ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CATTGGAATATTGAATGTCAAGGTGATTGGAGGCACCAACCTAGCCATCAGGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAGgtaattttggtcgttttgttagaatcacaacaaaataaacatatactttgttatcaaattacagcgccctcttgttgattgcag

Basic information

species	Zea mays
transcript	GRMZM2G138349_T03
intron #	7
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G138349_T04 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g10480.1 (Oryza sativa), 5'ss of exon 7

CATTGGAATATTGAATGTCAAGGTGATTGGAGGCACCAACCTAGCCATCAGGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAGgtaattttg---------gtcgttttgttagaatc---acaacaaaataaacatatactttgttat--caaattacagcgccctcttgttgattgcag----------------------------------------------
||| ||||||||||||||||||||||  ||||||||||||||||||||||| || |||||||||||||| |||||||| |||||||| ||||||||||||||| | ||              || || | |  ||    |||| || | || ||  | ||  |  |     |  |||  | | |||  || |   ||                                               
CATCGGAATATTGAATGTCAAGGTGAAAGGAGGCACCAACCTAGCCATCAGAGACATGTCAAGCAGTGATCCTTATGTAGTCCTGACCCTTGGGCAACAGgtagtattatgaaatcctaattttctgatggtttctgggcaactaattcaagatcgaattcatcgttttgtaccacattgtc-tctcattcagaacatgcagaaattcttgttctaaatttcaccatatcttcgctgtgtgcag

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|213172275|gb|FM186438.1|FM186438

EST:     GGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAG                         AAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAA
genomic: GGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAGgtaattttgg ... ttgattgcagAAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAA

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

EST:     GGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAG                         AAAGCACAAACTTCAGTAATCAATGGCAAC
genomic: GGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAGgtaattttgg ... ttgattgcagAAAGCACAAACTTCAGTAATCAATGGCAAC

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

EST:     GGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAG                         AAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAA
genomic: GGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAGgtaattttgg ... ttgattgcagAAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAA

EST: gi|50334442|gb|CO529568.1|CO529568

EST:     GGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAG                         AAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAA
genomic: GGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAGgtaattttgg ... ttgattgcagAAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAA

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

EST:     GGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAG                         AAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAA
genomic: GGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAGgtaattttgg ... ttgattgcagAAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAA

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

EST:     GGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAG                         AAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAA
genomic: GGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAGgtaattttgg ... ttgattgcagAAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAA

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

EST:     GGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAG                         AAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAA
genomic: GGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAGgtaattttgg ... ttgattgcagAAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAA

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

EST:     GGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAG                         AAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAA
genomic: GGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAGgtaattttgg ... ttgattgcagAAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAA

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

EST:     GGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAG                         AAAGCACAAACTTCAGTAAATCA-TGGCAACCTGAATCCTGTCTGGAATGA
genomic: GGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAGgtaattttgg ... ttgattgcagAAAGCACAAACTTCAGTAA-TCAATGGCAACCTGAATCCTGTCTGGAATGA

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), 47 (downstream exon)
Score: 126

CATTGGAATATTGAATGTCAAGGTGATTGGAGGCACCAACCTAGCCATCAGGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAGgtaattttgg ... ttgattgcagAAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAAGAACTGAAGCTCTCTGTTCCCCAGCAATATGGACCTCTGAAGCTG

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 330

Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 128