ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

ATCTAGAAGAAGATGAACAACCTAAAAAGAAGGTTAGATTAGGGAGCCCAGCGGCTCAATGGATTTCAGTTTATAATGCGAGGTGGCCCATCAAGCAGAGgtaattacaatcatttaattatatcagatgctacaatgcatgatagttatgttatacgcgctgcatatgctacaatgcatgatagttatgttatacgtgc...

Basic information

species	Zea mays
transcript	GRMZM2G082099_T01
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G082099_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os07g07560.2 (Oryza sativa), 5'ss of exon 12

ATCTAGAAGAAGATGAACAACCTAAAAAGAAGGTTAGATTAGGGAGCCCAGCGGCTCAATGGATTTCAGTTTATAATGCGAGGTGGCCCATCAAGCAGAGgtaattac----aatcatttaattatatcagatgcta-caatgcatgatagttatgttatacgcgctgcatatgctacaatgc--atgatagttatgttatacgtgc
| |  ||||||||||| ||||| || ||||| ||||||||||| |||||||| |||||||||||||| |||||||| || ||| || |||| ||||| ||||||||||    ||  | |  || |||| |      | | |       | |||  ||  || |  ||   | | ||   ||||  |  ||||| || | |       
ACCATGAAGAAGATGAGCAACCCAAGAAGAAAGTTAGATTAGGTAGCCCAGCAGCTCAATGGATTTCTGTTTATAACGCCAGGCGGGCCATGAAGCAAAGgtaattacatcaaagaactagatgatataaagcatgatcgacctgcatttgtttagtc-taggtacttgcttttcttggatgcaaacaatagtaatttgaa------

upper sequence: GRMZM2G082099_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA16G04580.1 (Glycine max), 5'ss of exon 12

ATCTAGAAGAAGATGAACAACCTAAAAAGAAGGTTAGATTAGGGAGCCCAGCGGCTCAATGGATTTCAGTTTATAATGCGAGGTGGCCCATCAAGCAGAGgtaattacaa--tcatttaat-tatatcagatgct-----acaatgcatgatagttatgttat-acgcgctgcatatgctacaatgcatga-tagttatgttatacgtgc
|||| ||||||||||| |||||||| ||||| ||  |||| ||||| || ||  |||| ||||| ||||| ||||||||  |  | ||||| |||||||||||||||  |  |||||   | | || |   | ||     |   ||||   || || |   || |    ||     ||||   |||||  |  ||||             
ATCTGGAAGAAGATGAGCAACCTAAGAAGAAAGTGCGATTGGGGAGTCCTGCTACTCAGTGGATATCAGTGTATAATGCTCGCCGTCCCATGAAGCAGAGgtaattaatacatcattctctgtctagcttgttcttaataatgttgcagattatttgttaaatcataaacttttcttgctttgatgcaaaagcagttgaa----------

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|61118494|gb|DN559455.1|DN559455

EST:     GCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGGCCCATGAAGCAGAG                         GTACCATTACAATGTGGCTGA
genomic: GCGGCTCAATGGATTTCAGTTTATAATGCGAGGTGGCCCATCAAGCAGAGgtaattacaa ... tgtttcttagGTACCATTACAATGTGGCTGA

EST: gi|61118493|gb|DN559454.1|DN559454

EST:     GCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGGCCCATGAAGCAGAG                         GTACCATTACAATGTGGCTGA
genomic: GCGGCTCAATGGATTTCAGTTTATAATGCGAGGTGGCCCATCAAGCAGAGgtaattacaa ... tgtttcttagGTACCATTACAATGTGGCTGA

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: 8 (upstream exon), 49 (downstream exon)
Score: 123

ATCTAGAAGAAGATGAACAACCTAAAAAGAAGGTTAGATTAGGGAGCCCAGCGGCTCAATGGATTTCAGTTTATAATGCGAGGTGGCCCATCAAGCAGAGgtaattacaa ... tgtttcttagGTACCATTACAATGTGGCTGACTCGAGGCTAAGCCAACATATAGAAAAGGGCAACGATGATGGGCTTTACATTAGCAGCATGGCTTCCTCGGCAAACCTT

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

Block sizes: 8 (upstream exon), 49 (downstream exon)
Score: 63