ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gtagttatgctagcattgcatgagctaatggctaatacataacatacacttgatcttgataaatctgacctatgttatttgctatttctatgtgcccacgtggtacttgatcatgctaaaatggaacacattttaaagtcaatttcaatgcttaatgcagGCATTGTGGAGCGTGACGGTCTAACTGGTCTTTATAGAGGTTTTGTGCCAAATGCGTTAAAAAATCTACCAAATAGCAG

Basic information

species	Zea mays
transcript	GRMZM2G178460_T01
intron #	8
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G178460_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g16040.1 (Oryza sativa), 3'ss of exon 8

gtagttatgctagcattgcatgagctaatggctaatacataacatacacttgatcttg-ataaatctgacctatgttatt---tgctatttctatgtgcccacgtggtacttgatcatg-----------ctaaaatggaacacattttaaagtcaatttcaatgcttaatgcagGCATTGTGGAGCGTGACGGTCTAACTGGTCTTTATAGAGGTTTTGTGCCAAATGCGTTAAAAAATCTACCAAATAGCAG
|||| |    ||    |       ||  ||    ||| | | |||    |   |  || ||||   | || |  | | |    ||| | |||||  ||| ||| ||   |||| || ||           ||||| || | ||  | ||||| |    |    |||| ||||||||||||||||| ||||| ||||||| ||| || || ||||||||||| |||||||| |||||||||||||||||||||||
gtagctgatttatatatagtccttctggtgttggataaacatcatcttttacttactgcataacgttcacttcagctctcagatgccagttctacatgctcacttgtagcttggtcttgtcctttatgggctaaactgaagcatttcttaaatttgtctc---tgctgaatgcagGCATTGTGGAACGTGATGGTCTAATTGGACTATACAGAGGTTTTGTTCCAAATGCATTAAAAAATCTACCAAATAGCAG

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|71423587|gb|DR806089.1|DR806089

EST:     GATGCAGATGAAAGGCACACCATACAATACTGTTTTTGATGCTATTCCAG                         GCATTGTGGAGCGTGACGGTCTAACTGGTCTTTATAGAGGTTTTGTGCCAA
genomic: GATGCAGATGAAAGGCACACCATACAATACTGTTTTTGATGCTATTCCAGgtagttatgc ... cttaatgcagGCATTGTGGAGCGTGACGGTCTAACTGGTCTTTATAGAGGTTTTGTGCCAA

EST: gi|50334119|gb|CO529245.1|CO529245

EST:     GATGCAGATGAAAGGCACACCATACAATACTGTTTTTGATGCTATTCCAG                         GCATTGTGGAGCGTGACGGTCTAACTGGTCTTTATAGAGGTTTTGTGCCAA
genomic: GATGCAGATGAAAGGCACACCATACAATACTGTTTTTGATGCTATTCCAGgtagttatgc ... cttaatgcagGCATTGTGGAGCGTGACGGTCTAACTGGTCTTTATAGAGGTTTTGTGCCAA

EST: gi|76919948|gb|DV167935.1|DV167935

EST:     GATGCAGATGAAAGGCACACCATACAATACTGTTTTTGATGCTATTCCAG                         GCATTGTGGAGCGTGACGGTCTAACTGGTCTTTATAGAGGTTTTGTGCCAA
genomic: GATGCAGATGAAAGGCACACCATACAATACTGTTTTTGATGCTATTCCAGgtagttatgc ... cttaatgcagGCATTGTGGAGCGTGACGGTCTAACTGGTCTTTATAGAGGTTTTGTGCCAA

EST: gi|60397321|gb|DN230137.1|DN230137

EST:     CATACAATACTGTTTTTGATGCTATTCCAG                         GCATTGTGGAGCGTGACGGTCTAACTGGTCTTTATAGAGGTTTTGTGCCAA
genomic: CATACAATACTGTTTTTGATGCTATTCCAGgtagttatgc ... cttaatgcagGCATTGTGGAGCGTGACGGTCTAACTGGTCTTTATAGAGGTTTTGTGCCAA

EST: gi|74236987|gb|DT644901.1|DT644901

EST:     CAATACTGTTTTTGATGCTATTCCAG                         GCATTGTGGAGCGTGACGGTCTAACTGGTCTTTATAGAGGTTTTGTGCCAA
genomic: CAATACTGTTTTTGATGCTATTCCAGgtagttatgc ... cttaatgcagGCATTGTGGAGCGTGACGGTCTAACTGGTCTTTATAGAGGTTTTGTGCCAA

EST: gi|60397862|gb|DN230678.1|DN230678

EST:     GATGCAGATGAAAGGCACACCATACAATACTGTTTTTGATGCTATTCCAG                         GCATTGTGGAGCGTGACGGTCTAACTGGTCTTTATAGAGGTTTTGTGCCAA
genomic: GATGCAGATGAAAGGCACACCATACAATACTGTTTTTGATGCTATTCCAGgtagttatgc ... cttaatgcagGCATTGTGGAGCGTGACGGTCTAACTGGTCTTTATAGAGGTTTTGTGCCAA

EST: gi|213170460|gb|FM192673.1|FM192673

EST:     TGATGCTATTCCAG                         GCA-TGTGGAGCGTGACGGTCTAACTGGTCTTTATAGAGGTTTTGTGCCAA
genomic: TGATGCTATTCCAGgtagttatgc ... cttaatgcagGCATTGTGGAGCGTGACGGTCTAACTGGTCTTTATAGAGGTTTTGTGCCAA

EST: gi|149004776|gb|EE039273.2|EE039273

EST:     GATGCAGATGAAAGGCACACCATACAATACTGTTTTTGATGCTATTCCAG                         GCATTGTGGAGCGTGACGGTCTAACTGGTCTTTATAGAGGTTTTGTGCCAA
genomic: GATGCAGATGAAAGGCACACCATACAATACTGTTTTTGATGCTATTCCAGgtagttatgc ... cttaatgcagGCATTGTGGAGCGTGACGGTCTAACTGGTCTTTATAGAGGTTTTGTGCCAA

EST: gi|74236988|gb|DT644902.1|DT644902

EST:     CAATACTGTTTTTGATGCTATTCCAG                         GCATTGTGGAGCGTGACGGTCTAACTGGTCTTTATAGAGGTTTTGTGCCAA
genomic: CAATACTGTTTTTGATGCTATTCCAGgtagttatgc ... cttaatgcagGCATTGTGGAGCGTGACGGTCTAACTGGTCTTTATAGAGGTTTTGTGCCAA

EST: gi|110951541|gb|EE171593.1|EE171593

EST:     GATGCAGATGAAAGGCACACCATACAATACTGTTTTTGATGCTATTCCAG                         GCATTGTGGAGCGTGACGGTCTAACTGGTCTTTATAGAGGTTTTGTGCCAA
genomic: GATGCAGATGAAAGGCACACCATACAATACTGTTTTTGATGCTATTCCAGgtagttatgc ... cttaatgcagGCATTGTGGAGCGTGACGGTCTAACTGGTCTTTATAGAGGTTTTGTGCCAA

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: 104

GCAACATTTGCAACTTTGATGTGTTATCCGCTGGACACTGTTAGGAGACAGATGCAGATGAAAGGCACACCATACAATACTGTTTTTGATGCTATTCCAGgtagttatgc ... cttaatgcagGCATTGTGGAGCGTGACGGTCTAACTGGTCTTTATAGAGGTTTTGTGCCAAATGCGTTAAAAAATCTACCAAATAGCAG

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 80

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 69

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 85

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

cttgatcatgctaaaatggaacacattttaaagtcaatttcaatgcttaatgcagGCATTGTGGAGCGTGACGGTCTAACTGGTCTTTATAGAGGTTTTGTGCCAAATGCGTTAAAAAATCTACCAAATAGCAG