ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TATTATATTTGCCTTGATGGAGCGTAGTGAGGCTGAGTTGGCAGAGCCCATTATACGGTTGCTTCCTGTTGCGCTTGGCCTTCTATACCTTGGAAAACAGgtaattctaagcatcctgtagatatggttctgatttcaatgtttacagctttgttcagtaatataagtaatagattgctgctaggcttaacatatccatc...

Basic information

species	Zea mays
transcript	GRMZM5G816609_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G816609_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g05340.1 (Oryza sativa), 5'ss of exon 17

TATTATATTTGCCTTGATGGAGCGTAGTGAGGCTGAGTTGGCAGAGCCCATTATACGGTTGCTTCCTGTTGCGCTTGGCCTTCTATACCTTGGAAAACAGgtaattct-aagcatcctgtagatatggttc----tgatttcaatgtttacagctttgttcagtaatataag--taatagattgctgctaggcttaacatatccatc
||| |||||||||||||||||||| |||||||||||| ||||||| |||||||||||  ||||||||||||||||||| ||||| || |||||||| |||||| || |  |||| |||  |    | ||||    |||||    | |||   ||| ||| || ||  ||  |  ||| | |   |   ||  |    | |       
TATCATATTTGCCTTGATGGAGCGCAGTGAGGCTGAGCTGGCAGAACCCATTATACGCCTGCTTCCTGTTGCGCTTGGTCTTCTGTATCTTGGAAAGCAGgtactttttgagcaaccttgaagcttagttccttttgattcattttttttgggctgtgtgcactagcatttgcttaaaaaaaatccagtattccctgctt-------

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|32929745|gb|CF034557.1|CF034557

EST:     TTATACGGTTGCTTCCTGTTGCGCTTGGCCTTCTATACCTTGGAAAACAG                         GATAGTGTGGAGGCTACCGCAGAGGTCTCTAAAACATTTGATGAAAAGATA
genomic: TTATACGGTTGCTTCCTGTTGCGCTTGGCCTTCTATACCTTGGAAAACAGgtaattctaa ... cctatttcagGATAGTGTGGAGGCTACCGCAGAGGTCTCTAAAACATTTGATGAAAAGATA

EST: gi|32911849|gb|CF016661.1|CF016661

EST:     GTTGCGCTTGGCCTTCTATACCTTGGAAAACAG                         GATAGTGTGGAGGCTACCGCAGAGGTCTCTAAAACATTTGATGAAAAGATA
genomic: GTTGCGCTTGGCCTTCTATACCTTGGAAAACAGgtaattctaa ... cctatttcagGATAGTGTGGAGGCTACCGCAGAGGTCTCTAAAACATTTGATGAAAAGATA

EST: gi|32935986|gb|CF040798.1|CF040798

EST:     TTATACGGTTGCTTCCTGTTGCGCTTGGCCTTCTATACCTTGGAAAACAG                         GATAGTGTGGAGGCTACCGCAGAGGTCTCTAAAACATTTGATGAAAGGATA
genomic: TTATACGGTTGCTTCCTGTTGCGCTTGGCCTTCTATACCTTGGAAAACAGgtaattctaa ... cctatttcagGATAGTGTGGAGGCTACCGCAGAGGTCTCTAAAACATTTGATGAAAAGATA

EST: gi|67041940|gb|CO468195.1|CO468195

EST:     ATACGGTTGCTTCCTGTTGCGCTTGGCCTTCTATACCTTGGAATTTTG                         GACACTGTGGAGGCTACCGCATAGGTCTCTAAAACATTTGATGAAAAGATA
genomic: ATACGGTTGCTTCCTGTTGCGCTTGGCCTTCTATACCTTGGAAAACAGgtaattctaa ... cctatttcagGATAGTGTGGAGGCTACCGCAGAGGTCTCTAAAACATTTGATGAAAAGATA

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), 49 (downstream exon)
Score: 224

TATTATATTTGCCTTGATGGAGCGTAGTGAGGCTGAGTTGGCAGAGCCCATTATACGGTTGCTTCCTGTTGCGCTTGGCCTTCTATACCTTGGAAAACAGgtaattctaa ... cctatttcagGATAGTGTGGAGGCTACCGCAGAGGTCTCTAAAACATTTGATGAAAAGATAGGGAAGTACTGTGATGTAACACTTATGTCGCTGGCATATGCCGGGACAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 192

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 176