ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gcatgccctcttcatctagtctcgttctcattcatttaaaatgccacccatgcatcttttatagctcagccagttaactgaatatgatttttcagTGCCGTCTTTCAACCACCATCCGCTGCCTTTCTCACCCAAGCGCGCACGTGCGCGCGCTCAGCATGTCCGTTCTCCGTGACATCCTGGACCACGGATCCG

Basic information

species	Zea mays
transcript	GRMZM5G844173_T01
intron #	14
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G844173_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os01g08700.6 (Oryza sativa), 3'ss of exon 14

gcatgccctcttcatctagtctcgttctcattcatttaaaatgccacccatgcatcttttatagctcagccagttaactgaatatgatttttcagTGCCGTCTTTCAACCACCATCCGCTGCCTTTCTCACCCAAGCGCGCACGTGCGCGCGCTCAGCATGTCCGTTCTCCGTGACATCCTGGACCACGGATCCG
||||| ||||||| |||  ||||  || | |||||   |||    || ||| |||| |  ||    || |    | ||||||| |   | | ||||||||||| ||||||||||||||||| ||||| ||||| |||||||| || || || |||||||||||||| || || |||||| || ||  ||||    
gcatgtcctcttc-tctgatctcactcacgttcatgccaaac-ttactcat-catcatccatgatccatcatcctgactgaatcttgatatgcagTGCCGTCTATCAACCACCATCCGCTGTCTTTCGCACCCCAGCGCGCATGTCCGTGCACTCAGCATGTCCGTCCTTCGCGACATCTTGAACAGCGGACAAA

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|67015070|gb|CO443819.1|CO443819

EST:     GGGGAGATCCAGGTTTATCAGTTGCTGATGGCCTTTCTAATCTGCTAAAG                         TGCCGTCTTTCAACCACCATCCGCTGCCTTTCTCACCCAAGCGCGCACGTG
genomic: GGGGAGATCCAGGTTTATCAGTTGCTGATGGCCTTTCTAATCTGCTAAAGgcatgccctc ... gatttttcagTGCCGTCTTTCAACCACCATCCGCTGCCTTTCTCACCCAAGCGCGCACGTG

EST: gi|16926698|gb|BM079766.1|BM079766

EST:     TTATCAGTTGCTGATGGCCTTTCTAATCTGCTAAAG                         TGCCGTCTTTCAACCACCATCCGCTGCCTTTCTCACCCAAGCGCGCACGTG
genomic: TTATCAGTTGCTGATGGCCTTTCTAATCTGCTAAAGgcatgccctc ... gatttttcagTGCCGTCTTTCAACCACCATCCGCTGCCTTTCTCACCCAAGCGCGCACGTG

EST: gi|60358929|gb|DN225902.1|DN225902

EST:     GGGGAGATCCAGGTTTATCAGTTGCTGATGGCCTTTCTAATCTGCTAAAG                         TGCCGTCTTTCAACCACCATCCGCTGCCTTTCTCACCCAAGCGCGCACGTG
genomic: GGGGAGATCCAGGTTTATCAGTTGCTGATGGCCTTTCTAATCTGCTAAAGgcatgccctc ... gatttttcagTGCCGTCTTTCAACCACCATCCGCTGCCTTTCTCACCCAAGCGCGCACGTG

EST: gi|149081338|gb|EE170453.2|EE170453

EST:     GGGGAGATCCAGGTTTATCAGTTGCTGATGGCCTTTCTAATCTGCTAAAG                         TGCCGTCTTTCAACCACCATCCGCTGCCTTTCTCACCCATGCGCGCACGTG
genomic: GGGGAGATCCAGGTTTATCAGTTGCTGATGGCCTTTCTAATCTGCTAAAGgcatgccctc ... gatttttcagTGCCGTCTTTCAACCACCATCCGCTGCCTTTCTCACCCAAGCGCGCACGTG

EST: gi|76017243|gb|DT944413.1|DT944413

EST:     GGGGAGATCCAGGTTTATCAGTTGCTGATGGCCTTTCTAATCTGCTAAAG                         TGCCGTCTTTCAACCACCATCCGCTGCCTTTCTCACCCAAGCGCGCACGTG
genomic: GGGGAGATCCAGGTTTATCAGTTGCTGATGGCCTTTCTAATCTGCTAAAGgcatgccctc ... gatttttcagTGCCGTCTTTCAACCACCATCCGCTGCCTTTCTCACCCAAGCGCGCACGTG

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), 49 (downstream exon)
Score: 205

CTTCTCGAAGTAACCGCTCGAGCAGTCCATCTTATTATTGAATGGGGAGATCCAGGTTTATCAGTTGCTGATGGCCTTTCTAATCTGCTAAAGgcatgccctc ... gatttttcagTGCCGTCTTTCAACCACCATCCGCTGCCTTTCTCACCCAAGCGCGCACGTGCGCGCGCTCAGCATGTCCGTTCTCCGTGACATCCTGGACCACGGATCCG

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 150

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 95

Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 193

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

atgccacccatgcatcttttatagctcagccagttaactgaatatgatttttcagTGCCGTCTTTCAACCACCATCCGCTGCCTTTCTCACCCAAGCGCGCACGTGCGCGCGCTCAGCATGTCCGTTCTCCGTGACATCCTGGACCACGGATCCG