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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTTTGAATGAGCTTTATGTTGAAGAGGAGGACTATGAGAGACTCCGTGAATCGGTTGATATGCATGACAACTTTGATCAGATAGGTCTTGCCCAAAAGgtaaagcgattatatgattgtactgcttattgatgttatttttccttttttattttattttgaataactaatggctggaatgccttgatcag

Basic information

species Oryza sativa
transcript LOC_Os11g01380.1
intron # 26
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 26
lower sequence: GRMZM2G395549_T01 (Zea mays), 5'ss of exon 11
AGCTTTGAATGAGCTTTATGTTGAAGAGGAGGACTATGAGAGACTCCGTGAATCGGTTGATATGCATGACAACTTTGATCAGATAGGTCTTGCCCAAAAGgtaaagcgattatatgattgtactgcttattgatgttattttt-ccttttttattttattttgaataactaatggctggaatgccttgatcag
                            |||||||||||||||||||||||||| ||||| | ||||||||||||||| ||||| ||||||||||| ||||||||   |  |||  || |  |     | |  ||  |||  |  |  |     |||   || ||||||   ||     |||   |||| |||
----------------------------GAGGACTATGAGAGACTCCGTGAATCAGTTGACACGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAGgtaaaataaaaataaaatag--ccagacagtcgtgcaattcctatcgctaccgcttttaatttaataacatgtgtt---aatttattgagcag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 26
lower sequence: GRMZM2G057576_T01 (Zea mays), 5'ss of exon 25
AGCTTTGAATGAGCTTTATGTTGAAGAGGAGGACTATGAGAGACTCCGTGAATCGGTTGATATGCATGACAACTTTGATCAGATAGGTCTTGCCCAAAAGgtaaagcgattatatgattgtactgcttattgatgttattttt-ccttttttattttattttgaataactaatggctggaatgccttgatcag
||| ||||||||||||||||| |||||||||||||| ||||||||||||||||| ||||| ||||||||||||||||| ||||| ||||||||||| ||||||||   |  |||  || |  |     | |  ||  |||  |  |  |     |||   || |||| |   ||     |||   |||| |||
AGCCTTGAATGAGCTTTATGTCGAAGAGGAGGACTACGAGAGACTCCGTGAATCAGTTGACATGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAGgtaaaataaaaataaaatag--ccagacagtcgtgcaattcctgtcgctaccgcttttaatttaatagcatgtgtt---aatttattgagcag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 26
lower sequence: GRMZM2G062042_T02 (Zea mays), 5'ss of exon 11
AGCTTTGAATGAGCTTTATGTTGAAGAGGAGGACTATGAGAGACTCCGTGAATCGGTTGATATGCATGACAACTTTGATCAGATAGGTCTTGCCCAAAAGgtaaagcgattatatgattgtactgcttattgatgttattttt-ccttttttattttattttgaataactaatggctggaatgccttgatcag
||| |||||||| |||||||| ||||| |||||||| ||||||||||||||||| ||||| ||||||||||||||||| ||||| ||||||||||| ||||||||   |  |||  || |  |     | |  ||  |||  |  |  |     |||   || ||||||   ||     |||   |||| |||
AGCCTTGAATGAACTTTATGTCGAAGATGAGGACTACGAGAGACTCCGTGAATCAGTTGACATGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAGgtaaaataaaaataaaatag--ccagacagtcgtgcaattcctatcgctaccgcttttaatttaataacatgtgtt---aatttattgagcag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 26
lower sequence: GRMZM5G804382_T01 (Zea mays), 5'ss of exon 3
AGCTTTGAATGAGCTTTATGTTGAAGAGGAGGACTATGAGAGACTCCGTGAATCGGTTGATATGCATGACAACTTTGATCAGATAGGTCTTGCCCAAAAGgta--aagcgattatatgattgtactgcttattgatgttatttt----------tccttttttattttattttgaat--aactaatggctggaatgccttgatcag
||| |||||||||||||||||||||||||| ||||||||||||||||||||||| ||||| ||||||||||||||||| || |||||||||||||| ||||||  || |    | |||   | | ||| ||||| |||| || |          | ||| ||  |  | |||| |||  || ||   |     ||  ||||| |||
AGCCTTGAATGAGCTTTATGTTGAAGAGGAAGACTATGAGAGACTCCGTGAATCAGTTGACATGCATGACAACTTTGACCAAATAGGTCTTGCCCAGAAGgtacaaaacagccagatg--cgcagtgcctattgttgttgttgtaatggtgtgatgcttattgttactgttttcaatttaattacctgtgttcatttcttgagcag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 26
lower sequence: GRMZM5G822591_T01 (Zea mays), 5'ss of exon 3
AGCTTTGAATGAGCTTTATGTTGAAGAGGAGGACTATGAGAGACTCCGTGAATCGGTTGATATGCATGACAACTTTGATCAGATAGGTCTTGCCCAAAAGgta--aagcgattatatgat--tgtactgcttattgatgttatttttccttttttattttattttgaataactaatggctgg-aatgccttgatcag------------------
||| ||||| || ||||||||||||||||| ||||| ||||||||||||||||| ||||||||||||||||||||||| || |||||||||||||| ||||||  ||      | || ||  || | ||| ||||| || |  | ||  | |  |  |    |    ||   || ||  |   |||    | | | |                  
AGCCTTGAACGAACTTTATGTTGAAGAGGAAGACTACGAGAGACTCCGTGAATCAGTTGATATGCATGACAACTTTGACCAAATAGGTCTTGCCCAGAAGgtacaaaatagccagataatcttgcagtgcctattgctgctgctgttgttgtaatcgtgcgatgcatattgttactgctttttaatttaataacctgtgtccatttctggagcag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 26
lower sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 26
AGCTTTGAATGAGCTTTATGTTGAAGAGGAGGACTATGAGAGACTCCGTGAATCGGTTGATATGCATGACAACTTTGATCAGATAGGTCTTGCCCAAAAGgtaaagcgattatatgattgtactgcttattgatgttatttttccttttttattttattttgaataactaatggctggaatgccttgat-cag
||| ||||||||| | |||||||| ||||| || ||||| ||| | || || ||  ||||| |||| || ||||||||||| ||||| ||||||||||||||   |  |||         | ||  | ||||    |||||||   ||||  || |         |  | ||  ||   |     |||| |||
AGCGTTGAATGAGATATATGTTGAGGAGGAAGATTATGATAGATTGCGCGAGTCAATTGATTTGCACGATAACTTTGATCAAATAGGCCTTGCCCAAAAGgtgtggaaatt---------tgctcttaattggaactatttttttgttttagttgtggaaatctcagattattactattactgtatgatgcag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 26
lower sequence: GLYMA11G06720.1 (Glycine max), 5'ss of exon 26
AGCTTTGAATGAGCTTTATGTTGAAGAGGAGGACTATGAGAGACTCCGTGAATCGGTTGATATGCATGACAACTTTGATCAGATAGGTCTTGCCCAAAAGgtaaagcgattatatgattgtactgcttattgatgttatt-----tttccttttttattttattttgaataactaatggctggaatgcc-ttgatcag----------------------
 |||||||||||  |||||| ||| || || |||||||| ||||||||||||||  | ||| ||||||| ||||| ||||||||||||||||| || ||||| || |     |||  ||   ||  || |     |||       |     |    || ||||    |||    |||   || | |    |||||  |                      
GGCTTTGAATGAAATTTATGCTGAGGAAGAAGACTATGACAGACTCCGTGAATCAATAGATCTGCATGATAACTTCGATCAGATAGGTCTTGCACAGAAGgtgaatcttacttatcttttgtcttattttgacaattagcaaaaatcgagatcagaatgttatgggaaatttaaaatatttgaattattattgattggcttcaacaatacacatgagcag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 26
lower sequence: GLYMA14G37510.1 (Glycine max), 5'ss of exon 24
AGCTTTGAATGAGCTTTATGTTGAAGAGGAGGACTATGAGAGACTCCGTGAATCGGTTGATATGCATGACAACTTTGATCAGATAGGTCTTGCCCAAAAGgtaaagcgattatatgattgtactgcttattgatgttatttttccttttttattttattttgaa-taactaa--tggctggaatgccttgatcag-----
||||||||||||  |||||||||| |||||||||||||| ||||| | ||||||  | ||| ||||||||||||| ||||||||||||||||| || ||||| || |     |||  ||  | |   ||    ||  || |     ||  |     | || |   | | |    | |  | ||||  ||  |        
AGCTTTGAATGAAATTTATGTTGAGGAGGAGGACTATGATAGACTTCATGAATCAATAGATCTGCATGACAACTTCGATCAGATAGGTCTTGCACAGAAGgtgaatcttccgtatctttcaaattgctaaaattgaaatctgaatcttactgagaaacttaggggtcatttggtttgaagaaatgtttttttttttttct

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 26
lower sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 26
AGCTTTGAATGAGCTTTATGTTGAAGAGGAGGACTATGAGAGACTCCGTGAATCGGTTGATATGCATGACAACTTTGATCAGATAGGTCTTGCCCAAAAGgtaaagcgattatatgatt-gtactgctta--ttgatgtt--atttttccttttttattttattttgaataactaatggctggaatgcct-tgatcag--
||||||||||||  |||||||||| |||||||||||||| ||||| | ||||||  | ||| ||||||||||||| ||||||||||||||||| || ||||| || |     |||  ||   | |||| |  ||||  |   | | || |      ||||   | ||  |   |      |  | |  || |  |||   
AGCTTTGAATGAAATTTATGTTGAGGAGGAGGACTATGATAGACTTCATGAATCAATAGATCTGCATGACAACTTCGATCAGATAGGTCTTGCACAGAAGgtgaatcttccttatctttcaaattgctaaaattgaaatctgaatcttaccgagacatttgggtgtgtttggtttgcattttcattttctgttttcattt

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 26
lower sequence: GLYMA01G38580.1 (Glycine max), 5'ss of exon 26
AGCTTTGAATGAGCTTTATGTTGAAGAGGAGGACTATGAGAGACTCCGTGAATCGGTTGATATGCATGACAACTTTGATCAGATAGGTCTTGCCCAAAAGgtaaagc--gattatatgat----tgtactgcttattgatgttatttttccttttttattttattttgaataactaatggctggaatgcc-ttgatcag--------------------
||||||||||||  |||||||||| || || ||||| || |||||||| |||||  | ||| ||||||||||||||||||||||||||||||| || ||||| || |  | |||| |  |    | |  ||   |||      || |    |     | || ||    |||    ||||  || | |    |||||  |                    
AGCTTTGAATGAAATTTATGTTGAGGAAGAAGACTACGACAGACTCCGAGAATCAATAGATTTGCATGACAACTTTGATCAGATAGGTCTTGCACAGAAGgtgaatctcggttatcttttgtcttattttgacaattagcaaaatctgagatcaggaagtt-atggaaaatttaaaatgtttgaattattattgattggcttcaacaatacatgagcag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 26
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 26
AGCTTTGAATGAGCTTTATGTTGAAGAGGAGGACTATGAGAGACTCCGTGAATCGGTTGATATGCATGACAACTTTGATCAGATAGGTCTTGCCCAAAAGgtaaagcgattatatgattgtactgcttattgatgttatttttccttttttattttattttgaataactaa--tggctggaatgc-cttgatcag
 |||||||||| | |||||||||| ||||| |||||||| ||||| ||||||||  ||||||||||||| |||||||||||||| || ||||| || |||||  ||  || || |  ||    |||  |||| | || ||| |  || | |    |  ||    | |  |   | | ||| |||   |||| |||
GGCTTTGAATGGGATTTATGTTGAGGAGGAAGACTATGACAGACTGCGTGAATCAATTGATATGCATGATAACTTTGATCAGATTGGCCTTGCACAGAAGgtggagt-ataatttcttta-ggtgca-attgtttttctttgtggttctatgcactggttgatttcataagccttgttggtatgtgtttgagcag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 26
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 26
AGCTTTGAATGAGCTTTATGTTGAAGAGGAGGACTATGAGAGACTCCGTGAATCGGTTGATATGCATGACAACTTTGATCAGATAGGTCTTGCCCAAAAGgtaa-agcgattatatgattgtactgcttattgatgttatttttcctttttt-attttattttgaataactaatggctggaatgccttgatcag
||| || ||||   || |||| || |||||||||||||| ||||| || |||||  | ||||||||||| |||||||| |||||||| ||||| || ||||| | || ||||  ||  || |  || ||| || || ||   ||| |      |   | |    || | ||| ||    |  ||    |     
AGCATTAAATGGTATTCATGTAGAGGAGGAGGACTATGATAGACTTCGGGAATCAATAGATATGCATGATAACTTTGACCAGATAGGCCTTGCACAGAAGgtgagagagattgaat--ttattttg-ttaatgttggtaggcttcataagcagaacatgtacataagatctagtgatgcgtgtggacag-----

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|12622957|gb|AU173170.1|AU173170
EST:     AATCGGTTGATATGCATGACAACTTTGATCAGATAGGTCTTGCCCAAAAG                         CTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTAC
genomic: AATCGGTTGATATGCATGACAACTTTGATCAGATAGGTCTTGCCCAAAAGgtaaagcgat ... ccttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTAC
EST: gi|5005228|gb|AU070390.1|AU070390
EST:     AATCGGTTGATATGCATGACAACTTTGATCAGATAGGTCTTGCCCAGAAG                         CTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTAC
genomic: AATCGGTTGATATGCATGACAACTTTGATCAGATAGGTCTTGCCCAAAAGgtaaagcgat ... ccttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTAC
EST: gi|29685119|gb|CB681394.1|CB681394
EST:     AATCGGTTGATATGCATGACAACTTTGATCATATAGGTCTTGCCCAGAAG                         CTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTAC
genomic: AATCGGTTGATATGCATGACAACTTTGATCAGATAGGTCTTGCCCAAAAGgtaaagcgat ... ccttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTAC
EST: gi|29664581|gb|CB660856.1|CB660856
EST:     AATCGGTTGATATGCATGACAACTTTGATCAGATAGGTCTTGCCCAAAAG                         CTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTAC
genomic: AATCGGTTGATATGCATGACAACTTTGATCAGATAGGTCTTGCCCAAAAGgtaaagcgat ... ccttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTAC
EST: gi|87017011|gb|CI286147.1|CI286147
EST:     AATCGGTTGATATGCATGACAACTTTGATCAGATAGGTCTTGCCCAAAAG                         CTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTAC
genomic: AATCGGTTGATATGCATGACAACTTTGATCAGATAGGTCTTGCCCAAAAGgtaaagcgat ... ccttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTAC

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: 74 (upstream exon), 75 (downstream exon)
Score: 106

AGCTTTGAATGAGCTTTATGTTGAAGAGGAGGACTATGAGAGACTCCGTGAATCGGTTGATATGCATGACAACTTTGATCAGATAGGTCTTGCCCAAAAGgtaaagcgat ... ccttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA




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