ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CGCCAGCGTGGCAGAAGCTGACAAAGAAGACGTGGACTTGGCAGTGAGGGCAGCCAGGGCCGCTTTCGACCACGGCGAGTGGCCACGCATGTCTGGATCCgtacgatgctcctcgacccctctgtagtctgtacacgtactacgcaactgccttggtagttagtgtggccgatgatgactattgactagcgacgacgtgggcaacgcaacattaactggcag

Basic information

species	Zea mays
transcript	GRMZM2G122172_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G122172_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os06g39230.1 (Oryza sativa), 5'ss of exon 1

CGCCAGCGTGGCAGAAGCTGACAAAGAAGACGTGGACTTGGCAGTGAGGGCAGCCAGGGCCGCTTTCGACCACGGCGAGTGGCCACGCATGTCTGGATCCgtacgatgctcctcgacccctctgtagtctgtacacgtactacgcaactgccttggtagttagtgtggccgatgatgactattgactagcgacgacgtgggcaacgcaacattaactggcag
|||| |||| || ||||  ||||| || ||||| ||| |||| |||| ||| || ||||  || |||||||||||||| ||||| |||||||| ||||| ||||| |  || ||  |  |     | || || ||          || || || |  ||| |  |    | |||  |  | ||| | |  |  |                            
CGCCCGCGTCGCCGAAGGCGACAAGGAGGACGTCGACCTGGCGGTGAAGGCGGCGAGGGAAGCATTCGACCACGGCGAATGGCCTCGCATGTCGGGATCAgtacggtcatcttcttcttcctctcaatc-gtgcaaa--------aaatggctggaaagtgaccg--atcaatggcgcat-ttgtcaaatgcag----------------------------

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|76936946|gb|DV174974.1|DV174974

EST:     CAGCCAGGGCCGCTTTCGACCACGGCGAGTGGCCACGCATGTCTGGATCC                         GAACGGGGGCGGATCATGGCGAGGCTGGCCGACCTGGTGGAGGAGCGCGCG
genomic: CAGCCAGGGCCGCTTTCGACCACGGCGAGTGGCCACGCATGTCTGGATCCgtacgatgct ... taactggcagGAACGGGGGCGGATCATGGCGAGGCTGGCCGACCTGGTGGAGGAGCGCGCG

EST: gi|148948770|gb|EC894171.2|EC894171

EST:     CAGCCAGGGCCGCTTTCGACCACGGCGAGTGGCCACGCATGTCTGGATCC                         GAACGGGGGCGGATCATGGCGAGGCTGGCCGACCTGGTGGAGGAGCGCGCG
genomic: CAGCCAGGGCCGCTTTCGACCACGGCGAGTGGCCACGCATGTCTGGATCCgtacgatgct ... taactggcagGAACGGGGGCGGATCATGGCGAGGCTGGCCGACCTGGTGGAGGAGCGCGCG

EST: gi|149087183|gb|EE176720.2|EE176720

EST:     CAGCCAGGGCCGCTTTCGACCACGGCGAGTGGCCACGCATGTCTGGATCC                         GAACGGGGGCGGATCATGGCGAGGCTGGCCGACCTGGTGGAGGAGCGCGCG
genomic: CAGCCAGGGCCGCTTTCGACCACGGCGAGTGGCCACGCATGTCTGGATCCgtacgatgct ... taactggcagGAACGGGGGCGGATCATGGCGAGGCTGGCCGACCTGGTGGAGGAGCGCGCG

EST: gi|76020437|gb|DT947607.1|DT947607

EST:     CAGCCAGGGCCGCTTTCCACCACGGCGAGTGGCCACGCATGTCTGGATCC                         GAACGGGGGCGGATCATGGCGAGGCTGGCCCGACCTGGTGGAGGAGCGCGC
genomic: CAGCCAGGGCCGCTTTCGACCACGGCGAGTGGCCACGCATGTCTGGATCCgtacgatgct ... taactggcagGAACGGGGGCGGATCATGGCGAGGCTGGCC-GACCTGGTGGAGGAGCGCGC

EST: gi|149009496|gb|EE041490.2|EE041490

EST:     CAGCCAGGGCCGCTTTCGACCACGGCGAGTGGCCACGCATGTCTGGATCC                         GAACGGGGGCGGATCATGGCGAGGCTGGCCGACCTGGTGGAGGAGCGCGCG
genomic: CAGCCAGGGCCGCTTTCGACCACGGCGAGTGGCCACGCATGTCTGGATCCgtacgatgct ... taactggcagGAACGGGGGCGGATCATGGCGAGGCTGGCCGACCTGGTGGAGGAGCGCGCG

EST: gi|148959028|gb|EE010537.2|EE010537

EST:     CAGCCAGGGCCGCTTTCGACCACGGCGAGTGGCCACGCATGTCTGGATCC                         GAACGGGGGCGGATCATGGCGAGGCTGGCCGACCTGGTGGAGGAGCGCGCG
genomic: CAGCCAGGGCCGCTTTCGACCACGGCGAGTGGCCACGCATGTCTGGATCCgtacgatgct ... taactggcagGAACGGGGGCGGATCATGGCGAGGCTGGCCGACCTGGTGGAGGAGCGCGCG

EST: gi|94478183|gb|EB707141.1|EB707141

EST:     CAGCCAGGGCCGCTTTCGACCACGGCGAGTGGCCACGCATGTCTGGATCC                         GAACGGGGGCGGATCATGGCGAGGCTGGCCGACCTGGTGGAGGAGCGCGCG
genomic: CAGCCAGGGCCGCTTTCGACCACGGCGAGTGGCCACGCATGTCTGGATCCgtacgatgct ... taactggcagGAACGGGGGCGGATCATGGCGAGGCTGGCCGACCTGGTGGAGGAGCGCGCG

EST: gi|211099338|gb|FL362938.1|FL362938

EST:     CAGCCAGGGCCGCTTTCGACCACGGCGAGTGGCCACGCATGTCTGGATCC                         GAACGGGRGCGGATCATGGCGAAGGCTGGCCGACCTGGTGGA
genomic: CAGCCAGGGCCGCTTTCGACCACGGCGAGTGGCCACGCATGTCTGGATCCgtacgatgct ... taactggcagGAACGGGGGCGGATCATGGCGA-GGCTGGCCGACCTGGTGGA

EST: gi|148942565|gb|EC887584.2|EC887584

EST:     CAGCCAGGGCCGCTTTCGACCACGGCGAGTGGCCACGCATGTCTGGATCC                         GAACGGGGGCGGATCATGGCGAGGCTGGCCGACCTGGTGGAGGAGCGCGCG
genomic: CAGCCAGGGCCGCTTTCGACCACGGCGAGTGGCCACGCATGTCTGGATCCgtacgatgct ... taactggcagGAACGGGGGCGGATCATGGCGAGGCTGGCCGACCTGGTGGAGGAGCGCGCG

EST: gi|148993481|gb|EE033800.2|EE033800

EST:     CAGCCAGGGCCGCTTTCGACCACGGCGAGTGGCCACGCATGTCTGGATCC                         GAACGGGGGCGGATCATGGCGAGGCTGGCCGACCTGGTGGAGGAGCGCGCG
genomic: CAGCCAGGGCCGCTTTCGACCACGGCGAGTGGCCACGCATGTCTGGATCCgtacgatgct ... taactggcagGAACGGGGGCGGATCATGGCGAGGCTGGCCGACCTGGTGGAGGAGCGCGCG

EST: gi|71317748|gb|DR795633.1|DR795633

EST:     CAGCCAGGGCCGCTTTCGACCACGGCGAGTGGCCACGCATGTCTGGATCC                         GAACGGGGGCGGATCATGGCGAGGCTGGCCGACCTGGTGGAGGAGCGCGCG
genomic: CAGCCAGGGCCGCTTTCGACCACGGCGAGTGGCCACGCATGTCTGGATCCgtacgatgct ... taactggcagGAACGGGGGCGGATCATGGCGAGGCTGGCCGACCTGGTGGAGGAGCGCGCG

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: 47 (upstream exon), 9 (downstream exon)
Score: 3

CGCCAGCGTGGCAGAAGCTGACAAAGAAGACGTGGACTTGGCAGTGAGGGCAGCCAGGGCCGCTTTCGACCACGGCGAGTGGCCACGCATGTCTGGATCCgtacgatgct ... taactggcagGAACGGGGGCGGATCATGGCGAGGCTGGCCGACCTGGTGGAGGAGCGCGCGGACGAGCTGGCGGCCCTGGAGAGCCTGGACGCCGGCAAGCACCCGGCCG

Block sizes: 46 (upstream exon), 43 (downstream exon)
Score: 12

Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 8