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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATGCTGATATATATGATAAAAATGCTTTCCATGTGGATGGATTTGATGGCTCTTTGGTTGAATTCATGGTTAGAGAAACCGAAAAACTACATCAACAGgtagagcagggttgtaactagcaatataattgttcattgtatgccaaaaattgcaaaatgttgatggttctggccatcttgtgtag

Basic information

species Oryza sativa
transcript LOC_Os01g55870.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55870.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G116087_T02 (Zea mays), 5'ss of exon 2
CAATGCTGATATATATGATAAAAATGCTTTCCATGTGGATGGATTTGATGGCTCTTTGGTTGAATTCATGGTTAGAGAAACCGAAAAACTACATCAACAGgtagagcag---gg------ttgtaactagcaatataattgttcattgtatgccaaaaattgcaaaatgttgatggttctggccatcttgtgtag
||| ||||| | ||||||||  |||||||||||  ||||||| ||||  || |||||||||||||  |||||||||||||| ||||| || |||  ||||||  |   |   ||      || |||  | |||   ||||| |  | | |||| ||| | |   | |||   ||| || || | ||         
CAACGCTGACACATATGATAGCAATGCTTTCCACATGGATGGTTTTGGAGGGTCTTTGGTTGAATATATGGTTAGAGAAACTGAAAAGCTCCATGCACAGgtgaattcgtttggacttctttttaaaaaccaaagcaattgatagtggcatgcgaaagaataacatatgcaaatgtttttgac-atag-------

upper sequence: LOC_Os01g55870.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G028369_T01 (Zea mays), 5'ss of exon 2
CAATGCTGATATATATGATAAAAATGCTTTCCATGTGGATGGATTTGATGGCTCTTTGGTTGAATTCATGGTTAGAGAAACCGAAAAACTACATCAACAGgtagagcagggttg---------taactagcaatataattgttcattgtatgccaaaaattgcaaaatgttgatggttctggccatcttgtgtag
||||||||||| ||||||||  |||||||||||  ||||||| ||||  ||||||||||||||||  |||||||||||||| ||||| || |||  |||||| ||      |||         |||  |  || | | ||| |||| | |||| ||| | |   | | | |  || || |  | ||         
CAATGCTGATACATATGATAGCAATGCTTTCCACATGGATGGTTTTGGCGGCTCTTTGGTTGAATATATGGTTAGAGAAACTGAAAAGCTCCATGCACAGgtggaattcatttggacattttttaagaacaaaaacagttgatcatggcatgcaaaagaataacatacgctattgtttttaac-atag-------

upper sequence: LOC_Os01g55870.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G124365_T01 (Zea mays), 5'ss of exon 2
CAATGCTGATATATATGATAAAAATGCTTTCCATGTGGATGGATTTGATGGCTCTTTGGTTGAATTCATGGTTAGAGAAACCGAAAAACTACATCAACAGgtagagca----gggttgt----aactagcaatataattgttcattgtatgccaaaaattgcaaaatgttgatggttctggccatcttgtgtag
||||||||||| ||||||||  |||||||||||  ||||||| ||||  || |||||||||||||  || ||||||||||| ||||| || |||  ||||||  | |     || ||      ||  | ||| | ||||| |||| | |||| ||| | |   |  || | ||| || |  | ||         
CAATGCTGATACATATGATAGCAATGCTTTCCACATGGATGGTTTTGGAGGATCTTTGGTTGAATATATAGTTAGAGAAACTGAAAAGCTCCATGCACAGgtgaatccatttggatttctttaaaaaaacaaaacaattgatcatggcatgcgaaagaataacatgtgctaatgtttgtaac-atag-------

upper sequence: LOC_Os01g55870.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv01s0010g00480.t01 (Vitis vinifera), 5'ss of exon 2
CAATGCTGATATATATGATAAAAATGCTTTCCATGTGGATGGATTTGATGGCTCTTTGGTTGAATTCATGGTTAGAGAAACCGAAAAACTACATCAACAGgtagagcagggttgtaactagcaatataattgttcattgtatgccaaaaattgcaaaatgttgat----ggttctggccatcttgtgtag--------
|||||| || | ||||||  |  |||| |||      ||||| ||| |||||||||||||||| |||||| | | |||||| |||||||| |||   ||||||    ||  || || |||     | ||  | | |    |      | ||  |||  | ||  |      |||||     | | | | |        
CAATGCAGACACATATGACCATCATGCCTTCTCCAAAGATGGGTTTCATGGCTCTTTGGTTGAGTTCATGATCAAAGAAACTGAAAAACTTCATGCCCAGgtattttagt-ttctagctaatgtaaaaagagctaaaaaaaatgttgatatctcaattttttattttttatttctgattggccttttttgcaagtcag

upper sequence: LOC_Os01g55870.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv14s0108g01330.t01 (Vitis vinifera), 5'ss of exon 2
CAATGCTGATATATATGATAAAAATGCTTTCCATGTGGATGGATTTGATGGCTCTTTGGTTGAATTCATGGTTAGAGAAACCGAAAAACTACATCAACAGgtagagcagggttgtaactagcaat--ataattgttcat---------------tgtatgccaaaaattgcaa----aatgttgatggttctggccatcttgtgtag---------------
|||||| || | |||||||    |||||||     ||||||| ||  ||||||||||||||||||||||||| || ||||||||||| || |||   ||||||    |   ||  | | | |||   | |||  || |                ||   |  ||| |  | ||    |||| || |  | ||||   |||  |  |                
CAATGCCGAGACATATGATCCCGATGCTTTGTCAATGGATGGGTTCCATGGCTCTTTGGTTGAATTCATGGTCAGGGAAACCGAAAAGCTTCATGCTCAGgtatgttacatttaaacccatcaaagaagaatgattgaaagaaaagaaggaagatgagagggaaagaagggaagaggaatgatgttattgctggttttctgatccacttttaattaacatag

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|29614868|gb|CB619881.1|CB619881
EST:     GCTCTTTGGTTGAATTCATGGTTAGAGAAACCGAAAAACTACATCAACAG                         GTTGGGAGATACAAGAGCCCTGATGAGCACCCATTCTTTCCGGAGGATCTG
genomic: GCTCTTTGGTTGAATTCATGGTTAGAGAAACCGAAAAACTACATCAACAGgtagagcagg ... tcttgtgtagGTTGGGAGATACAAGAGCCCTGATGAGCACCCATTCTTTCCGGAGGATCTG
EST: gi|29614869|gb|CB619882.1|CB619882
EST:     GCTCTTTGGTTGAATTCATGGTTAGAGAAACCGAAAAACTACATCAACAG                         GTTGGGAGATACAAGAGCCCTGATGAGCACCCATTCTTTCCGGAGGATCTG
genomic: GCTCTTTGGTTGAATTCATGGTTAGAGAAACCGAAAAACTACATCAACAGgtagagcagg ... tcttgtgtagGTTGGGAGATACAAGAGCCCTGATGAGCACCCATTCTTTCCGGAGGATCTG
EST: gi|88334481|gb|CI676255.1|CI676255
EST:     TGGTTAGAGAAACCGAAAAACTACATCAACAG                         GTTGGGAGATACAAGAGCCCTGATGAGCACCCATTCTTTCCGGAGGATCTG
genomic: TGGTTAGAGAAACCGAAAAACTACATCAACAGgtagagcagg ... tcttgtgtagGTTGGGAGATACAAGAGCCCTGATGAGCACCCATTCTTTCCGGAGGATCTG
EST: gi|25798291|gb|CA754252.1|CA754252
EST:     GCTCTTTGGTTGAATTCATGGTTAGAGAAACCGAANAACTACATCAACAG                         GTTGGGAGATACAAGAGCCCTGATGAGCACCCATTCTTTCCGGAGGATCTG
genomic: GCTCTTTGGTTGAATTCATGGTTAGAGAAACCGAAAAACTACATCAACAGgtagagcagg ... tcttgtgtagGTTGGGAGATACAAGAGCCCTGATGAGCACCCATTCTTTCCGGAGGATCTG
EST: gi|11442834|gb|BF430733.1|BF430733
EST:     GCTCTTTGGTTGAATTCATGGTTAGAGAAACCGAAAAACTACATCAACAG                         GTTGGGAGATACAAGAGCCCTGATGAGCACCCATTCTTTCCGGAGGATCTG
genomic: GCTCTTTGGTTGAATTCATGGTTAGAGAAACCGAAAAACTACATCAACAGgtagagcagg ... tcttgtgtagGTTGGGAGATACAAGAGCCCTGATGAGCACCCATTCTTTCCGGAGGATCTG
EST: gi|29617584|gb|CB622596.1|CB622596
EST:     TGGTTGAATTCATGGTTAGAGAAACCGAAAAACTACATCAACAG                         GTTGGGAGATACAAGAGCCCTGATGAGCACCCATTCTTTCCGGAGGATCTG
genomic: TGGTTGAATTCATGGTTAGAGAAACCGAAAAACTACATCAACAGgtagagcagg ... tcttgtgtagGTTGGGAGATACAAGAGCCCTGATGAGCACCCATTCTTTCCGGAGGATCTG

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), 73 (downstream exon)
Score: 37

CAATGCTGATATATATGATAAAAATGCTTTCCATGTGGATGGATTTGATGGCTCTTTGGTTGAATTCATGGTTAGAGAAACCGAAAAACTACATCAACAGgtagagcagg ... tcttgtgtagGTTGGGAGATACAAGAGCCCTGATGAGCACCCATTCTTTCCGGAGGATCTGCCTGAACCACTGTTGCCACCTCTCCAGTATCCAAAG




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