ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtcgtagacaagacttctttaattgcttttctgtaacagtggttactaaataaacatgttattctttgactgttacagACTAAGCCTGCTCTGCCAGCACTTGCACGACTTATCCATTCCAACGATGAGGAAGTTCTCACTGATGCTTGCTGGGCTTTGTCATACTTATCTGACGGCA

Basic information

species	Zea mays
transcript	GRMZM2G091119_T02
intron #	5
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G091119_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g14950.1 (Oryza sativa), 3'ss of exon 5

gtcgtagacaagacttctttaattgcttttct-----gtaacagtggttactaaataaacatgttattctttgactgtta-cagACTAAGCCTGCTCTGCCAGCACTTGCACGACTTATCCATTCCAACGATGAGGAAGTTCTCACTGATGCTTGCTGGGCTTTGTCATACTTATCTGACGGCA
||  | |||||   ||||||     ||  | |     |||      |  | |   | |||||| | ||  |||  ||| |  |||||| ||||||||| |||||||| ||||| ||||| || ||||| ||||||||||||||||||||||| ||||||||| | ||||| |||||||| ||||
gtt-tggacaaagtttctttgtactctactgtagttagtagggaaagacagttccttaacatgatgtttattgggtgtcaatagACTAGGCCTGCTCTTCCAGCACTGGCACGGCTTATTCACTCCAATGATGAGGAAGTTCTCACTGATGCGTGCTGGGCTCTTTCATATTTATCTGATGGCA

upper sequence: GRMZM2G091119_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA10G29000.1 (Glycine max), 3'ss of exon 5

------------gtcgtagacaagacttctttaattgctttt---ctgtaacagtg----gttactaaataaacatgttattctttgactgttac---agACTAAGCCTGCTCTGCCAGCACTTGCACGACTTATCCATTCCAACGATGAGGAAGTTCTCACTGATGCTTGCTGGGCTTTGTCATACTTATCTGACGGCA
            ||    | |  |  ||   | |||  || |   |||  |  |||     || |  | |  | |  |||| |||||  | || |   ||  ||| ||||| || || || ||||| || ||||||||||| |||||||| |||||| | |||||||| || |||||  |||||||  | ||||| || |
cattggtcttttgtttatgtcctgcttttactgatttattataagctgctattgtgttttatttcacagttcatacattatactttgtttttttcttcagGTTAAACCTGCACTTCCTGCTCTTGCCCGTCTTATCCATTCGAACGATGAAGAAGTTTTGACTGATGCATGTTGGGCACTGTCATATCTTTCTGATGGTA

upper sequence: GRMZM2G091119_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT4G02150.1 (Arabidopsis thaliana), 3'ss of exon 5

--gtcgtagacaagacttctttaattgcttttctgtaacagtggttactaaata---aacatgttattctttga----ctgtt---acagACTAAGCCTGCTCTGCCAGCACTTGCACGACTTATCCATTCCAACGATGAGGAAGTTCTCACTGATGCTTGCTGGGCTTTGTCATACTTATCTGACGGCA
   || |  |  | ||    || ||||  | ||   || | |  |||  |        | || || ||  || |     | ||    |||||  | || ||| | ||||  ||||  || ||| | || || |  ||||| ||||||||||| ||||| ||||||||| |||||||| | || ||     
gtttccttaaatatacacactttattgaatctccacaatattttttaacatgcttctgatattttgttacttaaaacatttttcgagcagACACAACCAGCTTTACCAGTTCTTGAGCGCCTTGTGCAATCAATGGATGAAGAAGTTCTCACAGATGCATGCTGGGCTCTGTCATACCTCTCGGATAATT

upper sequence: GRMZM2G091119_T02 (Zea mays), 3'ss of exon 5
lower sequence: EFJ31557 (Selaginella moellendorffii), 3'ss of exon 5

gtcgtagacaagacttctttaattgcttttctgtaacagtggttactaaataaacatgttattctttgactgttacagACTAAGCCTGCTCTGCCAGCACTTGCACGACTTATCCATTCCAACGATGAGGAAGTTCTCACTGATGCTTGCTGGGCTTTGTCATACTTATCTGACGGCA
   |||     | | | | ||      |   |  ||   || |   |         |||| ||  |||       ||| | |  |||||| |  | || || | |   || || ||||| |  || || ||||| || |||||||| |||||||||||||||||| |||| || || |
---gtatgtgggtcatttgtaggcatgtcgatacaaatttgatcgttggtcg---gtgttgtttcttg-------cagTCGAGACCTGCTTTATCTGCTCTAGAAAAGCTGATTCATTCGACTGACGAAGAAGTCCTTACTGATGCATGCTGGGCTTTGTCATACATATCCGATGGTA

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|211094922|gb|FL161920.1|FL161920

EST:     GGACTCTTTCCAACTTTTGCAGGGGAAAGCCACAGCCATCATTTGATCAG                         ACTAAGCCTGCTCTGCCAGCACTTGCACGACTTATCCATTCCANCGATGAG
genomic: GGACTCTGTCCAACTTTTGCAGGGGAAAGCCACAGCCATCATTTGATCAGgtcgtagaca ... actgttacagACTAAGCCTGCTCTGCCAGCACTTGCACGACTTATCCATTCCAACGATGAG

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), 49 (downstream exon)
Score: 1006

AGCCCAGTTGAATGAGCATGCGAAGCTCTCCATGTTGAGGAATGCCACCTGGACTCTGTCCAACTTTTGCAGGGGAAAGCCACAGCCATCATTTGATCAGgtcgtagaca ... actgttacagACTAAGCCTGCTCTGCCAGCACTTGCACGACTTATCCATTCCAACGATGAGGAAGTTCTCACTGATGCTTGCTGGGCTTTGTCATACTTATCTGACGGCA

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 414

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 443

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 427

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tgcttttctgtaacagtggttactaaataaacatgttattctttgactgttacagACTAAGCCTGCTCTGCCAGCACTTGCACGACTTATCCATTCCAACGATGAGGAAGTTCTCACTGATGCTTGCTGGGCTTTGTCATACTTATCTGACGGCA