ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

ACCGGCTGCTGCATCCGCCTCTGGCCCGTCGGGACATGCCCTCCGCCGCCGCAGAGGTCCAAGGTCGACACCTCCACCAGCAGCGCCAGCACGCACGGGGgtagacgtctctttctctcctgtcacctggatactcactcgcattgtgctttctttgctgtcttgctcgcgtggtagatgggatttgctcctctaagtga...

Basic information

species	Zea mays
transcript	GRMZM2G132184_T01
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G132184_T03 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os09g19700.1 (Oryza sativa), 5'ss of exon 1

---ACCGGCTGCTGCATCCGCCTCTGGCCCGTCGGGACATGCCCTCCGCCGCCGCAGAGGTCCAAGGTCGACACCTCCACCAGCAGCGCCAGCACGCACGGGGgtagacgtctctttctctcctgtcacctggatactcactcgcattgtgctttctttgctgtcttg--ctcgcgtggtagatgggatttgctcctctaagtga
   ||||| ||||||||||| || |||||  | ||||  ||||| ||||||||||   |||||||||| |||||||||||||||||||||||||||||||| |||| ||||| |||||   | |   |        || ||  |||  |  || |  |||   | | |     |    ||| ||||  ||||  | |  |  || 
GCCACCGGGTGCTGCATCCGGCTGTGGCCGATGGGGAGCTGCCCACCGCCGCCGC---GGTCCAAGGTGGACACCTCCACCAGCAGCGCCAGCACGCACGGCGgta-acgtccctttcgtcctttctaaagatgagctaacctgcaacg-actataattggaatttggaatctgttatgtaaatggattttggccataaatatgt

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|149104047|gb|EE289479.2|EE289479

EST:     GCAGAGGTCCAAGGTCGACACCTCCACCAGCAGCGCCAGCACGCACGGGG                         CAGAGAAGTCAACAGAAAATG
genomic: GCAGAGGTCCAAGGTCGACACCTCCACCAGCAGCGCCAGCACGCACGGGGgtagacgtct ... catgtaacagCAGAGAAGTCAACAGAAAATG

EST: gi|148930993|gb|EC873532.2|EC873532

EST:     GCAGAGGTCCAAGGTCGACACCTCCACCAGCAGCGCCAGCACGCACGGGG                         CAGAGAAGTCAACAGAAAATGGTAGTAGGAATCAACCGGTGGCATTGGTAG
genomic: GCAGAGGTCCAAGGTCGACACCTCCACCAGCAGCGCCAGCACGCACGGGGgtagacgtct ... catgtaacagCAGAGAAGTCAACAGAAAATGGTAGTAGGAATCAACCGGTGGCATTGGTAG

EST: gi|89762820|gb|DY690260.1|DY690260

EST:     GCAGAGGTCCAAGGTCGACACCTCCACCAGCAGCGCCAGCACGCACGGGG                         -AGA-A-GTCCACAGAAAATGGTAGTAGGAATCAACCGGGTGGCATTGGTA
genomic: GCAGAGGTCCAAGGTCGACACCTCCACCAGCAGCGCCAGCACGCACGGGGgtagacgtct ... catgtaacagCAGAGAAGTCAACAGAAAATGGTAGTAGGAATCAACCGG-TGGCATTGGTA

EST: gi|71773309|gb|DR971217.1|DR971217

EST:     GCAGAGGTCCAAGGTCGACACCTCCACCAGCAGCGCCAGCACGCACGGGG                         -AGA-A-GTCAACAGAAAATGGTAGTAGGAATCAACCGGGGGGCATTGGTA
genomic: GCAGAGGTCCAAGGTCGACACCTCCACCAGCAGCGCCAGCACGCACGGGGgtagacgtct ... catgtaacagCAGAGAAGTCAACAGAAAATGGTAGTAGGAATCAACCGGTGG-CATTGGTA

EST: gi|211069315|gb|FL193614.1|FL193614

EST:     GCAGAGGTCCAAGGTCGACACCTCCAC-AGCAGCGCCAGCACGCACGGGG                         -AGA-A-GTCAACAGAAAATGGTAGTAGGAATCAACCGGTGGGCATTGGTA
genomic: GCAGAGGTCCAAGGTCGACACCTCCACCAGCAGCGCCAGCACGCACGGGGgtagacgtct ... catgtaacagCAGAGAAGTCAACAGAAAATGGTAGTAGGAATCAACCGGTGG-CATTGGTA

EST: gi|71441100|gb|DR822150.1|DR822150

EST:     CAGAGGTCCAAGGTCGACACCTCCCAC-AGCAGCGCCAGCACGCACGGGG                         CAGAGAAGTCAACAGAAAA
genomic: CAGAGGTCCAAGGTCGACACCTCC-ACCAGCAGCGCCAGCACGCACGGGGgtagacgtct ... catgtaacagCAGAGAAGTCAACAGAAAA

EST: gi|76916337|gb|DV166341.1|DV166341

EST:     GCAGAGGTCCA-GGTCGACACCTCCACCAGCAGCGCCAGCACGCACGGGG                         CAGAGAAGTCAACA
genomic: GCAGAGGTCCAAGGTCGACACCTCCACCAGCAGCGCCAGCACGCACGGGGgtagacgtct ... catgtaacagCAGAGAAGTCAACA

EST: gi|76934438|gb|DV173883.1|DV173883

EST:     GCAGAGGTCCAAGGTCGACACCTCCACCAGCAGCGCCAGCACGCACGGGG                         CAGAGAAGTCAACAGAAAATGGTAGTAGGAATCAACCGGTGGCATTGGTAG
genomic: GCAGAGGTCCAAGGTCGACACCTCCACCAGCAGCGCCAGCACGCACGGGGgtagacgtct ... catgtaacagCAGAGAAGTCAACAGAAAATGGTAGTAGGAATCAACCGGTGGCATTGGTAG

EST: gi|211069314|gb|FL193613.1|FL193613

EST:     GCAGAGGTCCAAGGTCGACACCTCCACCAGCAGCGCCAGCACGCACGGGG                         -A-AGA-GTCAACNAGTAA-TGGTAGTAGGAATCA
genomic: GCAGAGGTCCAAGGTCGACACCTCCACCAGCAGCGCCAGCACGCACGGGGgtagacgtct ... catgtaacagCAGAGAAGTCAAC-AGAAAATGGTAGTAGGAATCA

EST: gi|211072047|gb|FL193622.1|FL193622

EST:     GCAGAGGTCCAAGGTCGACACCTCCACCAGCAGCGCCAGCACGCACGGGG                         --GAGA-GTCAACAGAA
genomic: GCAGAGGTCCAAGGTCGACACCTCCACCAGCAGCGCCAGCACGCACGGGGgtagacgtct ... catgtaacagCAGAGAAGTCAACAGAA

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), 43 (downstream exon)
Score: 52

ACCGGCTGCTGCATCCGCCTCTGGCCCGTCGGGACATGCCCTCCGCCGCCGCAGAGGTCCAAGGTCGACACCTCCACCAGCAGCGCCAGCACGCACGGGGgtagacgtct ... catgtaacagCAGAGAAGTCAACAGAAAATGGTAGTAGGAATCAACCGGTGGCATTGGTAGTCTCAGGTTCTACAACTACTAGTAATGCTGAAAGCAGTTCATCTGCATC

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 40

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 31