ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaggtttcaatattccacctgcagtctgtatcccattatttggttcctcacattttgattgtttaagtaaatatgactatttatgcaaatgctagAATTGGCATTACAAGTGAAGATTTGAAGAATACAATAGAGAAGACATTGGGTGGTGCAGGACTAGCTCTTTCATCTCCAAGGCTTATAATTCCTGCCGTG

Basic information

species	Zea mays
transcript	GRMZM2G060842_T01
intron #	7
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G060842_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g20640.1 (Oryza sativa), 3'ss of exon 7

gtaggtttcaatattccacctgcagtctgtatcccattatttggttcctcacattttgattgtttaagtaaatatgactatttatgcaaatgctagAATTGGCATTACAAGTGAAGATTTGAAGAATACAATAGAGAAGACATTGGGTGGTGCAGGACTAGCTCTTTCATCTCCAAGGCTTATAATTCCTGCCGTG
|||||||| || ||   |       | | |   | ||  ||||   |||||| || | |||  ||      ||||       | ||  ||||||||||| ||||| | ||| || ||||||||||||||||||||||||   |||||||||     | |||||||||| |||||||||||| | || || ||  | 
gtaggtttgaaaatgttaatcattttttattatcaatcttttg--ccctcactttgtcattaattgtccctatata------tgtgacaatgctagAATCGGCATAAGAAGCGAGGATTTGAAGAATACAATAGAGAAGGTGTTGGGTGGTATTTCAGTAGCTCTTTCGTCTCCAAGGCTTGTGATACCCGCTATA

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|88755364|gb|DY539505.1|DY539505

EST:     CTATCAAAGGAAGATATTCCAGAAGTTTTTCTAAAGAAGAAAGTGAAGAA                         AATTGGCATTACAAGTGAAGATTTGAAGAATACAATAGAGAAGACATTGGG
genomic: CTATCAAAGGAAGATATTCCAGAAGTTTTTCTAAAGAAGAAAGTGAAGAAgtaggtttca ... caaatgctagAATTGGCATTACAAGTGAAGATTTGAAGAATACAATAGAGAAGACATTGGG

EST: gi|50327397|gb|CO522523.1|CO522523

EST:     CTATCAAAGGAAGATATTCCAGAAGTTTTTCTAAAGAAGAAAGTGAAGAA                         AATTGGCATTACAAGTGAAGATTTGAAGAATACAATAGAGAAG
genomic: CTATCAAAGGAAGATATTCCAGAAGTTTTTCTAAAGAAGAAAGTGAAGAAgtaggtttca ... caaatgctagAATTGGCATTACAAGTGAAGATTTGAAGAATACAATAGAGAAG

EST: gi|76280844|gb|DV020412.1|DV020412

EST:     CTATCAAAGGAAGATATTCCAGAAGTTTTTCTAAAGAAGAAAGTGAAGAA                         AATTGGCATTACAAGTGAAGATTTGAAGAATACAATAGAGAAGACATTGGG
genomic: CTATCAAAGGAAGATATTCCAGAAGTTTTTCTAAAGAAGAAAGTGAAGAAgtaggtttca ... caaatgctagAATTGGCATTACAAGTGAAGATTTGAAGAATACAATAGAGAAGACATTGGG

EST: gi|18170857|gb|BM340697.1|BM340697

EST:     TTTTTCTAAAGAAGAAAGTGAAGAA                         AATTGGCATTACAAGTGAAGATTTGAAGAAT-CAATAGAGAAGACATTGGG
genomic: TTTTTCTAAAGAAGAAAGTGAAGAAgtaggtttca ... caaatgctagAATTGGCATTACAAGTGAAGATTTGAAGAATACAATAGAGAAGACATTGGG

EST: gi|50326968|gb|CO522094.1|CO522094

EST:     CTATCAAAGGAAGATATTCCAGAAGTTTTTCTAAAGAAGAAAGTGAAGAA                         AATTGGCATTACAAGTGAAGATTTGAAGAATACA
genomic: CTATCAAAGGAAGATATTCCAGAAGTTTTTCTAAAGAAGAAAGTGAAGAAgtaggtttca ... caaatgctagAATTGGCATTACAAGTGAAGATTTGAAGAATACA

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), 47 (downstream exon)
Score: 31

TTGCTTGTATCTTCAACTTCTGTATCAACATGCTGATAACCTATCAAAGGAAGATATTCCAGAAGTTTTTCTAAAGAAGAAAGTGAAGAAgtaggtttca ... caaatgctagAATTGGCATTACAAGTGAAGATTTGAAGAATACAATAGAGAAGACATTGGGTGGTGCAGGACTAGCTCTTTCATCTCCAAGGCTTATAATTCCTGCCGTG

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 85

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 78

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 56

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tggttcctcacattttgattgtttaagtaaatatgactatttatgcaaatgctagAATTGGCATTACAAGTGAAGATTTGAAGAATACAATAGAGAAGACATTGGGTGGTGCAGGACTAGCTCTTTCATCTCCAAGGCTTATAATTCCTGCCGTG