ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGGGACATCCTCTCCAACGGTGGCGCAGTCCAAGAAATGGCTCATATTGCAAACGGCCGGGACCATGGCAACTGCGTCTCCCTTCTTCGTGTCAATgcaagtgctcgatcgttcaattcgcgtgcctttcttttcatttgtgtcattttacatgtaacaatcggatcatccattgttttgtgattattgtgtgttatattaccatgtacag

Basic information

species	Zea mays
transcript	GRMZM2G118063_T02
intron #	10
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G118063_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os08g08820.2 (Oryza sativa), 5'ss of exon 10

TGGGACATCCTCTCCAACGGTGGCGCAGTCCAAGAAATGGCTCATATTGCAAACGGCCGGGACCATGGCAACTGCGTCTCCCTTCTTCGTGTCAATgcaagtgctcgatcgttcaattcgcgtgcctttcttttcatttgtgtcatt--ttacatgtaacaatcggatcatccattgttttgtgattattgtgtgttatattaccatgtacag
|||||||| || |||||||| ||||| ||||||||||||||||| ||||| |||||||| |||||||||||||  ||||| |||||||||||||||| ||||||         ||||| |      || ||  ||||    |  ||   |  ||||||||  |||| |     |||  | | ||  ||  |  |   | || | || | ||  
TGGGACATTCTGTCCAACGGCGGCGCCGTCCAAGAAATGGCTCACATTGCCAACGGCCGTGACCATGGCAACTCTGTCTCGCTTCTTCGTGTCAATgtaagtgc---------caattag------ttactactcatcaaggcaataaatagcatgtaacggtcgg-tagcgaattagtgtctgggtagcggattgcaaat-agcaggcacta

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|26558595|gb|CA830830.1|CA830830

EST:     TTGCAAACGGCCGGGACCATGGCAACTGCGTCTCCCTTCTTCGTGTCAAT                         AGCCCAAACTCCAACCAGAGCAACATGCTGATCCTCCAGGAGAGCTGCACG
genomic: TTGCAAACGGCCGGGACCATGGCAACTGCGTCTCCCTTCTTCGTGTCAATgcaagtgctc ... ccatgtacagAGCGCAAACTCCAACCAGAGCAACATGCTGATCCTCCAGGAGAGCTGCACG

EST: gi|87156118|gb|DY400907.1|DY400907

EST:     TTGCTAACGGCCGGGACCATGGCAACTGCGTCTCCCTTCTTCGTGTCAAT                         AGCCCAAGCTCCTACCAGAGCAACTTGCTGATCCTCCGGGAGAGCTGCTCG
genomic: TTGCAAACGGCCGGGACCATGGCAACTGCGTCTCCCTTCTTCGTGTCAATgcaagtgctc ... ccatgtacagAGCGCAAACTCCAACCAGAGCAACATGCTGATCCTCCAGGAGAGCTGCACG

EST: gi|22472184|gb|BU036664.1|BU036664

EST:     TTGCAAACGGCCGGGACCATGGCAACTGCGTCTCCCTTCTTCGTGTCAAT                         AGCCCAAACTCCAACCAGAGCAACATGCTGATCCTCCAGGAGAGCTGCACG
genomic: TTGCAAACGGCCGGGACCATGGCAACTGCGTCTCCCTTCTTCGTGTCAATgcaagtgctc ... ccatgtacagAGCGCAAACTCCAACCAGAGCAACATGCTGATCCTCCAGGAGAGCTGCACG

EST: gi|76017721|gb|DT944891.1|DT944891

EST:     TTGCAAACGGCCGGGACCATGGCAACTGCGTCTCCCTTCTTCGTGTCAAT                         AGCGCAAACTCCAACCAGAGCAACATGCTGATCCTCCAGGAGAGCTGCACG
genomic: TTGCAAACGGCCGGGACCATGGCAACTGCGTCTCCCTTCTTCGTGTCAATgcaagtgctc ... ccatgtacagAGCGCAAACTCCAACCAGAGCAACATGCTGATCCTCCAGGAGAGCTGCACG

EST: gi|5566756|gb|AI881622.1|AI881622

EST:     TTGCAAACGGCCGGGACCATGGCAACTGCGTCTCCCTTCTTCGTGTCAAT                         AGCCCAAACTCCAAC
genomic: TTGCAAACGGCCGGGACCATGGCAACTGCGTCTCCCTTCTTCGTGTCAATgcaagtgctc ... ccatgtacagAGCGCAAACTCCAAC

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 3 RNA-Seq libraries.

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 599

TGGGACATCCTCTCCAACGGTGGCGCAGTCCAAGAAATGGCTCATATTGCAAACGGCCGGGACCATGGCAACTGCGTCTCCCTTCTTCGTGTCAATgcaagtgctc ... ccatgtacagAGCGCAAACTCCAACCAGAGCAACATGCTGATCCTCCAGGAGAGCTGCACGGACGCATCGGGCTCATACGTGGTGTACGCGCCGGTGGATGTGGTGGCCA

Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 78