ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGAATGGGAACTTCTGAATGATATGAAGGCTGTATGGCTTCGCAGCCCGAAGGAGGTTACTGATGAGGAATACTCGAAGTTTTACCACTCACTAGCCAAGgtaatactgtagtgatgaattagtagtaccgaatgatttttttattttttttggtcaaagaaagcttttgtttgttggtcttgttgatgaaacatttgtataacttcataataattatttttcag

Basic information

species	Zea mays
transcript	GRMZM2G399073_T02
intron #	11
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G399073_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os06g50300.1 (Oryza sativa), 5'ss of exon 9

TGAATGGGAACTTCTGAATGATATGAAGGCTGTATGGCTTCGCAGCCCGAAGGAGGTTACTGATGAGGAATACTCGAAGTTTTACCACTCACTAGCCAAGgta---atactgtagtgatgaattagtagtaccgaatgatttttttattttttttggtcaaagaaagcttttgtttgttggtcttgttgatgaaacatttgtataacttcataataattatttttcag
||| ||||| |||||||||||| |||||||| |||||||||| ||||| |||||||||||||| || |||||| | ||||||||||||||||| || ||||||   | |||| |||||||||||   || | |  || |  ||||   |     | |   ||||||||   |      |  | |  |  || |||   || | ||                       
TGAGTGGGAGCTTCTGAATGATGTGAAGGCTATATGGCTTCGTAGCCCTAAGGAGGTTACTGAAGAAGAATACACAAAGTTTTACCACTCACTTGCTAAGgtacacagactgcagtgatgaatttacaggagc--ataacattttatgtaagccttgcagaagaaagcaagtaacc--tcatttaat--atcaaattattttgtag----------------------

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|211478283|gb|FL245116.1|FL245116

EST:     GAAGTTTTACCACTCACTAGCCAAG                         GACTTCAGTGATGACAAGCCTATGGGGTGGAGCCACTTCACTGCTGAAGGA
genomic: GAAGTTTTACCACTCACTAGCCAAGgtaatactgt ... tatttttcagGACTTCGGTGATGACAAGCCTATGGGTTGGAGCCACTTCACTGCTGAAGGA

EST: gi|22489665|gb|BU049575.1|BU049575

EST:     AGGAGGTTACTGACGAAGAATACTCAAAGTTTTACCACTCACTAGCCAAG                         GACTTCGGTGATGACAAGCCTATGGGTTGGAGCCACTTCACTGCTGAAGGA
genomic: AGGAGGTTACTGATGAGGAATACTCGAAGTTTTACCACTCACTAGCCAAGgtaatactgt ... tatttttcagGACTTCGGTGATGACAAGCCTATGGGTTGGAGCCACTTCACTGCTGAAGGA

EST: gi|19822479|gb|BQ048503.1|BQ048503

EST:     GGAGGTTACTGCCGAAGAATACTCAAAGTTTT-CCACTTCACTAGCCAAG                         GACTTCGGTGATGACAAGCCTATGGGTTGGAGCCACTTCACTGCTGAAGGA
genomic: GGAGGTTACTGATGAGGAATACTCGAAGTTTTACCAC-TCACTAGCCAAGgtaatactgt ... tatttttcagGACTTCGGTGATGACAAGCCTATGGGTTGGAGCCACTTCACTGCTGAAGGA

EST: gi|211478285|gb|FL245118.1|FL245118

EST:     GAAGTTTTACCACTCACTAGCCAAG                         GACTTCAGTGATGACAAGCCTATGGGTTGGAGCCACTTCACTGCTGAAGGA
genomic: GAAGTTTTACCACTCACTAGCCAAGgtaatactgt ... tatttttcagGACTTCGGTGATGACAAGCCTATGGGTTGGAGCCACTTCACTGCTGAAGGA

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), 48 (downstream exon)
Score: 804

TGAATGGGAACTTCTGAATGATATGAAGGCTGTATGGCTTCGCAGCCCGAAGGAGGTTACTGATGAGGAATACTCGAAGTTTTACCACTCACTAGCCAAGgtaatactgt ... tatttttcagGACTTCGGTGATGACAAGCCTATGGGTTGGAGCCACTTCACTGCTGAAGGAGATGTTGAGTTCAAAGCTTTGCTCTTCATTCCACCGAAGGCTCCGCATG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 671

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 498