ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

ATGGACCCAGCAAGTGCAAGAGATGCTGAACACAAAGAAGTTTGGTGACATTGCATTTAGAGACAAGGATTTTAAGACTGCAATTGACTACTATTCCAAGgtatcagcatacctgttctctattttcgcgtaattatggtaggagactaggggtgctaacggatcacgatccaaatatttcacaatttcttagggcctaa...

Basic information

species	Zea mays
transcript	GRMZM2G169080_T01
intron #	9
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G169080_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os10g42110.1 (Oryza sativa), 5'ss of exon 9

ATGGACCCAGCAAGTGCAAGAGATGCTGAACACAAAGAAGTTTGGTGACATTGCATTTAGAGACAAGGATTTTAAGACTGCAATTGACTACTATTCCAAGgtatcagcatacctgttctctattttcgcgtaattatggtaggagactaggggtgctaacggatcacgatccaaatattt------cacaattt--cttagggcctaa
|||||| ||||||||||||||||||||||| || |||||||||||||||||||||||||||||||||||||| |||||||||||||||||||| ||||||||||||       |||| ||| ||  |  |    |      | |   | |   || | ||   |  |    | | | |||      ||||| ||   || | || |  
ATGGACTCAGCAAGTGCAAGAGATGCTGAATACCAAGAAGTTTGGTGACATTGCATTTAGAGACAAGGATTTCAAGACTGCAATTGACTACTACTCCAAGgtatca------ttgttttctcttacctaggctatgctaccgtacctttgcaatgttgacattttgcttcacgattgtttgtttgacacaagttgttttggagctt--

upper sequence: GRMZM2G169080_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA05G06140.1 (Glycine max), 5'ss of exon 9

ATGGACCCAGCAAGTGCAAGAGATGCTGAACACAAAGAAGTTTGGTGACATTGCATTTAGAGACAAGGATTTTAAGACTGCAATTGACTACTATTCCAAGgtatcagcatacctgttctctattttcgcgtaattatgg-----taggagactaggggtgctaacgg----atcacgatccaaa--tatttcacaatttcttagggcctaa-------------------------------
|||||| || ||||||||||| ||  |||||||||| |||||||| || |||||||| |||||||||||||| || | ||||||||| || || || ||||||  |   |   | |   || ||||    |  || |||     | |  | ||     || | |       |  | | ||  ||  ||| |  | ||| || | | | ||                                
ATGGACACAACAAGTGCAAGATATCTTGAACACAAAAAAGTTTGGGGATATTGCATTCAGAGACAAGGATTTCAAAAATGCAATTGAGTATTACTCTAAGgtag-attctctgtttcacctttttttaactggttttggcttattggttgcctcaaaatgttcataatctcaatatgttcttaaggtatattcctatt-ctgaagtcatagtctgagccctttatttctttgcattaagcag

upper sequence: GRMZM2G169080_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA17G16420.1 (Glycine max), 5'ss of exon 9

ATGGACCCAGCAAGTGCAAGAGATGCTGAACACAAAGAAGTTTGGTGACATTGCATTTAGAGACAAGGATTTTAAGACTGCAATTGACTACTATTCCAAGgtatcagcatacctgttctctattttcgcgtaattatggtaggagactaggggtgctaacggatcacgatccaaatatttcacaat-ttcttagggcctaa---------------------------------------------------
|||||| || ||||| ||||| ||  |||||||||| |||||||| || |||||||| |||||||||||||| || | |||||| || || ||||| ||||||    ||    |   || |  |||    |||           |  | ||  |  | |  | || | ||  ||| || |||  || |||||| |   ||                                                    
ATGGACACAACAAGTACAAGATATCTTGAACACAAAAAAGTTTGGGGATATTGCATTCAGAGACAAGGATTTCAAAAATGCAATCGAGTATTATTCTAAGgtagattcactgtttcacttttcttttttttaaccg--------gttttggcttattgattg-tctcaatataaaaatctcaatatgttcttaagatatattcctattctgaagtcatagtctgactgccctttatttctttgcattaacag

upper sequence: GRMZM2G169080_T01 (Zea mays), 5'ss of exon 9
lower sequence: AT5G46570.1 (Arabidopsis thaliana), 5'ss of exon 7

ATGGACCCAGCAAGTGCAAGAGATGCTGAACACAAAGAAGTTTGGTGACATTGCATTTAGAGACAAGGATTTTAAGACTGCAATTGACTACTATTCCAAGgtatcagcatacctgttctctattttcgcgtaattat-ggtaggagactaggggtgctaacggatcacgatccaaatatttcacaatttcttagggcctaa
|||||| || |||||||| |||||||| |||||||| ||||| || |||||||| || |||||||||||||| ||||   ||||||| ||||| ||||||||   || | |     |  | |      | ||||| | |||    ||  ||   | |||||   ||   ||| |    || ||                  
ATGGACACAACAAGTGCAGGAGATGCTTAACACAAAAAAGTTCGGGGACATTGCTTTCAGAGACAAGGATTTCAAGAACTCAATTGAATACTACTCCAAGgtgagaggaaa-----tagcaacaaatccataattctcggtgttcgaaaagaatttctaac--ctctgtatctatggtttccag-----------------

upper sequence: GRMZM2G169080_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv02s0012g01140.t01 (Vitis vinifera), 5'ss of exon 9

ATGGACCCAGCAAGTGCAAGAGATGCTGAACACAAAGAAGTTTGGTGACATTGCATTTAGAGACAAGGATTTTAAGACTGCAATTGACTACTATTCCAAGgtatcagcatacctgttctctattttcgcgtaattat--ggtaggagact---aggggtgctaacggatcacgatccaaatatttcacaatttcttagggcctaa
|||||| || ||||||||||||||| ||||||||||||| || || || ||||||||||| ||||||||||| |||| ||||||||| || ||||| |||||||   |    |  |   ||  | |     ||  ||  ||| |  || |        || ||   | | |    |||| |  ||    || |||    |     
ATGGACACAACAAGTGCAAGAGATGTTGAACACAAAGAAATTCGGGGATATTGCATTTAGGGACAAGGATTTCAAGAGTGCAATTGATTATTATTCAAAGgtattgtcccttcactgaacttgtcttcatcaagcattgggtggtggatttttgaaaatgatatttgttgagttaccaattgattggatatctctccttg-----

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|50336037|gb|CO531163.1|CO531163

EST:     CTGCATTTAGAGACAAGGATTTTAAGACTGCAATTGACTACTATTCCAAG                         CTAGTCGCAATGATGTCGACGCCTTCGGCTACCGTTTTTGCTAGGCGCAGT
genomic: TTGCATTTAGAGACAAGGATTTTAAGACTGCAATTGACTACTATTCCAAGgtatcagcat ... tctaatgcagCTAGTCGCAATGATGTCGACGCCTTCGGCTACCGTTTTTGCTAGGCGCAGT

EST: gi|78021489|gb|DV489876.1|DV489876

EST:     TTGCATTTAGAGACAAGGATTTTAAGACTGCAATTGACTACTATTCCAAG                         CTAGTCGCAATGATGTCGACGCCTTCGGCTACCGTTTTTGCTAGGCGCAGT
genomic: TTGCATTTAGAGACAAGGATTTTAAGACTGCAATTGACTACTATTCCAAGgtatcagcat ... tctaatgcagCTAGTCGCAATGATGTCGACGCCTTCGGCTACCGTTTTTGCTAGGCGCAGT

EST: gi|71437024|gb|DR818074.1|DR818074

EST:     TTGCATTTAGAGACAGGGATTTTAAGACTGCAAATGACTACTATTCCAAG                         CTAGTCGCAATGATGT
genomic: TTGCATTTAGAGACAAGGATTTTAAGACTGCAATTGACTACTATTCCAAGgtatcagcat ... tctaatgcagCTAGTCGCAATGATGT

EST: gi|71758345|gb|DR956282.1|DR956282

EST:     TGCAATTGACTACTATTCCAAG                         CTAGTCGCAATGATGTCGACGCCTTCGGCTACCGTTTTTGCTAGGCGCAGT
genomic: TGCAATTGACTACTATTCCAAGgtatcagcat ... tctaatgcagCTAGTCGCAATGATGTCGACGCCTTCGGCTACCGTTTTTGCTAGGCGCAGT

EST: gi|71774299|gb|DR972177.1|DR972177

EST:     TTGCATTTAGAGACAAGGATTTTAAGACTGCAATTGACTACTATTCCAAG                         CTAGTCGCAATGATGTCGACGCCTTCGGCTACCGTTTTTGCTAGGCGCAGT
genomic: TTGCATTTAGAGACAAGGATTTTAAGACTGCAATTGACTACTATTCCAAGgtatcagcat ... tctaatgcagCTAGTCGCAATGATGTCGACGCCTTCGGCTACCGTTTTTGCTAGGCGCAGT

EST: gi|101394044|gb|EB818955.1|EB818955

EST:     TTGCATTTAGAGACAAGGATTTTAAGACTGCAATTGACTACTATTCCAAG                         CTAGTCGCAATGATGTCGACGCCTTCGGCTACCGTTTTTGCTAGGCGCAGT
genomic: TTGCATTTAGAGACAAGGATTTTAAGACTGCAATTGACTACTATTCCAAGgtatcagcat ... tctaatgcagCTAGTCGCAATGATGTCGACGCCTTCGGCTACCGTTTTTGCTAGGCGCAGT

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 4 RNA-Seq libraries.

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 94

ATGGACCCAGCAAGTGCAAGAGATGCTGAACACAAAGAAGTTTGGTGACATTGCATTTAGAGACAAGGATTTTAAGACTGCAATTGACTACTATTCCAAGgtatcagcat ... tctaatgcagCTAGTCGCAATGATGTCGACGCCTTCGGCTACCGTTTTTGCTAGGCGCAGTTTTTCCTACTTGATGAATGAGCAAGCAGAGCTTGCTCTACGGGACGCAA

Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 14

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 21