ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGGCAGAGTTCCCTTCGGCAAAGCCTCCACTAGGAGTCTTCTTTGCAGCTGTTGCCCCTCGACTTCAACCAAGATATTATTCTATTTCATCTTCACCTAGgtaaatagccccactcataatttttccttctcatcatgaatatttgttttcctgttgacttacatttcctttcatctggcag

Basic information

species	Zea mays
transcript	AC217947.4_FGT002
intron #	11
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: AC217947.4_FGT002 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os08g14570.1 (Oryza sativa), 5'ss of exon 11

TGGCAGAGTTCCCTTCGGCAAAGCCTCCACTAGGAGTCTTCTTTGCAGCTGTTGCCCCTCGACTTCAACCAAGATATTATTCTATTTCATCTTCACCTAGgtaaatagccccactcataatttttccttctcatcatgaa-----tatttgttttcctgttgacttacatttcctttcatctggcag
|||||||||||||||| |||||||||||||||||||||||||||||||| ||||| ||||| ||||| || ||||| || || ||||||||||||||||||||||    || ||| ||  |||||| | |||||  | ||     |  ||   ||  | ||||| | |||||||||   ||   |||
TGGCAGAGTTCCCTTCAGCAAAGCCTCCACTAGGAGTCTTCTTTGCAGCCGTTGCTCCTCGTCTTCAGCCGAGATACTACTCAATTTCATCTTCACCTAGgtaaaatatcctacttatgctttttcttcctcattttaaaattgttccttacctttttattgacatgcatttccttct-tccatcag

upper sequence: AC217947.4_FGT002 (Zea mays), 5'ss of exon 11
lower sequence: Vv11s0052g00880.t01 (Vitis vinifera), 5'ss of exon 12

TGGCAGAGTTCCCTTCGGCAAAGCCTCCACTAGGAGTCTTCTTTGCAGCTGTTGCCCCTCGACTTCAACCAAGATATTATTCTATTTCATCTTCACCTAGgtaaatagccccactcat--aatttttccttctcatcatg--aatatttgttttcct----gttgact-tacatttc-ctttcatctggcag--------
|||| || ||||| || || ||||||||||| ||||| ||||||||||| ||||| || ||  | || || ||||||||||| || |||||||| || | || | ||   |    | |  || | ||   || |||| |     | ||  |    ||    ||  ||| |  | | | || | ||   | |         
TGGCTGAATTCCCATCAGCCAAGCCTCCACTTGGAGTTTTCTTTGCAGCAGTTGCTCCACGCTTGCAGCCCAGATATTATTCCATATCATCTTCCCCAAAgtgagtatttctgtcctttcaaatattagatcgcatctttttgctgttaatacctctagatgtcaactgtgtaatacactatgattccgtaaaactgtaa

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|211060797|gb|FL421770.1|FL421770

EST:     CATCTTCACCTAG                         TATGGCACCAACCAGGATTCATGTCACATGTGCGCTCGTGCGCGAAACAAC
genomic: CATCTTCACCTAGgtaaatagcc ... catctggcagTATGGCACCAACCAGGATTCATGTCACATGTGCGCTCGTGCGCGAAACAAC

EST: gi|76932021|gb|DV172915.1|DV172915

EST:     GTTGCCCCTCGACTTCAACCAAGATATTATTCTATTTCATCTTCACCTAG                         TATGGCACCAACCAGGATTCATGTCACATGTGCGCTCGTGCGCGAAACAAC
genomic: GTTGCCCCTCGACTTCAACCAAGATATTATTCTATTTCATCTTCACCTAGgtaaatagcc ... catctggcagTATGGCACCAACCAGGATTCATGTCACATGTGCGCTCGTGCGCGAAACAAC

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: 44 (upstream exon), 47 (downstream exon)
Score: 71

TGGCAGAGTTCCCTTCGGCAAAGCCTCCACTAGGAGTCTTCTTTGCAGCTGTTGCCCCTCGACTTCAACCAAGATATTATTCTATTTCATCTTCACCTAGgtaaatagcc ... catctggcagTATGGCACCAACCAGGATTCATGTCACATGTGCGCTCGTGCGCGAAACAACACCCGCTGGAAGGGTACATAAGGGAGTTTGCTCAACTTGGATTAAG

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 216

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 213