ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaaggttctttcctgtaatgtttctttctctgagtaactcaactcaagtgccattaacggggatcaaacaatctcctgtgcagGTGGTAGATGCGCTATCCCTGTCGAAGGCAACGATGGCAAAAGTTCACCAAAATTTGGCCTGGGCAGTGGCATATAACATAGTAGCCATTCCAATTGCCG

Basic information

species	Zea mays
transcript	GRMZM5G855347_T02
intron #	9
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G855347_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g08070.1 (Oryza sativa), 3'ss of exon 14

gtaaggttctttcctgtaatgtttctttctctgagtaactcaactcaagtgc-cattaacggggatcaaacaatctcctgtgcagGTGGTAGATGCGCTATCCCTGTCGAAGGCAACGATGGCAAAAGTTCACCAAAATTTGGCCTGGGCAGTGGCATATAACATAGTAGCCATTCCAATTGCCG
||| | |||| | || || || |  | |  |||  ||  |||| |    | |    |||     |  || ||  || | |   ||||  | |||||  |||| || ||||| ||||| ||||| ||||||||||||||||| |||||||| || ||||||||||||||||| || || |||||||
gtaggattctgttctcta-tgatattgtaactgcatagttcaagtggcattcgtgctaataaacaagaaccaccctacggcttagGTAATGGATGCTTTATCACTTTCGAAAGCAACTATGGCCAAAGTTCACCAAAATTTAGCCTGGGCTGTCGCATATAACATAGTAGCTATCCCTATTGCCG

upper sequence: GRMZM5G855347_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA04G05900.1 (Glycine max), 3'ss of exon 14

------gtaaggttctt----tcctgtaatgtttctttctctgagtaa---ctcaactcaagtgccattaacggggatcaaacaatctcctgt---gcagGTGGTAGATGCGCTATCCCTGTCGAAGGCAACGATGGCAAAAGTTCACCAAAATTTGGCCTGGGCAGTGGCATATAACATAGTAGCCATTCCAATTGCCG
       |||  | ||     | |   | | | || ||| ||   |     |||   ||||        |  |    |  | |||  | || |    ||||| || |||||||||   ||  |  ||||||| |||| ||||||  ||||||||||| | |||||||| ||||||||  | || |||||||| ||||| |
cggataataacatactcaaaattcaaaattctctccttcccttcattttctctccgttcaaacaaatggagggttagtttaccaactttctatttgacagGTTGTCGATGCGCTAGATCTAGCACAGGCAACAATGGGAAAAGTGTACCAAAATTTGTCTTGGGCAGTCGCATATAATGTCGTTGCCATTCCCATTGCTG

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|60353203|gb|DN220176.1|DN220176

EST:     CTGCCTCTGATGCAGCTTCAGTTGTTCTACTAGGCAACAGACTTTCTCAG                         GTGGTAGATGCGCTATCCCTGTCGAAGGCAACGATGGCAAAAGTTCACCAA
genomic: CTGCCTCTGATGCAGCTTCAGTTGTTCTACTAGGCAACAGACTTTCTCAGgtaaggttct ... tcctgtgcagGTGGTAGATGCGCTATCCCTGTCGAAGGCAACGATGGCAAAAGTTCACCAA

EST: gi|32835068|gb|CD974746.1|CD974746

EST:     CTGCCTCTGATGCAGCTTCAGTTGTTCTACTAGGCAACAGACTTTCTCAG                         GTGGTAGATGCGCTATCCCTGTCGAAGGCAACGATGGCAAAAGTTCACCAA
genomic: CTGCCTCTGATGCAGCTTCAGTTGTTCTACTAGGCAACAGACTTTCTCAGgtaaggttct ... tcctgtgcagGTGGTAGATGCGCTATCCCTGTCGAAGGCAACGATGGCAAAAGTTCACCAA

EST: gi|211367137|gb|FL432362.1|FL432362

EST:     TGCAGCTTCAGTTGTTCTACTAGGCAACAGACTTTCTCAG                         GTGGGTAGATGCGCTATCCCTGTCGAAGGCAACGATGGCAAAAGTTCACCA
genomic: TGCAGCTTCAGTTGTTCTACTAGGCAACAGACTTTCTCAGgtaaggttct ... tcctgtgcagGT-GGTAGATGCGCTATCCCTGTCGAAGGCAACGATGGCAAAAGTTCACCA

EST: gi|5525756|gb|AI861649.1|AI861649

EST:     CTG-CTCTGATGCAGCTTCAGTTGTTCTNCTAGGCANCAGNCTTTCTCAG                         GTGGTAGATGCGCTATCCCTGTCGAAGGCAACGATGGCAAAAGTTCNCCAA
genomic: CTGCCTCTGATGCAGCTTCAGTTGTTCTACTAGGCAACAGACTTTCTCAGgtaaggttct ... tcctgtgcagGTGGTAGATGCGCTATCCCTGTCGAAGGCAACGATGGCAAAAGTTCACCAA

EST: gi|5847391|gb|AW000470.1|AW000470

EST:     CTGCCTCTGATGCAGCTTCAGTTGTTCTACTAGGCAACAGACTTTCTCAG                         GTGGTAGATGCGCTATCCCTGTCGAAGGCAACGATGGCAAA
genomic: CTGCCTCTGATGCAGCTTCAGTTGTTCTACTAGGCAACAGACTTTCTCAGgtaaggttct ... tcctgtgcagGTGGTAGATGCGCTATCCCTGTCGAAGGCAACGATGGCAAA

EST: gi|60358034|gb|DN225007.1|DN225007

EST:     CTGCCTCTGATGCAGCTTCAGTTGTTCTACTAGGCAACAGACTTTCTCAG                         GTGGTAGATGCGCTATCCCTGTCGAAGGCAACGATGGCAAAAGTTCACCAA
genomic: CTGCCTCTGATGCAGCTTCAGTTGTTCTACTAGGCAACAGACTTTCTCAGgtaaggttct ... tcctgtgcagGTGGTAGATGCGCTATCCCTGTCGAAGGCAACGATGGCAAAAGTTCACCAA

EST: gi|32832471|gb|CD972149.1|CD972149

EST:     CTGCCTCTGATGCAGCTTCAGTTGTTCTACTAGGCAACAGACTTTCTCAG                         GTGGTAGATGCGCTATCCCTGTCGAAGGCAACGATGGCAAAAGTTCACCAA
genomic: CTGCCTCTGATGCAGCTTCAGTTGTTCTACTAGGCAACAGACTTTCTCAGgtaaggttct ... tcctgtgcagGTGGTAGATGCGCTATCCCTGTCGAAGGCAACGATGGCAAAAGTTCACCAA

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), 48 (downstream exon)
Score: 182

AGCAGCCGCAGATGTTGGAATAGCCATGCGAACTCATTCAAAAGAGAACGCTGCCTCTGATGCAGCTTCAGTTGTTCTACTAGGCAACAGACTTTCTCAGgtaaggttct ... tcctgtgcagGTGGTAGATGCGCTATCCCTGTCGAAGGCAACGATGGCAAAAGTTCACCAAAATTTGGCCTGGGCAGTGGCATATAACATAGTAGCCATTCCAATTGCCG

Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 137

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 70

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 141

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tctgagtaactcaactcaagtgccattaacggggatcaaacaatctcctgtgcagGTGGTAGATGCGCTATCCCTGTCGAAGGCAACGATGGCAAAAGTTCACCAAAATTTGGCCTGGGCAGTGGCATATAACATAGTAGCCATTCCAATTGCCG