAAA
EST: gi|88328438|gb|CI676643.1|CI676643
EST:     ACTCTTGCATTCTTAGCAGGTGTCATGATTTGGTCACAG                         ATCACAGACTTACCATTCTCTCTTTATTCAACATTTGTTATTGAAGCTAAA
genomic: ACTCTTGCATTCTTAGCAGGTGTCATGATTTGGTCACAGgtatagaata ... tgcaatgcagATCACAGACTTACCATTCTCTCTTTATTCAACATTTGTTATTGAAGCTAAA

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), 66 (downstream exon)
Score: 26

AAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATACTACACACTCTTGCATTCTTAGCAGGTGTCATGATTTGGTCACAGgtatagaata ... tgcaatgcagATCACAGACTTACCATTCTCTCTTTATTCAACATTTGTTATTGAAGCTAAACATGGTTTTAACAAG




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