ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CATTGGTGCAAACTCAGCCGCGGGTGCTCCTGGCTTGTCACCAAGCTCTTCAATAGGATCTCTTACCGCTGAAAAATCGACTTTGAACCCTAATGCTAAGgtctgactgatatgaagttgtttatgtcttctttgatcacttttcatgatgagtctgctagtaccaaatcttaagttaatatacacaacttttatgtatt...

Basic information

species	Zea mays
transcript	GRMZM5G829738_T01
intron #	11
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G829738_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os02g27950.1 (Oryza sativa), 5'ss of exon 11

CATTGGTGCAAACTCAGCCGCGGGTGCTCCTGGCTTGTCACCAAGCTCTTCAATAGGATCTCTTACCGCTGAAAAATCGACTTTGAACCCTAATGCTAAGgtctgactgatatgaagttgtttatgtcttctttgatcacttttcatga----tgagtctgctagtaccaaatcttaagttaatatacacaacttttatgtatt------
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CATTGCTGCAAGCTCAGTTGCATGTGCTCCAGGCTTGTCCCCGAGCTCTTCAATGGGTTCTCTTAGCTCAGAAAAATCATCTTTGAACCCGAATGCTAAGgtctatcgtatactacatc-tggctgcttttgtgcatggatattgataggcatctattcctctgatcatttgtgtcgcaaggtcactgacaactgttatttctaaaccag

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|31363999|gb|CD448354.1|CD448354

EST:     AATCGACTTTGAACCCTAATGCTAAG                         GAATTCAAGCTAAATCCTAATGCCAAGAGTTTCACTCCGTCAGCATCTCTG
genomic: AATCGACTTTGAACCCTAATGCTAAGgtctgactga ... ttctaatcagGAATTCAAGCTAAATCCTAATGCCAAGAGTTTCACTCCGTCAGCATCTCTG

EST: gi|116815752|gb|EC858445.1|EC858445

EST:     CTCTTACTGCTGAAAAATCGACTTTGAACCCTAATGCTAAG                         GAATTCAAGCTAAATCCTAATGCCAAGAGTTTCACTCCGTCAGCATCTCTG
genomic: CTCTTACCGCTGAAAAATCGACTTTGAACCCTAATGCTAAGgtctgactga ... ttctaatcagGAATTCAAGCTAAATCCTAATGCCAAGAGTTTCACTCCGTCAGCATCTCTG

EST: gi|60344962|gb|DN211935.1|DN211935

EST:     GACTTTG-ACCCTAATGCTAAG                         GAATTCAAGCTAAATCCTAATGCCAAGAGTTTCACTCCGTCAGCATCTCTG
genomic: GACTTTGAACCCTAATGCTAAGgtctgactga ... ttctaatcagGAATTCAAGCTAAATCCTAATGCCAAGAGTTTCACTCCGTCAGCATCTCTG

EST: gi|116826672|gb|EC870479.1|EC870479

EST:     CTCTTA-CGCTGAAAAAT--ACTTTGAA-CCTAATGCTAAG                         GACATTCAAGCTAAATCCTAATGCCAAGAGTTTCACTCCCGTCAGCATCTC
genomic: CTCTTACCGCTGAAAAATCGACTTTGAACCCTAATGCTAAGgtctgactga ... ttctaatcagGA-ATTCAAGCTAAATCCTAATGCCAAGAGTTTCACT-CCGTCAGCATCTC

EST: gi|74234144|gb|DT642058.1|DT642058

EST:     CAATAGGATCTCTTACCGCTGAAAAATCGACTTTGAACCCTAATGCTAAG                         GAATTCAAGCTAAATCCTAATGCCAAGAGTTTCACTCCGTCAGCATCTCTG
genomic: CAATAGGATCTCTTACCGCTGAAAAATCGACTTTGAACCCTAATGCTAAGgtctgactga ... ttctaatcagGAATTCAAGCTAAATCCTAATGCCAAGAGTTTCACTCCGTCAGCATCTCTG

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: 160

CATTGGTGCAAACTCAGCCGCGGGTGCTCCTGGCTTGTCACCAAGCTCTTCAATAGGATCTCTTACCGCTGAAAAATCGACTTTGAACCCTAATGCTAAGgtctgactga ... ttctaatcagGAATTCAAGCTAAATCCTAATGCCAAGAGTTTCACTCCGTCAGCATCTCTGAGGCCACCACACCCTACATCATCTGATGCATCATATTACTATCCTAATA

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 113

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 97