ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GGAATTTCTGAAGCCAAGCTTGCGCATTGTTTCTCATCAGCCTAGTGACTCTGGAAAACATGCCGGAAATGCTTCTCATTCTGATGGTTCCAAGAGTCAAgtatggctgcccaaattgaacatttactatatgtatggtcactaatttgttgcccggtatttgggtgtagtgattcttttttttcgtttttgcag

Basic information

species	Zea mays
transcript	GRMZM2G138349_T03
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G138349_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g10480.3 (Oryza sativa), 5'ss of exon 7

GGAATTTCTGAAGCCAAGCTTGCGCATTGTTTCTCATCAGCCTAGTGACTCTGGAAAACATGCCGGAAATGCTTCTCATTCTGATGGTTCCAAGAGTCAAgtatg----gctgccc--aaattgaacatt-tactatatg-tatggtcactaatttgttgcccggtatttgggtgtagtgattcttttttttcgtt---tttgcag
 || |||||  |||||||| | || ||||||||||||||| |||| ||||| || |||||||| || | ||| || |||||||   ||||||||||  ||||| |     ||| ||  ||| || | |||  | | | |  ||   |   ||   ||||   ||    || | |  |    |  |  |      ||   |||||||
AGAGTTTCTTGAGCCAAGCCTACGGATTGTTTCTCATCAGTCTAGCGACTCCGGGAAACATGCAGGCAGTGCCTCCCATTCTGTCAGTTCCAAGAGCGAAgtaggcagcactgtcctaaaactgcaaattgcattttgttctaccttacttagcatgttctgcgactcttagattcaaatttagtaatccccgatttgatttgcag

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|60672574|gb|DN475276.1|DN475276

EST:     CTGGAAAACATGCCGGAAATGCTTCTCATTCTGATGGTTCCNAGAGTCAA                         GTCGGCATGATCGAGTTCATTGGAATATTGAATGTCAGGGTGATTGGAGGC
genomic: CTGGAAAACATGCCGGAAATGCTTCTCATTCTGATGGTTCCAAGAGTCAAgtatggctgc ... gtttttgcagGTCGGCATGATCGAGTTCATTGGAATATTGAATGTCAAGGTGATTGGAGGC

EST: gi|213172275|gb|FM186438.1|FM186438

EST:     CTGGAAAACATGCCGGAAATGCTTCTCATTCTGATGGTTCCAAGAGTCAA                         GTCGGCATGATCGAGTTCATTGGAATATTGAATGTCAAGGTGATTGGAGGC
genomic: CTGGAAAACATGCCGGAAATGCTTCTCATTCTGATGGTTCCAAGAGTCAAgtatggctgc ... gtttttgcagGTCGGCATGATCGAGTTCATTGGAATATTGAATGTCAAGGTGATTGGAGGC

EST: gi|71768791|gb|DR966728.1|DR966728

EST:     CTGGAAAACATGCCGGAAATGCTTCTCATTCTGATGGTTCCAAGAGTCAA                         GTCGGCATGATCGAGTTCATTGGAATATTGAATGTCAAGGTGATTGGAGGC
genomic: CTGGAAAACATGCCGGAAATGCTTCTCATTCTGATGGTTCCAAGAGTCAAgtatggctgc ... gtttttgcagGTCGGCATGATCGAGTTCATTGGAATATTGAATGTCAAGGTGATTGGAGGC

EST: gi|78179014|gb|DV549387.1|DV549387

EST:     CTGGAAAACATGCCGAAAATGCTTCTCATTCTGATGGTTCCAAGAGTCAA                         GTCGGCATGATCGAGTTCATTGGAATATTGAATGTCAAGGTGATTGGAGGC
genomic: CTGGAAAACATGCCGGAAATGCTTCTCATTCTGATGGTTCCAAGAGTCAAgtatggctgc ... gtttttgcagGTCGGCATGATCGAGTTCATTGGAATATTGAATGTCAAGGTGATTGGAGGC

EST: gi|12046228|gb|BF728367.1|BF728367

EST:     CTGGAAAACATGCCGAAAATGCTTCTCATTCTGATGGTTCCAAGAGTCAA                         GTCGGCATGATCGAGTTCATTGGAATATTGAATGTCAAGGTGATTGGAGGC
genomic: CTGGAAAACATGCCGGAAATGCTTCTCATTCTGATGGTTCCAAGAGTCAAgtatggctgc ... gtttttgcagGTCGGCATGATCGAGTTCATTGGAATATTGAATGTCAAGGTGATTGGAGGC

EST: gi|211245510|gb|FK953342.1|FK953342

EST:     CT-GAAAACATGCCGGAAATGCTTCTCATTCTGATGGTTCCAAGAGTCAA                         GTCGGCATGATCGAGTTCATTGGAATATTGAATGTCAAGGTGATTGGAGGC
genomic: CTGGAAAACATGCCGGAAATGCTTCTCATTCTGATGGTTCCAAGAGTCAAgtatggctgc ... gtttttgcagGTCGGCATGATCGAGTTCATTGGAATATTGAATGTCAAGGTGATTGGAGGC

EST: gi|6918414|gb|AW399944.1|AW399944

EST:     CTGGAAAACATGCCGAAAATGCTTCTCATTCTGATGGTTCCAAGAGTCAA                         GTCGGCATGATCGAGTTCATTGGAATATTGAATGTCAAGGTGATTGGAGGC
genomic: CTGGAAAACATGCCGGAAATGCTTCTCATTCTGATGGTTCCAAGAGTCAAgtatggctgc ... gtttttgcagGTCGGCATGATCGAGTTCATTGGAATATTGAATGTCAAGGTGATTGGAGGC

EST: gi|78087463|gb|DV515856.1|DV515856

EST:     GATGGTTCCAAGAGTCAA                         GTCGGCATGATCGAGTTCATTGGAATATTGAATGTCAAGGTGATTGGAGGC
genomic: GATGGTTCCAAGAGTCAAgtatggctgc ... gtttttgcagGTCGGCATGATCGAGTTCATTGGAATATTGAATGTCAAGGTGATTGGAGGC

EST: gi|31250107|gb|CD219131.1|CD219131

EST:     CTGGAAAACATGCCGGAAATGCTTCTCATTCTGATGGTTCCAAGAGTCAA                         GTCGGCATGATCGAGTTCATTGGAATATTGAATGTCAAGGTGAT
genomic: CTGGAAAACATGCCGGAAATGCTTCTCATTCTGATGGTTCCAAGAGTCAAgtatggctgc ... gtttttgcagGTCGGCATGATCGAGTTCATTGGAATATTGAATGTCAAGGTGAT

EST: gi|78087464|gb|DV515857.1|DV515857

EST:     CTGGAAAACATGCCGGAAATGCTTCTCATTCTGATGGTTCCAAGAGTCAA                         GTCGGCATGATCGAGTTCATTGGAATATTGAATGTCAAGGTGATTGGAGGC
genomic: CTGGAAAACATGCCGGAAATGCTTCTCATTCTGATGGTTCCAAGAGTCAAgtatggctgc ... gtttttgcagGTCGGCATGATCGAGTTCATTGGAATATTGAATGTCAAGGTGATTGGAGGC

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: 43 (upstream exon), 49 (downstream exon)
Score: 66

GGAATTTCTGAAGCCAAGCTTGCGCATTGTTTCTCATCAGCCTAGTGACTCTGGAAAACATGCCGGAAATGCTTCTCATTCTGATGGTTCCAAGAGTCAAgtatggctgc ... gtttttgcagGTCGGCATGATCGAGTTCATTGGAATATTGAATGTCAAGGTGATTGGAGGCACCAACCTAGCCATCAGGGATATGTCAAGCAGTGACCCTTATGTCGTCC

Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 158

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 143