ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

AATTGCTTGGCTACCATCTTCTTACTTTTGTTTGCCATGGTCTCATATTCTCTCTGGGTGTTCTCTTTCTCTGGTCTAATGCTTCATCGTTTATCCACAAgtaagagatcacctcagtatcataaactgctcaaactataaaacatacaagtttgtccattgctagttagatgggcataggctaatttcatgatgtgaaattctgcccatcaattcag

Basic information

species	Zea mays
transcript	GRMZM2G359018_T02
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G359018_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g12650.1 (Oryza sativa), 5'ss of exon 2

AATTGCTTGGCTACCATCTTCTTACTTTTGTTTGCCATGGTCTCATATTCTCTCTGGGTGTTCTCTTTCTCTGGTCTAATGCTTCATCGTTTATCCACAAgtaaga---gatcacctcagtatcataaactgctcaaactataa-aacatacaagtttgtccattgctagttagatgggcataggctaatttcatgatgtgaaattctgcccatcaattcag
|||||||||||||||| || || ||||| ||||||||||| |||||||||||| ||||| |||||||||||||||||||||| ||||| |||||  ||||||||||     |  | ||  ||||| ||  || ||||  | |   ||   | ||   ||| |      || |||||    | |    |  |   |      ||| | ||||| |   |||||
AATTGCTTGGCTACCACCTCCTGACTTTCGTTTGCCATGGGCTCATATTCTCTTTGGGTCTTCTCTTTCTCTGGTCTAATGCCTCATCATTTATTAACAAgtaagattgtttttcatctctatcacaacttgttcaagttttggcaaagcataatcatgttccac---aggtagataattacataaaaggtctct------aaactgtgccctttctttcag

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|88757769|gb|DY541910.1|DY541910

EST:     TCTCTGGGTGTTCTCTTTCTCTGGTCTAATGCTTCATCGTTTATCCACAA                         GTCTCCCCCAAAGATCCCAGAGGTGGTCATTCCTGAAGATTTAGTTGTCAA
genomic: TCTCTGGGTGTTCTCTTTCTCTGGTCTAATGCTTCATCGTTTATCCACAAgtaagagatc ... atcaattcagGTCTCCCCCAAAGATCCCAGAGGTGGTCATTCCTGAAGATTTAGTTGTCAA

EST: gi|29543942|gb|CB604322.1|CB604322

EST:     TGTTCTCTTTCTCTGGTCTAATGCTTCATCGTTTATCCACAA                         GTCTCCCCCAAAGATCCCAGAGGTGGTCATTCCTGAAGATTTAGTTGTCAA
genomic: TGTTCTCTTTCTCTGGTCTAATGCTTCATCGTTTATCCACAAgtaagagatc ... atcaattcagGTCTCCCCCAAAGATCCCAGAGGTGGTCATTCCTGAAGATTTAGTTGTCAA

EST: gi|32934217|gb|CF039029.1|CF039029

EST:     TCTCTGGGTGTTCTCTTTCTCTGGTCTAATGCTTCATCGTTTATCCACAA                         GTCTCCCCCAAAGATCCCAGAGGTGGTCATTCCTGAAGATTTAGTTGTCAA
genomic: TCTCTGGGTGTTCTCTTTCTCTGGTCTAATGCTTCATCGTTTATCCACAAgtaagagatc ... atcaattcagGTCTCCCCCAAAGATCCCAGAGGTGGTCATTCCTGAAGATTTAGTTGTCAA

EST: gi|60395596|gb|DN228466.1|DN228466

EST:     TCTTTCTCTGGTCTAATGCTTCATCGTTTATCCACAA                         GTCTCCCCCAAAGATCCCAGAGGTGGTCATTCCTGAAGATTTAGTTGTCAA
genomic: TCTTTCTCTGGTCTAATGCTTCATCGTTTATCCACAAgtaagagatc ... atcaattcagGTCTCCCCCAAAGATCCCAGAGGTGGTCATTCCTGAAGATTTAGTTGTCAA

EST: gi|31355597|gb|CD439954.1|CD439954

EST:     TCTCTGGGTGTTCTCTTTCTCTGGTCTAATGCTTCATCGTTTATCCACAA                         GTCTCCCCCAAAGATCCCAGAGGTGGTCATTCCTGAAGATTTAGTTGTCAA
genomic: TCTCTGGGTGTTCTCTTTCTCTGGTCTAATGCTTCATCGTTTATCCACAAgtaagagatc ... atcaattcagGTCTCCCCCAAAGATCCCAGAGGTGGTCATTCCTGAAGATTTAGTTGTCAA

EST: gi|22546350|gb|BU098661.1|BU098661

EST:     TCTCTGGGTGTTCTCTTTCTCTGGTCTAATGCTTCATCGTTTATCCACAA                         GTCTCCCCCAAAGATCCCAGAGGTGGTCATTCCTGAAGATTTAGTTGTCAA
genomic: TCTCTGGGTGTTCTCTTTCTCTGGTCTAATGCTTCATCGTTTATCCACAAgtaagagatc ... atcaattcagGTCTCCCCCAAAGATCCCAGAGGTGGTCATTCCTGAAGATTTAGTTGTCAA

EST: gi|29543376|gb|CB603772.1|CB603772

EST:     TCTCTGGTCTAATGCTTCATCGTTTATCCACAA                         GTCTCCCCCAAAGATCCCAGAGGTGGTCATTCCTGAAGATTTAGTTGTCAA
genomic: TCTCTGGTCTAATGCTTCATCGTTTATCCACAAgtaagagatc ... atcaattcagGTCTCCCCCAAAGATCCCAGAGGTGGTCATTCCTGAAGATTTAGTTGTCAA

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), 47 (downstream exon)
Score: 239

AATTGCTTGGCTACCATCTTCTTACTTTTGTTTGCCATGGTCTCATATTCTCTCTGGGTGTTCTCTTTCTCTGGTCTAATGCTTCATCGTTTATCCACAAgtaagagatc ... atcaattcagGTCTCCCCCAAAGATCCCAGAGGTGGTCATTCCTGAAGATTTAGTTGTCAACATTGCGGTATCCACTCGTTATGAGATCAACAGGGCCTTTGCTAATCTC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 72

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 59