ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CTAATAGGTCAGATGAGGATTTTTCACGGTATTGCTTCTCGATGGCATACATTGTGGCTCTACTGCATGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagcatattcagcacgccatagtgaaatttactcccaagtgatctagttcgctcatctaatttaattttctcctgatcag

Basic information

species	Zea mays
transcript	GRMZM2G056944_T01
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G056944_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g26080.1 (Oryza sativa), 5'ss of exon 7

CTAATAGGTCAGATGAGGATTTTTCACGGTATTGCTTCTCGATGGCATACATTGTGGCTCTACTGCATGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagcatatt-cagcacgcca------tagtgaaatttactcccaagtgatctagttcgctcatctaatttaattttctcctgatcag----------
||||| |||||||||| ||||||||||| |||||||||||    ||||| ||||| ||||||||||| ||||||||||||||||||||||||||||||||||||| |||     ||||  ||         ||||||| ||||   || |||||  |  ||| | ||| ||| |  ||    || ||            
CTAATCGGTCAGATGATGATTTTTCACGTTATTGCTTCTCATCCGCATATATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagaataccatggcacatcaatcttccgctgaaattcactcttcagcgatcttatatgcttacctacttttaaatttaaatgttcttatatccgcag

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|211248170|gb|FL432278.1|FL432278

EST:     ATTGTGGCTCTACTGCATGACAGTCTTGGTGTACCACTGGATGACAAGAG                         GATTGAGTATTCAAACCAGGTTGGAGACATTCAGGTTGAATGGGCTCTAGG
genomic: ATTGTGGCTCTACTGCATGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagcatat ... tcctgatcagGATTGAGTATTCAAACCAGGTTGGAGACATTCAGGTTGAATGGGCTCTAGG

EST: gi|50333273|gb|CO528399.1|CO528399

EST:     CTGGATGACAAGAG                         GATTGAGTATTCAAACCAGGTTGGAGACATTCAGGTTGAATGGGCTTTAGG
genomic: CTGGATGACAAGAGgcaagcatat ... tcctgatcagGATTGAGTATTCAAACCAGGTTGGAGACATTCAGGTTGAATGGGCTCTAGG

EST: gi|166431836|gb|EG289982.1|EG289982

EST:     ATTGGGGCTCTACTGCATGACAGTCTTGGTGTACCACTGGATGACAAGAG                         GATTGAGTATTCAAACCAGGTTGGAGACATTCAGGTT
genomic: ATTGTGGCTCTACTGCATGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagcatat ... tcctgatcagGATTGAGTATTCAAACCAGGTTGGAGACATTCAGGTT

EST: gi|78116868|gb|DV535255.1|DV535255

EST:     ATTGTGGCTTTACTGCATGACAGTCTTGGTGTACCACTGGATGACAAGAG                         GATTGAGTATTCAAACCAGGTTGGAGACATTCAGGTTGAATGGGCTCTAGG
genomic: ATTGTGGCTCTACTGCATGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagcatat ... tcctgatcagGATTGAGTATTCAAACCAGGTTGGAGACATTCAGGTTGAATGGGCTCTAGG

EST: gi|149069897|gb|EE158294.2|EE158294

EST:     ATTGTGGCTTTACTGCATGACAGTCTTGGTGTACCACTGGATGACAAGAG                         GATTGAGTATTCAAACCAGGTTGGAGACATTCAGGTTGAATGGGCTTTAGG
genomic: ATTGTGGCTCTACTGCATGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagcatat ... tcctgatcagGATTGAGTATTCAAACCAGGTTGGAGACATTCAGGTTGAATGGGCTCTAGG

EST: gi|4573154|gb|AI438507.2|AI438507

EST:     TACTGCATGACAGTCTTGGTGTACCACTGGATGACAAGAG                         GATTGAGTATTCAAACCAGGTTGGAGACATTCAGGTTGAATGGGCTCTAGG
genomic: TACTGCATGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagcatat ... tcctgatcagGATTGAGTATTCAAACCAGGTTGGAGACATTCAGGTTGAATGGGCTCTAGG

EST: gi|166604134|gb|EG222272.1|EG222272

EST:     GTCTTGGTGTACCACTGGATGACAAGAG                         GATTGAGTATTCAAACCAGGTTGGAGACATTCAGGTTGAATGGGCTCTAGG
genomic: GTCTTGGTGTACCACTGGATGACAAGAGgcaagcatat ... tcctgatcagGATTGAGTATTCAAACCAGGTTGGAGACATTCAGGTTGAATGGGCTCTAGG

EST: gi|60341251|gb|DN208224.1|DN208224

EST:     ATTGTGGCTCTACTGCATGACAGTCTTGGTGTACCACTGGATGACAAGAG                         GATTGAGTATTCAAACCAGGTTGGAGACATTCAGGTTGAATGGGCTCTAGG
genomic: ATTGTGGCTCTACTGCATGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagcatat ... tcctgatcagGATTGAGTATTCAAACCAGGTTGGAGACATTCAGGTTGAATGGGCTCTAGG

EST: gi|148987020|gb|EE030843.2|EE030843

EST:     ATTGTGGCTCTACTGCATGACAGTCTTGGTGTACCACTGGATGACAAGAG                         GATTGAGTATTCAAACCAGGTTGGAGACATTCAGGTTGAATGGGCTCTAGG
genomic: ATTGTGGCTCTACTGCATGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagcatat ... tcctgatcagGATTGAGTATTCAAACCAGGTTGGAGACATTCAGGTTGAATGGGCTCTAGG

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), 46 (downstream exon)
Score: 63

CTAATAGGTCAGATGAGGATTTTTCACGGTATTGCTTCTCGATGGCATACATTGTGGCTCTACTGCATGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagcatat ... tcctgatcagGATTGAGTATTCAAACCAGGTTGGAGACATTCAGGTTGAATGGGCTCTAGGAGCTTTCATCACACTGATGCAAAATACGAGTTTAAAGCCATTACACACC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 155

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 203