ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

AATGGGTTACAAGAATCCCATTCTACTACTACATCCCTTAGGTGGTTATACCAAAGCGGATGATGTCCCACTGCCAGTTAGAATGGAACAACACAGTAAGgtatacatttgtcgtcttaatcttagctgtttaccggatgtattatgcaaattgctgaagtttatcatgcacag

Basic information

species	Zea mays
transcript	GRMZM2G158147_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G158147_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os04g02050.1 (Oryza sativa), 5'ss of exon 2

AATGGGTTACAAGAATCCCATTCTACTACTACATCCCTTAGGTGGTTATACCAAAGCGGATGATGTCCCACTGCCAGTTAGAATGGAACAACACAGTAAGgtatacatttgtcgtcttaatcttagctgtttaccggat-gtattatgcaaattgctgaagtttatcatgca-cag
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AATGGGCTTCAAGAATCCCATTCTACTGCTGCACCCTTTAGGTGGCTTCACGAAAGCTGATGATGTCCCGTTGCCTGTGAGAATGGAACAACACAGCAAGgtaatcatttgt----ttatgc--agttatttgctagttcaaactgtgcaaattactaaa-ttgatcatatggcag

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|60338703|gb|DN205676.1|DN205676

EST:     CCAAAGCGGATGATGTCCCACTGCCAGTTAGAATGGAACAACACAGTAAG                         GTTTTAGAAGATGGAGTGCTTGATCCTGAGACTACTATAGTGTCTATATTT
genomic: CCAAAGCGGATGATGTCCCACTGCCAGTTAGAATGGAACAACACAGTAAGgtatacattt ... tcatgcacagGTTTTAGAAGATGGAGTGCTTGATCCTGAGACTACTATAGTGTCTATATTT

EST: gi|211399264|gb|FL448232.1|FL448232

EST:     AGCGGATGATGTCCCACTGCCAGTTAGAATGGAACAACACAGT-AG                         GTTTTTAGAAGATGGAGTGCTTGATCCTGAGACTACTATAGTGTCTATATT
genomic: AGCGGATGATGTCCCACTGCCAGTTAGAATGGAACAACACAGTAAGgtatacattt ... tcatgcacagG-TTTTAGAAGATGGAGTGCTTGATCCTGAGACTACTATAGTGTCTATATT

EST: gi|32941956|gb|CF046775.1|CF046775

EST:     CCAAAGCGGATGATGTCCCACTGCCAGTTAGAATGGAACAACACAGTAAG                         GTTTTAGAAGATGGAGTGCTTGATCCTGAGACTACTATAGTGTCTATATTT
genomic: CCAAAGCGGATGATGTCCCACTGCCAGTTAGAATGGAACAACACAGTAAGgtatacattt ... tcatgcacagGTTTTAGAAGATGGAGTGCTTGATCCTGAGACTACTATAGTGTCTATATTT

EST: gi|78180099|gb|DV550472.1|DV550472

EST:     CCAAAGCGGATGATGTCCCACTGCCAGTTAGAATGGAACAACACAGTAAG                         GTTTTAGAAGATGGAGTGCTTGATCCTGAGACTACTATAGTGTCTATATTT
genomic: CCAAAGCGGATGATGTCCCACTGCCAGTTAGAATGGAACAACACAGTAAGgtatacattt ... tcatgcacagGTTTTAGAAGATGGAGTGCTTGATCCTGAGACTACTATAGTGTCTATATTT

EST: gi|32940782|gb|CF045601.1|CF045601

EST:     CCAAAGCGGATGATGTCCCACTGCCAGTTAGAACGGAACAACACAGTAAG                         GTTTTAGAAGATGGAGTGCTTGATCCTGAGACTACTATAGTGTCTATATTT
genomic: CCAAAGCGGATGATGTCCCACTGCCAGTTAGAATGGAACAACACAGTAAGgtatacattt ... tcatgcacagGTTTTAGAAGATGGAGTGCTTGATCCTGAGACTACTATAGTGTCTATATTT

EST: gi|32942406|gb|CF047225.1|CF047225

EST:     CCAAAGCGGATGATGTCCCACTGCCAGTTAGAATGGAACAACACAGTAAG                         GTTTTAGAAGATGGAGTGCTTGATCCTGAGACTACTATAGTGTCTATATTT
genomic: CCAAAGCGGATGATGTCCCACTGCCAGTTAGAATGGAACAACACAGTAAGgtatacattt ... tcatgcacagGTTTTAGAAGATGGAGTGCTTGATCCTGAGACTACTATAGTGTCTATATTT

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: 118

AATGGGTTACAAGAATCCCATTCTACTACTACATCCCTTAGGTGGTTATACCAAAGCGGATGATGTCCCACTGCCAGTTAGAATGGAACAACACAGTAAGgtatacattt ... tcatgcacagGTTTTAGAAGATGGAGTGCTTGATCCTGAGACTACTATAGTGTCTATATTTCCCTCACCAATGCATTATGCTGGTCCAACAGAAGTGCAGTGGCATGCAA

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 165

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 54