ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GTTGCGGGATCGTCTTGTGAAAATTGTGACGGATTACCGGACAGAAACTTCATTGCGAAATGGATGCAACGATATACTTAAGgtttactttctttcgtatactgtgctgctccatgtctcaaccatcttgaattttggacattttcatccgaaacttgctttgttcag

Basic information

species	Zea mays
transcript	GRMZM2G040247_T01
intron #	18
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G040247_T01 (Zea mays), 5'ss of exon 18
lower sequence: LOC_Os04g11880.1 (Oryza sativa), 5'ss of exon 18

GTTGCGGGATCGTCTTGTGAAAATTGTGACGGATTACCGGACAGAAACTTCATTGCGAAATGGATGCAACGATATACTTAAGgtttactttctttcgtatactgtgct----gctccatgtct--caaccatcttgaattttggacattttcatccga--aacttgctttgttcag
|||||||||||| ||||||||||||||||| || || || ||||||||||||||  || |||| ||||| ||||||||||||||| |  |||      |   | | ||    | |   |||||    |  | |    || |   |  ||  | |  ||  | | |||  ||| |||
GTTGCGGGATCGCCTTGTGAAAATTGTGACAGACTATCGAACAGAAACTTCATTAAGACATGGGTGCAATGATATACTTAAGgttaatattcaagaaaaagatatacttaaggttagttgtctatttattaccccacatct---atcttgacgtttgatgaccctgccatgtacag

upper sequence: GRMZM2G040247_T01 (Zea mays), 5'ss of exon 18
lower sequence: LOC_Os04g11880.3 (Oryza sativa), 5'ss of exon 16

GTTGCGGGATCGTCTTGTGAAAATTGTGACGGATTACCGGACAGAAACTTCATTGCGAAATGGATGCAACGATATACTTAAGgtttactttctttcgtatactgtgct----gctccatgtc--tcaaccatcttgaattttggacattttcatccga--aacttgctttgttcag
             ||||||||||||||||| || || || ||||||||||||||  || |||| ||||| ||||||||||||||| |  |||      |   | | ||    | |   ||||  |  |  | |    || |   |  ||  | |  ||  | | |||  ||| |||
------------CCTTGTGAAAATTGTGACAGACTATCGAACAGAAACTTCATTAAGACATGGGTGCAATGATATACTTAAGgttaatattcaagaaaaagatatacttaaggttagttgtctatttattaccccacatct---atcttgacgtttgatgaccctgccatgtacag

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|211348416|gb|FL045968.1|FL045968

EST:     ATTACCGGACAGAAACTTCATTGCGAAATGGATGCAACGATATACTTAAG                         GCTGACTGTGTTAACCTTTTGGTTAAATACTACCACGAGGCTCGGCGTGGG
genomic: ATTACCGGACAGAAACTTCATTGCGAAATGGATGCAACGATATACTTAAGgtttactttc ... ctttgttcagGCTGACTGTGTTAACCTTTTGGTTAAATACTACCACGAGGCTCGGCGTGGG

EST: gi|71445370|gb|DR826420.1|DR826420

EST:     ATTACCGGACAGAAACTTCATTGCGAAATGGATGCAACGATATACTTAAG                         GCTGACTGTGTTAACCTTTTGGTTAAATACTACCACGAGGCTCGGCGTGGG
genomic: ATTACCGGACAGAAACTTCATTGCGAAATGGATGCAACGATATACTTAAGgtttactttc ... ctttgttcagGCTGACTGTGTTAACCTTTTGGTTAAATACTACCACGAGGCTCGGCGTGGG

EST: gi|40303669|gb|CK348056.1|CK348056

EST:     ATTACCGGACAGAAACTTCATTGCGAAATGGATGCAACGATATACTTAAG                         GCTGACTGTGTTAACCTTTTGGTTAAATACTACCACGAGGCTCGGCGTGGG
genomic: ATTACCGGACAGAAACTTCATTGCGAAATGGATGCAACGATATACTTAAGgtttactttc ... ctttgttcagGCTGACTGTGTTAACCTTTTGGTTAAATACTACCACGAGGCTCGGCGTGGG

EST: gi|74239642|gb|DT647556.1|DT647556

EST:     ATTACCGGACAGAAACTTCATTGCGAAATGGATGCAACGATATACTTAAG                         GCTGACTGTGTTAACCTTTTGGTTAAATACTACCACGAGGCTCGGCGTGGG
genomic: ATTACCGGACAGAAACTTCATTGCGAAATGGATGCAACGATATACTTAAGgtttactttc ... ctttgttcagGCTGACTGTGTTAACCTTTTGGTTAAATACTACCACGAGGCTCGGCGTGGG

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: 47 (upstream exon), 49 (downstream exon)
Score: 44

GTTGCGGGATCGTCTTGTGAAAATTGTGACGGATTACCGGACAGAAACTTCATTGCGAAATGGATGCAACGATATACTTAAGgtttactttc ... ctttgttcagGCTGACTGTGTTAACCTTTTGGTTAAATACTACCACGAGGCTCGGCGTGGGGTATACATGGTAAGCATGGACGAGGAGGTACACGGAAACAGAGCTGACG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 76

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 107