ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CAAGAGGTGGCAGCTTCAGCTGGTGAGAGCAGCTTTAGATCCTTTATGATTGCTGTGCAGCGTTGTACCAGTAGCGTAGCTATTCTTCAGCAGgtaatcttcgctgatccatcaagttgcaaccttggcttgcatatgaagtcaataaagcatgcttgaatttctctgtttcctctgtag

Basic information

species	Zea mays
transcript	GRMZM5G823484_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G823484_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os12g13590.1 (Oryza sativa), 5'ss of exon 17

CAAGAGGTGGCAGCTTCAGCTGGTGAGAGCAGCTTTAGATCCTTTATGATTGCTGTGCAGCGTTGTACCAGTAGCGTAGCTATTCTTCAGCAGgtaatcttcgctgatccatcaagttgcaaccttggcttgcatatgaagtcaataaagcatgcttgaatttctctgtttcctctgtag
  ||||| ||||||| | || |||||||| |||||||||||||| ||||||||||||||||||||| | || || || |||||||||||||||||||| | |   | ||||  |   |  |  ||  |||  || | ||      | || ||||||    || |||  | ||  | |   
GCAGAGGCGGCAGCTGCTGCAGGTGAGAGTAGCTTTAGATCCTTCATGATTGCTGTGCAGCGTTGTGCTAGCAGTGTGGCTATTCTTCAGCAGgtaatatgcagag-tccactagactttacactaagctgccaaacga------tgaaccatgctgattttcctccttctctccag---

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|9566477|gb|BE475986.1|BE475986

EST:     CGTAGCTATTCTTCAGCAG                         TACTTCTCAAATACCATATCTCGGCTCTTGCTACCTGTTGATGGTGCTCAT
genomic: CGTAGCTATTCTTCAGCAGgtaatcttcg ... tcctctgtagTACTTCTCAAATACCATATCTCGGCTCTTGCTACCTGTTGATGGTGCTCAT

EST: gi|32802642|gb|CD954878.1|CD954878

EST:     TTATGATTGCTGTGCAGCGTTGTACCAGTAGCGTAGCTATTCTTCAGCAG                         TACTTCTCAAATACCATATCTCGGCTCTTGCTACCTGTTGATGGTGCTCAT
genomic: TTATGATTGCTGTGCAGCGTTGTACCAGTAGCGTAGCTATTCTTCAGCAGgtaatcttcg ... tcctctgtagTACTTCTCAAATACCATATCTCGGCTCTTGCTACCTGTTGATGGTGCTCAT

EST: gi|32804847|gb|CD957083.1|CD957083

EST:     TTATGATTGCTGTGCAGCGTTGTACCAGTAGCGTAGCTATTCTTCAGCAG                         TACTTCTCAAATACCATATCTCGGCTCTTGCTACCTGTTGATGGTGCTCAT
genomic: TTATGATTGCTGTGCAGCGTTGTACCAGTAGCGTAGCTATTCTTCAGCAGgtaatcttcg ... tcctctgtagTACTTCTCAAATACCATATCTCGGCTCTTGCTACCTGTTGATGGTGCTCAT

EST: gi|71434510|gb|DR815560.1|DR815560

EST:     TTATGATTGCTGTGCAGCGTTGTACCAGTAGCGTAGCTATTCTTCAGCAG                         TACTTCTCAAATACCATATCTCGGCTCTTGCTACCTGTTGATGGTGCTCAT
genomic: TTATGATTGCTGTGCAGCGTTGTACCAGTAGCGTAGCTATTCTTCAGCAGgtaatcttcg ... tcctctgtagTACTTCTCAAATACCATATCTCGGCTCTTGCTACCTGTTGATGGTGCTCAT

EST: gi|5847426|gb|AW000505.1|AW000505

EST:     GCTGTGCAGCGTTGTACCAGTAGCGTAGCTATTCTTCAGCAG                         TACTTCTCAAATACCATATCTCGGCTCTTGCTACCTGTTGATGGTGCTCAT
genomic: GCTGTGCAGCGTTGTACCAGTAGCGTAGCTATTCTTCAGCAGgtaatcttcg ... tcctctgtagTACTTCTCAAATACCATATCTCGGCTCTTGCTACCTGTTGATGGTGCTCAT

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: 227

CAAGAGGTGGCAGCTTCAGCTGGTGAGAGCAGCTTTAGATCCTTTATGATTGCTGTGCAGCGTTGTACCAGTAGCGTAGCTATTCTTCAGCAGgtaatcttcg ... tcctctgtagTACTTCTCAAATACCATATCTCGGCTCTTGCTACCTGTTGATGGTGCTCATCCGTCTGCTTGTGAAGATATGGGGTCAGCAGTATCAGTAGTTGAGGCTG

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 175

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 239