ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TTCCTCTGCCATATCAAGTGCTGATCTATTTGGCCATCCAGCAAACAATTCTAGCGTGGATCTCAGTGCTTCAGATTTGATCAACAGAATATCATTCCAGgtaacagttgggtagaataatgttgtctccttgactccttggcttacttgcattaacgcattgttgtgtttgtcttggcag

Basic information

species	Zea mays
transcript	GRMZM2G134045_T01
intron #	7
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G134045_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os10g42420.1 (Oryza sativa), 5'ss of exon 6

TTCCTCTGCCATATCAAGTGCTGATCTATTTGGCCATCCAGCAAACAATTCTAGCGTGGATCTCAGTGCTTCAGATTTGATCAACAGAATATCATTCCAGgtaacagttgggtagaataatgttgtctccttgactccttggcttacttgcattaacgcattgttgtgtttgtcttggcag
 || |||||||| |||||||||||||||||||| |||||| | || | ||| | ||||||||| ||||||||||||||||||||| |  | || ||||||||||     | |||| ||| |   |     || | |  | | | ||     ||| | |  ||||| | | |||        
ATCTTCTGCCATTTCAAGTGCTGATCTATTTGGTCATCCAACCAATAGTTCCAACGTGGATCTGAGTGCTTCAGATTTGATCAACCGGCTTTCTTTCCAGgtaaattaagagtagcatagtacagctgggtttattgatagacctatg---attgatgtcttgttatctctgtag------

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|87155179|gb|DY399968.1|DY399968

EST:     GCCATCCAGCAAACAATTCTAGCGTGGATCTCAGTGCTTCAGATTTGATCAACAGAATATCATTCCAG        
genomic: CTAGCGTGGATCTCAGTGCTTCAGATTTGATCAACAGAATATCATTCCAGgtaacagttg ... gtcttggcagG

EST: gi|78082818|gb|DV511211.1|DV511211

EST:     GCCATCCAGCAAACAATTCTAGCGTGGATCTCAGTGCTTCAGATTTGATCAACAGAATATCATTCCAG        
genomic: CTAGCGTGGATCTCAGTGCTTCAGATTTGATCAACAGAATATCATTCCAGgtaacagttg ... gtcttggcagG

EST: gi|86467876|gb|DY234246.1|DY234246

EST:     CTAGCGTGGATCTCAGTGCTTCAGATTTGATCAACAGAATATCATTCCAG                         GCCACTCAAGATCTGTCTTCTTTCAAGAACATGGCAGGGGAAACTGGGAAA
genomic: CTAGCGTGGATCTCAGTGCTTCAGATTTGATCAACAGAATATCATTCCAGgtaacagttg ... gtcttggcagGCCACTCAAGATCTGTCTTCTCTCAAGAACATGGCAGGGGAAACTGGGAAA

EST: gi|87154151|gb|DY398940.1|DY398940

EST:     GCCATCCAGCAAACAATTCTAGCGTGGATCTCAGTGCTTCAGATTTGATCAACAGAATATCATTCCAG        
genomic: CTAGCGTGGATCTCAGTGCTTCAGATTTGATCAACAGAATATCATTCCAGgtaacagttg ... gtcttggcagG

EST: gi|78110556|gb|DV528966.1|DV528966

EST:     GCCATCCAGCAAACAATTCTAGCGTGGATCTCAGTGCTTCAGATTTGATCAACAGAATATCATTCCAG        
genomic: CTAGCGTGGATCTCAGTGCTTCAGATTTGATCAACAGAATATCATTCCAGgtaacagttg ... gtcttggcagG

EST: gi|50329244|gb|CO524370.1|CO524370

EST:     GCCATCCAGCAAACAATTCTAGCGTGGATCTCAGTGCTTCAGATTTGATCAACAGAATATCATTCCAG        
genomic: CTAGCGTGGATCTCAGTGCTTCAGATTTGATCAACAGAATATCATTCCAGgtaacagttg ... gtcttggcagG

EST: gi|78027266|gb|DV495653.1|DV495653

EST:     CTAGCGTGGATCTCAGTGCTTCAGATTTGATCAACAGAATATCATTCCAG                         GCCACTCAAGATCTGTCTTCTCTCAAGAACATGGCAGGGGAAACTGGGAAA
genomic: CTAGCGTGGATCTCAGTGCTTCAGATTTGATCAACAGAATATCATTCCAGgtaacagttg ... gtcttggcagGCCACTCAAGATCTGTCTTCTCTCAAGAACATGGCAGGGGAAACTGGGAAA

EST: gi|17931094|gb|BM268054.1|BM268054

EST:     CTAGCGTGGATCTCAGTGCTTCAGATTTGATCAACAGAATATCATTCCAG                         GCCACTCAAGATCTGTCTTCTCTCAAGAACATGGCAGGGGAAACTGGGAAA
genomic: CTAGCGTGGATCTCAGTGCTTCAGATTTGATCAACAGAATATCATTCCAGgtaacagttg ... gtcttggcagGCCACTCAAGATCTGTCTTCTCTCAAGAACATGGCAGGGGAAACTGGGAAA

EST: gi|26455703|gb|CA827286.1|CA827286

EST:     GCCATCCAGCAAACAATTCTAGCGTGGATCTCAGTGCTTCAGATTTGATCAACAGAATATCATTCCAG        
genomic: CTAGCGTGGATCTCAGTGCTTCAGATTTGATCAACAGAATATCATTCCAGgtaacagttg ... gtcttggcagG

EST: gi|22545199|gb|BU097558.1|BU097558

EST:     GCCATCCAGCAAACAATTCTAGCGTGGATCTCAGTGCTTCAGATTTGATCAACAGAATATCATTCCAG        
genomic: CTAGCGTGGATCTCAGTGCTTCAGATTTGATCAACAGAATATCATTCCAGgtaacagttg ... gtcttggcagG

EST: gi|211356763|gb|FL443096.1|FL443096

EST:     CTAGCGTGGATCTCAGTGCTTCAGATTTGATCAACAGAATATCATTCCAG                         GCCACTCAAGATCTGTCTTCTCTCAAGAACATGGCAGGGGAAACTGGGAAA
genomic: CTAGCGTGGATCTCAGTGCTTCAGATTTGATCAACAGAATATCATTCCAGgtaacagttg ... gtcttggcagGCCACTCAAGATCTGTCTTCTCTCAAGAACATGGCAGGGGAAACTGGGAAA

EST: gi|89759290|gb|DY688159.1|DY688159

EST:     CTAGCGTGGATCTCAGTGCTTCAGATTTGATCAACAGAATATCATTCCAG                         GCCACTCAAGATCTGTCTTCTCTCAAGAACATGGCAGGGGAAACTGGGAAA
genomic: CTAGCGTGGATCTCAGTGCTTCAGATTTGATCAACAGAATATCATTCCAGgtaacagttg ... gtcttggcagGCCACTCAAGATCTGTCTTCTCTCAAGAACATGGCAGGGGAAACTGGGAAA

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: 45 (upstream exon), 48 (downstream exon)
Score: 27

TTCCTCTGCCATATCAAGTGCTGATCTATTTGGCCATCCAGCAAACAATTCTAGCGTGGATCTCAGTGCTTCAGATTTGATCAACAGAATATCATTCCAGgtaacagttg ... gtcttggcagGCCACTCAAGATCTGTCTTCTCTCAAGAACATGGCAGGGGAAACTGGGAAAAGGTTGACATCGATGGCATCCAACATCATCACTGATCTTCAGGACCGCA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 149

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 170