ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

AATGTTTGTTGATGCACTGGATGCACAAATGTATGACAAGCACCATCAAACTGGGCATTGCATCTTGAGTCTCCACAAGgtgaaccctttgcttcgtctttagataacattaaatatttttttttcaaatcctgtcccagagcaatagattttctgaagatagaataatcgatagtgcg...

Basic information

species	Zea mays
transcript	GRMZM2G053047_T02
intron #	14
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G053047_T02 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os01g43380.1 (Oryza sativa), 5'ss of exon 8

AATGTTTGTTGATGCACTGGATGCACAAATGTATGACAAGCACCATCAAACTGGGCATTGCATCTTGAGTCTCCACAAGgtgaaccctttgcttcgtctttagataacattaaatatttttttttcaaatcctgtcccaga-gcaatagatttt--ctgaagatagaataat-cgatagtgcg
||||||||| ||||| ||||||||||||||||| ||||| || ||| |||| ||||||||||| |||||||| |||| ||||   || |  |||   |||||  ||  || ||| |  |||  ||  |||  | |  |||  |||    | ||   |||||   |    |||  | |    | 
AATGTTTGTAGATGCTCTGGATGCACAAATGTACGACAAACATCATGAAACAGGGCATTGCATATTGAGTCTTCACAGGgtgcgtccatctctta--ctttatttag-atgaaacaaatttcattttaatgttctttcagttgcagcgcagttcagctgaattcaatgaaatatgctcacac-

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|60355160|gb|DN222133.1|DN222133

EST:     AGTCTCCACAAG                         GACCAGCACTGCTACTCCCGTCTTCTGGAGTTGATTGTGAATGTTTGGGCA
genomic: AGTCTCCACAAGgtgaaccctt ... ttttgtacagGACCAGCACTGCTACTCCCGTCTTCTGGAGTTGATTGTGAATGTTTGGGCA

EST: gi|20337002|gb|BQ172632.1|BQ172632

EST:     TGTATGACAAGCACCATCAAACTGGGCATTGCATCTTGAGTCTCCACAAG                         GACCAGCACTGCTACTCCCGTCTTCTGGAGTTGATTGTGAATGTTTGGGCA
genomic: TGTATGACAAGCACCATCAAACTGGGCATTGCATCTTGAGTCTCCACAAGgtgaaccctt ... ttttgtacagGACCAGCACTGCTACTCCCGTCTTCTGGAGTTGATTGTGAATGTTTGGGCA

EST: gi|60342418|gb|DN209391.1|DN209391

EST:     TGTATGACAAGCACCATCAAACTGGGCATTGCATCTTGAGTCTCCACAAG                         GACCAGCACTGCTACTCTCGTCTTCTGGAGTTGATTGTGAATGTTTGGGCA
genomic: TGTATGACAAGCACCATCAAACTGGGCATTGCATCTTGAGTCTCCACAAGgtgaaccctt ... ttttgtacagGACCAGCACTGCTACTCCCGTCTTCTGGAGTTGATTGTGAATGTTTGGGCA

EST: gi|60352494|gb|DN219467.1|DN219467

EST:     TGTATGACAAGCACCATCAAACTGGGCATTGCATCTTGAGTCTCCACAAG                         GACCAGCACTGCTACTCCCGTCTTCTGGAGTTGATTGTGAATGTTTGGGCA
genomic: TGTATGACAAGCACCATCAAACTGGGCATTGCATCTTGAGTCTCCACAAGgtgaaccctt ... ttttgtacagGACCAGCACTGCTACTCCCGTCTTCTGGAGTTGATTGTGAATGTTTGGGCA

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: 47 (upstream exon), 49 (downstream exon)
Score: 56

AATGTTTGTTGATGCACTGGATGCACAAATGTATGACAAGCACCATCAAACTGGGCATTGCATCTTGAGTCTCCACAAGgtgaaccctt ... ttttgtacagGACCAGCACTGCTACTCCCGTCTTCTGGAGTTGATTGTGAATGTTTGGGCATTCCACAGTGCACGACGGATGGTCTATGTTAATCCTGCAACTGGTCAAA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 24

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 46