ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtatgttttcgcagttctttaattcgtacattcagaagtcttggcaccacttcatctcaccaacactagcttatcacctcacgtttcttctgcaccatgcagACTTTGGATGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGTGGATACTCCCTCGATTCTGATGCGATTGGTCTACCAAGGGCTCATGGGCTTT

Basic information

species	Zea mays
transcript	GRMZM2G180335_T03
intron #	11
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G180335_T01 (Zea mays), 3'ss of exon 19
lower sequence: LOC_Os01g69130.2 (Oryza sativa), 3'ss of exon 19

gtatgttttcgcagttctttaattcgtacattcagaagtcttggcaccacttcatctcaccaacactagcttatcacctcacgtttcttctgcaccatgcagACTTTGGATGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGTGGATACTCCCTCGATTCTGATGCGATTGGTCTACCAAGGGCTCATGGGCTTT------
|||||||||  |||  ||    ||   |  || | |    ||   ||   || ||||    |||| ||  ||||    |  | ||       ||   | |||||||||||||||||||||||||| || ||  |||| ||||| ||       || ||||| ||| | ||||| |  |||||||||||||||||||||||||      
gtatgttttgtcagaactaagttttccattttaatagcatttcatactgattgatct----aacattaaattatttattggccttgtg---acatgcttcagACTTTGGATGAGATACCACTTGAAGCGGACACAGTTGAGAGAGGC------TATTCCCTGGATGCCGATGCAACAGGTCTACCAAGGGCTCATGGGCTTTCTTCAT

upper sequence: GRMZM2G180335_T01 (Zea mays), 3'ss of exon 19
lower sequence: LOC_Os01g69130.2 (Oryza sativa), 3'ss of exon 19

gtatgttttcgcagttctttaattcgtacattcagaagtcttggcaccacttcatctcaccaacactagcttatcacctcacgtttcttctgcaccatgcagACTTTGGATGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGTGGATACTCCCTCGATTCTGATGCGATTGGTCTACCAAGGGCTCATGGGCTTT------
|||||||||  |||  ||    ||   |  || | |    ||   ||   || ||||    |||| ||  ||||    |  | ||       ||   | |||||||||||||||||||||||||| || ||  |||| ||||| ||       || ||||| ||| | ||||| |  |||||||||||||||||||||||||      
gtatgttttgtcagaactaagttttccattttaatagcatttcatactgattgatct----aacattaaattatttattggccttgtg---acatgcttcagACTTTGGATGAGATACCACTTGAAGCGGACACAGTTGAGAGAGGC------TATTCCCTGGATGCCGATGCAACAGGTCTACCAAGGGCTCATGGGCTTTCTTCAT

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|211326562|gb|FL096798.1|FL096798

EST:     AGAGGAAGCAGATACGTGAAAATCTTAAGGTCCTTCAACAAGCTTACAAA                         ACTTTGGATGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGTGGA
genomic: AGAGGAAGCAGATACGTGAAAATCTTAAGGTCCTTCAACAAGCTTACAAAgtatgttttc ... caccatgcagACTTTGGATGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGTGGA

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: 48 (upstream exon), 48 (downstream exon)
Score: 134

AGATGATCTTTTGGAAGACTTGCTCAAAGAACCTGATGAGCTAACCATAAAGAGGAAGCAGATACGTGAAAATCTTAAGGTCCTTCAACAAGCTTACAAAgtatgttttc ... caccatgcagACTTTGGATGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGTGGATACTCCCTCGATTCTGATGCGATTGGTCTACCAAGGGCTCATGGGCTTT

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 104

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 151

Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 113

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

cacttcatctcaccaacactagcttatcacctcacgtttcttctgcaccatgcagACTTTGGATGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGTGGATACTCCCTCGATTCTGATGCGATTGGTCTACCAAGGGCTCATGGGCTTT