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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattaagagtagcatagtacagctgggtttattgatagacctatgattgatgtcttgttatctctgtagGCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAGAAGTTGACATCTTTGGCATCGAACATCATGTCTGATCTTCAAGACCGGA

Basic information

species Oryza sativa
transcript LOC_Os10g42420.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g42420.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G134045_T02 (Zea mays), 3'ss of exon 6
gtaaattaagagtagcatagtacagctgggtttattgatagacctatg---attgatgtcttgttatctctgt------agGCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAGAAGTTGACATCTTTGGCATCGAACATCATGTCTGATCTTCAAGACCGGA
||||     | |||| ||| |   |     || | |  | | | ||     ||| | |  ||||| | | |||      ||||  | || |||||||||||| ||||||||||||| |||||||||||||| | |||||||||  ||||||| ||||||||  |||||||||| ||||| |
gtaacagttgggtagaataatgttgtctccttgactccttggcttacttgcattaacgcattgttgtgtttgtcttggcagGCCACTCAAGATCTGTCTTCTCTCAAGAACATGGCAGGGGAAACTGGGAAAAGGTTGACATCGATGGCATCCAACATCATCACTGATCTTCAGGACCGCA

upper sequence: LOC_Os10g42420.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G094390_T01 (Zea mays), 3'ss of exon 6
gtaaattaagagtagcatagtacagctgggtttattgatagacctatgattgatgtcttgttatctctgt------agGCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAGAAGTTGACATCTTTGGCATCGAACATCATGTCTGATCTTCAAGACCGGA
||||   |   |    | | |  |  | | ||| ||  |   | | || || |||  ||| | | | |||      ||||  | ||||||||||||||| ||||||||||||| |||||||| ||||| |||||||||||  ||||||| ||||||||  |||||||||| ||||| |
gtaa-caagttgggtaagaatggattttgttttctttttgtgcttgtg-ttaatgcattgctgtgtttgtcttggcagGCCACTCAGGATCTGTCTTCTCTCAAGAACATGGCAGGGGAAACCGGGAAAAAGTTGACATCGATGGCATCCAACATCATCACTGATCTTCAGGACCGCA
















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|88274837|gb|CI388295.1|CI388295
EST:     CCAACGT-GATCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAG                         GCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
genomic: CCAACGTGGATCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAGgtaaattaag ... atctctgtagGCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
EST: gi|218493112|gb|FG943279.1|FG943279
EST:     CCAACGTGGATCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAG                         GCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
genomic: CCAACGTGGATCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAGgtaaattaag ... atctctgtagGCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
EST: gi|88906634|gb|CI375706.1|CI375706
EST:     CCAACGTGGATCTGAGTGCTTCAGATTTGATCAACC-GCTTTCTTTCCAG                         GCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
genomic: CCAACGTGGATCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAGgtaaattaag ... atctctgtagGCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
EST: gi|88261708|gb|CI365284.1|CI365284
EST:     GATCTGAGTGCTTCAGATTTGATCAACC-GCTTTCTTTCCA-                         GCTTCCCA-GATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
genomic: GATCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAGgtaaattaag ... atctctgtagGCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
EST: gi|88226112|gb|CI226028.1|CI226028
EST:     CCAACGTGGATCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAG                         GCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
genomic: CCAACGTGGATCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAGgtaaattaag ... atctctgtagGCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
EST: gi|88250385|gb|CI348615.1|CI348615
EST:     AACGTGGATCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAG                         GCTTCCCAGAATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
genomic: AACGTGGATCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAGgtaaattaag ... atctctgtagGCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
EST: gi|87022045|gb|CI259117.1|CI259117
EST:     CCAACGTGGATCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAG                         GCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
genomic: CCAACGTGGATCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAGgtaaattaag ... atctctgtagGCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
EST: gi|88906383|gb|CI375455.1|CI375455
EST:     GCAACGT-GATCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAG                         GCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
genomic: CCAACGTGGATCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAGgtaaattaag ... atctctgtagGCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
EST: gi|86868624|gb|CI333001.1|CI333001
EST:     AGATTTGATCAACCGGCTTTCTTTCCAG                         GCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCT-GGGAAACTGGGAAG
genomic: AGATTTGATCAACCGGCTTTCTTTCCAGgtaaattaag ... atctctgtagGCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
EST: gi|89182866|gb|CI045624.1|CI045624
EST:     CCAACGTGGATCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAG                         GCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
genomic: CCAACGTGGATCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAGgtaaattaag ... atctctgtagGCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
EST: gi|33654042|gb|CF276656.1|CF276656
EST:     CCAACGTGGATCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAG                         GCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
genomic: CCAACGTGGATCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAGgtaaattaag ... atctctgtagGCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
EST: gi|58610590|gb|CK038302.1|CK038302
EST:     CAACGT-GATTCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAG                         GCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
genomic: CAACGTGGA-TCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAGgtaaattaag ... atctctgtagGCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
EST: gi|88243030|gb|CI244152.1|CI244152
EST:     CCAACGTGGATCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAG                         GCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
genomic: CCAACGTGGATCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAGgtaaattaag ... atctctgtagGCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
EST: gi|86489006|gb|CI131639.1|CI131639
EST:     CCAACGTGGATCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAG                         GCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
genomic: CCAACGTGGATCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAGgtaaattaag ... atctctgtagGCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
EST: gi|86250851|gb|CI007714.1|CI007714
EST:     CCAACGTGGATCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAG                         GCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
genomic: CCAACGTGGATCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAGgtaaattaag ... atctctgtagGCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
EST: gi|86495273|gb|CI137906.1|CI137906
EST:     CCCACGTGGATCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAG                         GCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
genomic: CCAACGTGGATCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAGgtaaattaag ... atctctgtagGCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
EST: gi|218500046|gb|FG955203.1|FG955203
EST:     CCAACGTGGATCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAG                         GCTTCCCAGGATCTGTCTT
genomic: CCAACGTGGATCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAGgtaaattaag ... atctctgtagGCTTCCCAGGATCTGTCTT
EST: gi|88902693|gb|CI088231.1|CI088231
EST:     CCAACGTGGATCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAG                         GCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
genomic: CCAACGTGGATCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAGgtaaattaag ... atctctgtagGCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
EST: gi|86594982|gb|CI258236.1|CI258236
EST:     CCAACGTGGATCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAG                         GCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
genomic: CCAACGTGGATCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAGgtaaattaag ... atctctgtagGCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
EST: gi|86839725|gb|CI343654.1|CI343654
EST:     CTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAG                         GCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
genomic: CTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAGgtaaattaag ... atctctgtagGCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
EST: gi|86823611|gb|CI258687.1|CI258687
EST:     CCAACGTGGATCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAG                         GCTTCCNCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAA
genomic: CCAACGTGGATCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAGgtaaattaag ... atctctgtagGCTTCC-CAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAA
EST: gi|87034089|gb|CI187451.1|CI187451
EST:     CCAACGTGGATCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAG                         GCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
genomic: CCAACGTGGATCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAGgtaaattaag ... atctctgtagGCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
EST: gi|89176736|gb|CI111452.1|CI111452
EST:     CGGCTTTCTTTCCAG                         GCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG
genomic: CGGCTTTCTTTCCAGgtaaattaag ... atctctgtagGCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAG

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), 67 (downstream exon)
Score: 21

ATCTTCTGCCATTTCAAGTGCTGATCTATTTGGTCATCCAACCAATAGTTCCAACGTGGATCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAGgtaaattaag ... atctctgtagGCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAGAAGTTGACATCTTTGGCATCGAACATCATGTCTGATCTTCAAGACCGGA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtacagctgggtttattgatagacctatgattgatgtcttgttatctctgtagGCTTCCCAGGATCTGTCTTCTATCAAGAACATGGCTGGGGAAACTGGGAAGAAGTTGACATCTTTGGCATCGAACATCATGTCTGATCTTCAAGACCGGA
                                           ttatctct  CT-rich tract
             tttattgata  TA-rich tract