ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GAGAGGCCCATTCCTTGAAAGTGGAGAACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAGgttcttttcatttactgatatcagaaatataaatttcctttggctcctgttgtgtataaccttgtattttttgtgtgcag

Basic information

species	Zea mays
transcript	GRMZM2G120578_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G120578_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g15550.1 (Oryza sativa), 5'ss of exon 4

GAGAGGCCCATTCCTTGAAAGTGGAGAACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAGgttctt--------ttcatttactgatatcagaaatataaatttcctttggctcctgttgtgtataaccttgtattttt-tgtgtgcag----------------
|||||||||||||  ||||||| ||||| || ||||| |||||||| ||||||||||| |||||  | || |||||||||||          |||  || ||| | |  ||||| |||     | | |    | || |   |    ||  | | || ||||  | |                
GAGAGGCCCATTCACTGAAAGTTGAGAAGATCTTGTATCAGGGGAAGTCACCATACCAAGAAGTTTTAGTTTTTGAGgttctcaacttctcatcacctattgacagccaaaataaaaaaaaaatctagtatttattatactttgtattacagtgttgtgtgacctgttttttttttatgcag

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|211320667|gb|FL013191.1|FL013191

EST:     CATATTGTACCAGGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAG                         TCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT
genomic: CATATTGTACCAGGGG-AAATCACCATACCAGGAAGTCCTGGTCTTTGAGgttcttttca ... ttgtgtgcagTCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT

EST: gi|148956445|gb|EC902269.2|EC902269

EST:     ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAG                         TCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT
genomic: ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAGgttcttttca ... ttgtgtgcagTCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT

EST: gi|78117805|gb|DV536192.1|DV536192

EST:     ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAG                         TCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT
genomic: ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAGgttcttttca ... ttgtgtgcagTCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT

EST: gi|148931937|gb|EC875166.2|EC875166

EST:     ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAG                         TCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT
genomic: ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAGgttcttttca ... ttgtgtgcagTCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT

EST: gi|148930370|gb|EE284813.2|EE284813

EST:     ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAG                         TCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT
genomic: ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAGgttcttttca ... ttgtgtgcagTCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT

EST: gi|211322828|gb|FL013194.1|FL013194

EST:     ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAG                         TCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT
genomic: ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAGgttcttttca ... ttgtgtgcagTCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT

EST: gi|149072878|gb|EE161134.2|EE161134

EST:     ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAG                         TCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT
genomic: ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAGgttcttttca ... ttgtgtgcagTCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT

EST: gi|211322835|gb|FL013201.1|FL013201

EST:     CATATTGTACCAGGGGAAATCACCATACCAAGGAAGTCCTGGTCTTTGAG                         TCGTCAACCTATGGGGAAAAGTC-TTGTGNCTTGATGGTATTGTTCAATTG
genomic: CATATTGTACCAGGGGAAATCACCATACCA-GGAAGTCCTGGTCTTTGAGgttcttttca ... ttgtgtgcagTCGTCAACCTATGGG-AAA-GTCCTTGTG-CTTGATGGTATTGTTCAATTG

EST: gi|211322829|gb|FL013195.1|FL013195

EST:     ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAG                         TCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT
genomic: ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAGgttcttttca ... ttgtgtgcagTCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT

EST: gi|32865849|gb|CF005531.1|CF005531

EST:     ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAG                         TCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT
genomic: ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAGgttcttttca ... ttgtgtgcagTCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT

EST: gi|28188224|gb|CB179834.1|CB179834

EST:     ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAG                         TCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT
genomic: ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAGgttcttttca ... ttgtgtgcagTCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT

EST: gi|148963955|gb|EE015081.2|EE015081

EST:     ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAG                         TCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT
genomic: ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAGgttcttttca ... ttgtgtgcagTCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT

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: 48 (upstream exon), 48 (downstream exon)
Score: 160

GAGAGGCCCATTCCTTGAAAGTGGAGAACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAGgttcttttca ... ttgtgtgcagTCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACTGATAAGGATGAATGTGCGTACCAGGAAATGATTACTCACCTCCCACTCT

Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 115

Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 75