Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTGGTACATACTATGAAGGTTTCTTTAGAAGACCTGTATAATGGTACTACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatcttgcacattctcgagtggttctttcatactgaaaggattgttatttgttattgtcttgaattatgaatatatacaatttataataataata...

Basic information

species Oryza sativa
transcript LOC_Os02g43930.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g43930.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G118731_T01 (Zea mays), 5'ss of exon 4
ATGTGGTACATACTATGAAGGTTTCTTTAGAAGACCTGTATAATGGTACTACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatcttgcacattctcgagtggt----tctttcatactgaa-aggattgttat-ttgttattgtcttgaattatgaatatatacaatttataataataata
||||||| ||||||||||||||||| ||||| || ||||| ||||| || ||||| ||||| ||||| || |||| |||| ||||| | ||||||||||||||||| | ||   | ||||| |  |||    | | |  |  |||| ||  ||| | | ||| ||| ||    |||  || | |||||| | |  |   ||     
ATGTGGTGCATACTATGAAGGTTTCCTTAGACGATCTGTACAATGGGACAACCAAGAAACTATCTTTATCGCGGAGTGCTTTGTGCTCCAAGTGCAAGGGgtaagt-ttttcttcgttctcaataggtaaattgtcttctggtgaacagttttgctgtgttgatat-gtagccaatgctgcaaatatactaat-gtctcaact---
















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|29665502|gb|CB661777.1|CB661777
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|33797209|gb|CF324468.1|CF324468
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|27576325|gb|CA999019.1|CA999019
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|218489299|gb|FG965759.1|FG965759
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAAGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|58667485|gb|CK056171.1|CK056171
EST:     CCNNNNNNNCTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: CC-AAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|58661241|gb|CK049921.1|CK049921
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|58672684|gb|CK061370.1|CK061370
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|58677822|gb|CK066509.1|CK066509
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|58603501|gb|CK014029.1|CK014029
EST:     GTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: GTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|58687630|gb|CK076317.1|CK076317
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTG
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGT-GGGGCAGCAGCAACTTGCCATGGTTGTCATGGTG
EST: gi|58597866|gb|CK008394.1|CK008394
EST:     AAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAACGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTG
genomic: AAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAA-GGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTG
EST: gi|58695486|gb|CK084173.1|CK084173
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|218485257|gb|FG950272.1|FG950272
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAAGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|29619928|gb|CB624940.1|CB624940
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|13420811|gb|AU174901.1|AU174901
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|29673001|gb|CB669276.1|CB669276
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|29683463|gb|CB679738.1|CB679738
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|218492553|gb|FG956401.1|FG956401
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|116875639|gb|EC366147.1|EC366147
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|33795773|gb|CF323756.1|CF323756
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGNGTTGTCATGGTG
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATG-GTTGTCATGGTG
EST: gi|58601372|gb|CK011900.1|CK011900
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|3763799|gb|AU030551.1|AU030551
EST:     CGGAATGCTCTGTGCACAAAGT-NAAGGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTG
genomic: CGGAATGCTCTGTGCACAAAGTGCAA-GGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTG
EST: gi|27577056|gb|CA999750.1|CA999750
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|396941261|gb|HO188470.1|HO188470
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGGTG
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCAT-GGTG
EST: gi|58589635|gb|CF987943.1|CF987943
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAACGG                         TACCGGATCCAAGAGTGGGGC
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGC

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), 74 (downstream exon)
Score: 168

ATGTGGTACATACTATGAAGGTTTCTTTAGAAGACCTGTATAATGGTACTACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGCAGGAATGAGAACAATAACAAGACAAATTGGGCTTGGCATGATCCAACAG




<











<


<