ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GTTGGACCAGCACTTATCTTCTCAAGCGCAACTGCAATAAGTATGCTTGGGTGGGACAACAAAGTCCGATCAATCCTCTCCACTAGCTTCCCTCGCTCAGgtaagatccatttaagttactatacaatacaactctgtgacacttcctcctgctggcatgctatcaatatgttacaattttgtcttcttgcccagtctgtgctgaactaaaccatattcctgtgcatcttcag

Basic information

species	Zea mays
transcript	GRMZM2G150772_T02
intron #	18
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G150772_T02 (Zea mays), 5'ss of exon 18
lower sequence: LOC_Os09g24260.1 (Oryza sativa), 5'ss of exon 18

GTTGGACCAGCACTTATCTTCTCAAGCGCAACTGCAATAAGTATGCTTGGGTGGGACAACAAAGTCCGATCAATCCTCTCCACTAGCTTCCCTCGCTCAGgtaagatcc--atttaagttactatacaatacaactctgtgacacttcc-----------tcctgctggcatgctatcaatatgttacaattttgtcttcttgcccagtctgtgctgaactaaaccatattcctgtgcat--cttcag
||||||||||||||||||||||| || ||||||||||||||||||||||| |||||||||||||| ||||| ||||| || |||||||||||||| || ||||||||    || ||    | || | || || |  || |    ||||            | |   |  |||||| |  ||| | | | | ||  | || |   | ||| ||||||||||||||| ||||   | |  ||   | |||
GTTGGACCAGCACTTATCTTCTCTAGTGCAACTGCAATAAGTATGCTTGGATGGGACAACAAAGTTCGATCTATCCTTTCTACTAGCTTCCCTCGTTCTGgtaagattataatatattcaattaaaaaagactaacctatagtccttctgatgctcccagttcctttaacatgct-ttgatacgctgctacttcttattttcatc-agtttgtgctgaactaaacaatatgtgtttttatgcatgcag

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|13315888|gb|BG410236.1|BG410236

EST:     GTGGGACAACAAAGTCCGATCAATCCTCTCCACTAGCTTCCCTCGCTCAG                         TATTACTTGGTGCATTGAATGACCGCCTACTGCTTGTAAATCCGACGGATA
genomic: GTGGGACAACAAAGTCCGATCAATCCTCTCCACTAGCTTCCCTCGCTCAGgtaagatcca ... gcatcttcagTATTACTTGGTGCATTGAATGACCGCCTACTGCTTGTAAATCCGACGGATA

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: 362

GTTGGACCAGCACTTATCTTCTCAAGCGCAACTGCAATAAGTATGCTTGGGTGGGACAACAAAGTCCGATCAATCCTCTCCACTAGCTTCCCTCGCTCAGgtaagatcca ... gcatcttcagTATTACTTGGTGCATTGAATGACCGCCTACTGCTTGTAAATCCGACGGATATAAACCCAAGACAGAAAAAGGGAGTGGAAATAAGGGCCTGTTTAGTTGG

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 319

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 204