ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TCATATATTCTTTCAACAAAGGCATGGTCCAGGCCAAAGATCATTGTATAACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAGgtttgttttgagttcggtgacctattttttcagatagaaagatctctctggaataatattctattgtttacacaattcattttgcag

Basic information

species	Zea mays
transcript	GRMZM2G047223_T03
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G047223_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os08g31840.2 (Oryza sativa), 5'ss of exon 4

TCATATATTCTTTCAACAAAGGCATGGTCCAGGCCAAAGATCATTGTATAACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAGgtttgttttgagttcggtgacctattttttcagatagaaagatctctctggaataatattc--tattgtttacacaattcattttgcag
 ||||| ||||| ||||| || |||||||||||||||||||| ||||||||  || | |||||||| ||||| ||||| |||||||||||||| |||||||||||| || |    | ||||   ||||   | ||| |   || ||| | || ||||||    | |  ||| || ||| |||  |||||
ACATATTTTCTTCCAACAGAGACATGGTCCAGGCCAAAGATCCTTGTATAATGTTCTAAAAGCATACTCTGTTTATGATAGGGATGTTGGATACGTGCAGgtttgtgttaaaactgctgactagttttaggatataaacttat-tctgttgagtaatatgtgttctcttttgcataat-catgatgcag

upper sequence: GRMZM2G047223_T02 (Zea mays), 5'ss of exon 4
lower sequence: AT5G15930.1 (Arabidopsis thaliana), 5'ss of exon 4

TCATATATTCTTTCAACAAAGGCATGGTCCAGGCCAAAGATCATTGTATAACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAGgtttgttttgagttcggtgacctattttttcagatagaaagatctctctggaataatattctattgtttacacaattcattttgcag
 ||| | ||||| ||  | || ||||| ||||||||||||||||| || ||  || | |||||||| |||||||||||||| ||||| |||||||| ||||| | |   ||| ||  |  | |  || ||        |||||    ||  ||| |      | |  |   || |   ||  |||||
ACATGTTTTCTTCCAGAAGAGACATGGACCAGGCCAAAGATCATTATACAATGTTCTAAAAGCATACTCTGTCTATGACAGAGATGTCGGATATGTTCAGgtatttccagagatcttttcctttattcttatttgcccaagatggtact--aattacgaaagactcatggtactaaaaataatgcag

upper sequence: GRMZM2G047223_T02 (Zea mays), 5'ss of exon 4
lower sequence: Vv14s0083g00540.t01 (Vitis vinifera), 5'ss of exon 4

TCATATATTCTTTCAACAAAGGCATGGTCCAGGCCAAAGATCATTGTATAACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAGgtttg----ttttgagttcggtgacctattttttca--gatagaaagatctctctggaataatattctattgtttacacaattcattttgcag
 ||| | ||||| || || || ||||| || || ||||| ||  | || ||  ||||||| ||||| ||||| |||||||| |||||||||||||| ||||||||    |  ||  |    | ||   | | || |  | | | | |||       |||| | |||  ||||     |   ||     |||||
ACATGTTTTCTTCCAGCAGAGACATGGACCTGGTCAAAGGTCCCTCTACAATGTTTTGAAGGCATACTCTGTGTATGACAGAGATGTTGGATATGTTCAGgtttggatctcatgtatctcatcactcttctatttactgtttgtaggatact----gaatgacattggattg---gtatcgtttgaaatgcag

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|78113905|gb|DV532294.1|DV532294

EST:     ACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAG                         GGAATGGGATTTTTAGCTGGGTTGCTGCTTCTTTATATGAGTGAGGAGGAT
genomic: ACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAGgtttgttttg ... cattttgcagGGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGAT

EST: gi|211004390|gb|FL335892.1|FL335892

EST:     ACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAG                         GGAATGGGATTTT-AGCT
genomic: ACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAGgtttgttttg ... cattttgcagGGAATGGGATTTTTAGCT

EST: gi|61118400|gb|DN559361.1|DN559361

EST:     ACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAG                         GGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGAT
genomic: ACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAGgtttgttttg ... cattttgcagGGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGAT

EST: gi|89758012|gb|DY687355.1|DY687355

EST:     ACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAG                         GGAATGGGATTTTTAGCTGGGTTGCTGCTTCTTTATATGAGTGAGGAGGAT
genomic: ACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAGgtttgttttg ... cattttgcagGGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGAT

EST: gi|91874336|gb|EB404293.1|EB404293

EST:     ACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAG                         GGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGAT
genomic: ACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAGgtttgttttg ... cattttgcagGGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGAT

EST: gi|78117555|gb|DV535942.1|DV535942

EST:     ACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAG                         GGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGAT
genomic: ACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAGgtttgttttg ... cattttgcagGGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGAT

EST: gi|71771758|gb|DR969695.1|DR969695

EST:     ACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAG                         GGAATGGGATTTTTAGCTGGGGTGCTGCTTCTTTATATGAGTGAGGAGGAT
genomic: ACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAGgtttgttttg ... cattttgcagGGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGAT

EST: gi|78118515|gb|DV536899.1|DV536899

EST:     ACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAG                         GGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGAT
genomic: ACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAGgtttgttttg ... cattttgcagGGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGAT

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: 77

TCATATATTCTTTCAACAAAGGCATGGTCCAGGCCAAAGATCATTGTATAACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAGgtttgttttg ... cattttgcagGGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGATGCATTCTGGTTATTAGTCGCGTTGCTAAAGGGAGCTGTCCATGCACCAA

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 28

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 70