ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

...atcttgctatggattttttttctttttattatctttattatgcttgtttgctttggcctatttcactcaaatagtttacctgtggtcttgctacatttagATCGTTAAGGAGAATCAGAAGCTTCACAAAGGAAATGTTGAGATTGAAGGTGACTTGGCTACTCTTGCCGACAAGAGTATCTTTCCTGGGGATGTTCTTT

Basic information

species	Zea mays
transcript	GRMZM2G376074_T02
intron #	12
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G376074_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os03g09270.1 (Oryza sativa), 3'ss of exon 3

----------atcttgctatggattttttttctttttattatctttattatgcttgtttgctttggcctatttcactcaaatagtttacctgtggtcttgctacatttagATCGTTAAGGAGAATCAGAAGCTTCACAAAGGAAATGTTGAGATTGAAGGTGACTTGGCTACTCTTGCCGACAAGAGTATCTTTCCTGGGGATGTTCTTT
           | ||  ||| ||   ||  || || | | || |  ||||||||||||| |||| |   ||| || ||||||  ||         | |||| | ||| |||| ||||||||||| ||| |||||||||||||   |||||||||||||| ||| || ||||||||||| |||||| |||| |||||||| |||||||| |
cctttctccattttttttattgaaccttgctccttatttgatttacattatgcttgtttactttag---attgcattcaaattatt-------actgttgccatattcagATTGTTAAGGAGAACCAGGAGCTTCACAAAGGCTCTGTTGAGATTGAAGATGATTTTGCTACTCTTGCTGACAAGTGTATTTTTCCTGGAGATGTTCTAT

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|67025740|gb|CO454489.1|CO454489

EST:     GTTCCACATCCGTCTATCAGTTGAAACTCATGATATGGGAATCTTTAGGG                         ATCGTTAAGGAGAATCAGAAGCTTCACAAAGGAAATGTTGAGATTGAAGGT
genomic: GTTCCACATCCGTCTATCAGTTGAAACTCATGATATGGGAATCTTTAGGGgtatggtata ... ctacatttagATCGTTAAGGAGAATCAGAAGCTTCACAAAGGAAATGTTGAGATTGAAGGT

EST: gi|76284352|gb|DV023920.1|DV023920

EST:     GTTCCACATCCGTCTATCAGTTGAAACTCATGATATGGGAATCTTTAGGG                         ATCGTTAAGGAGAATCAGAAGCTTCACAAAGGAAATGTTGAGATTGAAGGT
genomic: GTTCCACATCCGTCTATCAGTTGAAACTCATGATATGGGAATCTTTAGGGgtatggtata ... ctacatttagATCGTTAAGGAGAATCAGAAGCTTCACAAAGGAAATGTTGAGATTGAAGGT

EST: gi|211478836|gb|FL266343.1|FL266343

EST:     GTTCTACATCCGTCTATCAGTTGAAACTCATGATATGGGAATCTTTAGGG                         ATCGTTAAGGAGAATCAGAAGCTTCACAAAGGAAATGTTGAGATTGAAGGT
genomic: GTTCCACATCCGTCTATCAGTTGAAACTCATGATATGGGAATCTTTAGGGgtatggtata ... ctacatttagATCGTTAAGGAGAATCAGAAGCTTCACAAAGGAAATGTTGAGATTGAAGGT

EST: gi|67022296|gb|CO451045.1|CO451045

EST:     GTTCCACATCCGTCTATCAGTTGAAACTCATGATATGGGAATCTTTAGGG                         ATCGTTNAGGA-AATCANAAGCTTCACAA-GGAA-TGTTGAGATTGA-GGT
genomic: GTTCCACATCCGTCTATCAGTTGAAACTCATGATATGGGAATCTTTAGGGgtatggtata ... ctacatttagATCGTTAAGGAGAATCAGAAGCTTCACAAAGGAAATGTTGAGATTGAAGGT

EST: gi|60345273|gb|DN212246.1|DN212246

EST:     CATGATATGGGAATCTTTAGGG                         ATCGTTAAGGAGAATCAGAAGCTTCACAAAGGAAATGTTGAGATTGAAGGT
genomic: CATGATATGGGAATCTTTAGGGgtatggtata ... ctacatttagATCGTTAAGGAGAATCAGAAGCTTCACAAAGGAAATGTTGAGATTGAAGGT

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: 48 (upstream exon), 49 (downstream exon)
Score: 166

GCGTTCCAGGAGGACAAGCTCTGGGAATTCAATCAGTTTGAAAGTCTCTGGTTCCACATCCGTCTATCAGTTGAAACTCATGATATGGGAATCTTTAGGGgtatggtata ... ctacatttagATCGTTAAGGAGAATCAGAAGCTTCACAAAGGAAATGTTGAGATTGAAGGTGACTTGGCTACTCTTGCCGACAAGAGTATCTTTCCTGGGGATGTTCTTT

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 86

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 66

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 139

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gtttgctttggcctatttcactcaaatagtttacctgtggtcttgctacatttagATCGTTAAGGAGAATCAGAAGCTTCACAAAGGAAATGTTGAGATTGAAGGTGACTTGGCTACTCTTGCCGACAAGAGTATCTTTCCTGGGGATGTTCTTT