ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GCTGAACCAATGCCATCGCTTGATGCAATTGCAGCACATCATAACATCTCATTGGGTGGCCTGCCACCTCTTCCCTTCCAGAAACAGGAGCGTTTGCAAGgtataattttatcaaccaccatcagcatgatgcctatttcatattcctgaagtgttaaagtggtatttctttgggttttccacttttcaatcattcaaacaagtgcttgaacatcctctttgttaattgcgtttcctgtag

Basic information

species	Zea mays
transcript	GRMZM2G033828_T01
intron #	11
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G033828_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os08g42600.1 (Oryza sativa), 5'ss of exon 10

GCTGAACCAATGCCATCGCTTGATGCAATTGCAGCACATCATAACATCTCATTGGGTGGCCTGCCACCTCTTCCCTTCCAGAAACAGGAGCGTTTGCAAGgtataattttatcaaccaccatcagcatgatgcctatttcatattcctgaagtgt-taaagtggtatttctttgggttttccacttttcaatcattcaaacaagtgcttgaacatcctctttgttaattgcgtttcctgtag
||||||||||||||||| |||||||| ||||| || || |||||||| ||| | |  || ||||||||||||||||| || || || || | ||  | |||||      |  ||    | | |  |||| | | |      |     | || | | | ||    |  ||     |   || ||  |||   |  |||    |                                        
GCTGAACCAATGCCATCACTTGATGCCATTGCGGCGCACCATAACATTTCACTCGAGGGGCTGCCACCTCTTCCCTTTCAAAAGCAAGAACATTCACCAGgtagcccactggca--tgctacct-catgtttcattgcctttgactttaaaatatatgaaagaatggtt-----gaacttacaaattttggtatttcttgtag---------------------------------------

upper sequence: GRMZM2G033828_T01 (Zea mays), 5'ss of exon 11
lower sequence: AT3G12280.2 (Arabidopsis thaliana), 5'ss of exon 10

GCTGAACCAATGCCATCGCTTGATGCAATTGCAGCACATCATAACATCTCATTGGGTGGCCTGCCACCTCTTCCCT-TCCAGAAACAGGAGCGTTTGCAAGgtataattttatcaaccaccatcagcatgatgcctatttcatattcctgaagtgttaaagtggtatttctttgggttttccacttttcaatcattcaaacaagtgcttgaacatcctctttgttaattgcgtttcctgtag
||||||||||||||||| || |||||||| ||||||| |  |||  |||| |   |  ||    ||    |   || | || || || ||   ||  | |||||   ||||||      |    |  |       | |   |  |      | || ||   |  | || |      || || | ||| |   |||  |                                            
GCTGAACCAATGCCATCTCTGGATGCAATCGCAGCACTTATTAATTTCTC-TGACGGAGCAAATCATGCATCATCTGTACAAAAGCATGAAACTTGTCCAGgta--gttttatttgtttctga-attaaagcagttttccaacctgttgttaatggtatgattttcttaccaaaaattgtcaaatttgctgccatatag-------------------------------------------

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|30087053|gb|CB885261.1|CB885261

EST:     GGGTGGCCTGCCACCTCTTCCCCTT-TAGAAACAGGAGCGTTTGCAAG                         ACAAAGATGAAGTCAGGTCTCCCAAAAGGGCATGCACTGAGAGGAGAAACG
genomic: GGGTGGCCTGCCACCTCTT-CCCTTCCAGAAACAGGAGCGTTTGCAAGgtataatttt ... tttcctgtagACAAAGATGAAGTCAGGTCTCCCAAAAGGGCATGCACTGAGAGGAGAAACG

EST: gi|67026333|gb|CO455082.1|CO455082

EST:     ATTGGGTGGCCTGCCACCTCTTCCTTTCCAGAAACAGGAGCGTTTGCAAG                         ACAAAGATGAAGTCAGGTCTCCCAAAAGGGCATGCACTGAGAGGAGAAACG
genomic: ATTGGGTGGCCTGCCACCTCTTCCCTTCCAGAAACAGGAGCGTTTGCAAGgtataatttt ... tttcctgtagACAAAGATGAAGTCAGGTCTCCCAAAAGGGCATGCACTGAGAGGAGAAACG

EST: gi|29167908|gb|CB411168.1|CB411168

EST:     ATTGGGTGGCCTGCCACCTCTTCCCTTCCAGAAACAGGAGCGTTTGCAAG                         ACAAAGATGAAGTCAGGTCTCCCAAAAGGGCATGCACTGAGAGGAGAAACG
genomic: ATTGGGTGGCCTGCCACCTCTTCCCTTCCAGAAACAGGAGCGTTTGCAAGgtataatttt ... tttcctgtagACAAAGATGAAGTCAGGTCTCCCAAAAGGGCATGCACTGAGAGGAGAAACG

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), 49 (downstream exon)
Score: 148

GCTGAACCAATGCCATCGCTTGATGCAATTGCAGCACATCATAACATCTCATTGGGTGGCCTGCCACCTCTTCCCTTCCAGAAACAGGAGCGTTTGCAAGgtataatttt ... tttcctgtagACAAAGATGAAGTCAGGTCTCCCAAAAGGGCATGCACTGAGAGGAGAAACGTGCTGGTGGACAGCAATTCATTGCGGTCACCAGTGAAGGATATTATTAA

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 10

Block sizes: 45 (upstream exon), 42 (downstream exon)
Score: 9