ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CGTCATCGCCGATGGCGTCGACAAGAACGGCAAGCCGCACAAGGTCAGGCTCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagctagccaatctctcctgctttctctctctctctcaagtctgaatcgactattctccgtcattttcttgagcatttctgcctgcag

Basic information

species	Zea mays
transcript	GRMZM2G168143_T02
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G168143_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os06g01850.1 (Oryza sativa), 5'ss of exon 2

CGTCATCGCCGATGGCGTCGACAAGAACGGCAAGCCGCACAAGGTCAGGCTCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagctagccaatct-ctcctgctttctctctctctctcaagtct---gaatcgactattctccgtcattttct-tgagcatttctgcctgcag------
|||||||||||| |||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||  ||||||||||||||||||||||||| ||||||  |   |   ||| ||||| |||  ||  ||||  ||         | |||||      | | |||       | | ||| |   | || |       
CGTCATCGCCGACGGCGTCGACAAGAACGGCAAGCCGCACAAGCTCAGGCTCTACTCCATCGCCAGCAGCGCTCTCGGCGACTTCGGCGACTCCAAGACCgtcagtccccctcttctcttctcctccttattcaatctcattccttctcatcggatcgatctcctttcttcacaccagataatcatcttcacttgtacctctag

upper sequence: GRMZM2G168143_T02 (Zea mays), 5'ss of exon 2
lower sequence: AT1G20020.2 (Arabidopsis thaliana), 5'ss of exon 3

----------------------------------CGTCATCGCCGATGGCGTCGACAAGAACGGCAAGCCGCACAAGGTCAGGCTCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagctagccaatctctcctgctttctctctctctctcaagtctgaatcgactattctccgtcattttcttgagcatttctgcctgcag
                                   || || || |||||  | |||||||| || ||||| ||||||||||| || |||||||| || ||||||||  | || ||  ||||| | ||  | || || |  | | |     | |  |    |||      || | |   |||||  |     | |    |  | ||  || ||               
GAGAAATCCCGTACAGAGAAGGACAATCTGTTGGTGTGATTGCAGATGGAATTGACAAGAATGGAAAGCCTCACAAGgtcagactttactccattgcaagcagcgctcttggagatctcggcaattctgaaaccgtaataaaccatttccttta-caaattttacgaggctttgttttgtctggttaagtgaatgaagg--agttgtttcag---------------

upper sequence: GRMZM2G168143_T02 (Zea mays), 5'ss of exon 2
lower sequence: AT1G20020.3 (Arabidopsis thaliana), 5'ss of exon 3

CGTCATCGCCGATGGCGTCGACAAGAACGGCAAGCCGCACAAGGTCAGGCTCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagctagccaatctctcctgctttctctctctctctcaagtctgaatcgactattctccgtcattttcttgagcatttctgcctgcag
 || || || |||||  | |||||||| || ||||| ||||||||||| || |||||||| || ||||||||  | || ||  ||||| | ||  | || || |  | | |     | |  |    |||      || | |   |||||  |     | |    |  | ||  || ||               
TGTGATTGCAGATGGAATTGACAAGAATGGAAAGCCTCACAAGGTCAGACTTTACTCCATTGCAAGCAGCGCTCTTGGAGATCTCGGCAATTCTGAAACCgtaataaaccatttccttta-caaattttacgaggctttgttttgtctggttaagtgaatgaagg--agttgtttcag---------------

upper sequence: GRMZM2G168143_T02 (Zea mays), 5'ss of exon 2
lower sequence: AT5G66190.2 (Arabidopsis thaliana), 5'ss of exon 3

CGTCATCGCCGATGGCGTCGACAAGAACGGCAAGCCGCACAAGGTCAGGCTCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagctagccaatctctcctgctttctctctctctctcaagtctgaatcgactattctccgtcattttcttgagcatttctgcctgcag
 || ||  | || ||  | ||||||||||| |||||||||||| ||||||| ||||| ||||| || || || || || ||||| || ||||||||||| || || |  |    |||| |||   |     ||  ||   | | |  | |    |  ||  ||  | || |     |     ||    |||||
AGTGATTCCAGAGGGAATAGACAAGAACGGGAAGCCGCACAAGCTCAGGCTTTACTCTATCGCGAGTAGTGCCATTGGTGACTTTGGAGACTCCAAGACCgtaagcaaat----aatccctctaac---aactaactaaataatgatttacaaaatgatcttctcttatctg--gaaatggatccttttgcag

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|71441572|gb|DR822622.1|DR822622

EST:     TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACA                         GTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC

EST: gi|93015751|gb|EB641271.1|EB641271

EST:     TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACA                         GTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC

EST: gi|148932036|gb|EC875356.2|EC875356

EST:     TCTACTCCATCGCCAGCAGCGCGATCGGCGAATTCGGCGACTTCAAGACA                         GTCTCGCTGTGTGTCAAGAGGCTCATCTACCCCAA-GAATGCCGGAGAGAT
genomic: TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGA-TGCCGGAGAGAT

EST: gi|74242655|gb|DT650569.1|DT650569

EST:     TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACA                         GTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC

EST: gi|50327429|gb|CO522555.1|CO522555

EST:     TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACA                         GTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC

EST: gi|94475152|gb|EB704110.1|EB704110

EST:     TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACA                         GTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC

EST: gi|91047927|gb|EB158345.1|EB158345

EST:     TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACA                         GTCTCGCTGTGTGTCAAGAGGCTCATCTA
genomic: TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTA

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), 44 (downstream exon)
Score: 14

CGTCATCGCCGATGGCGTCGACAAGAACGGCAAGCCGCACAAGGTCAGGCTCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCTTATGTACGTCTACGTCTCTTCACA

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 70

Block sizes: 46 (upstream exon), 44 (downstream exon)
Score: 5