ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

ATTGATTTACACAAATTCTGGTCTTGCTATCTTGGCTTTAACTTCAAGTGCTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAGgtgagatccgattcttatgtacatatagatgtgcataaatagtgttcagatcgctcatcttctctgcatatcattggtgaaaattgtgtatggtagattgttactaaattgttcagtttgctattcatcaatcttatag

Basic information

species	Zea mays
transcript	GRMZM2G550865_T01
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G550865_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g14980.2 (Oryza sativa), 5'ss of exon 19

ATTGATTTACACAAATTCTGGTCTTGCTATCTTGGCTTTAACTTCAAGTGCTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTC---TGGAAAGgtgagatccgattcttatgtacatatagatgtgcataaatagtgttcagatcgctcatcttctctgcatatcattggtgaaaattgtgtatggtagattgttactaaattgttcagtttgctattcatcaatcttatag
    |||||||||||||||||| | ||||||||||||||| |||||| |||||||||||| |||||||||||||| |||| ||| || || ||   ||||||||| | ||| |  |  | |   || ||| || ||| | | |  |    |  |      | | |   |     ||  ||  |  | | |||      |||||||||||| || ||  |||||||||| |    |||| |||
---TATTTACACAAATTCTGGTGTCGCTATCTTGGCTTTAGCTTCAAATGCTGTTCATCTGCTCTGGAAATGGCCTCGCAATGACCGAAACTCAAGTGGAAAGgttaaatctggattatttacgcacataaatatgc-tcagttttacctacctgctctgtataccaggt---ccaggggcaagcaatttgtgcatatgattgttactaactttttatgtttgctattgac---tcttctag

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|67042557|gb|CO468812.1|CO468812

EST:     CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAG                         GCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTG
genomic: CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAGgtgagatccg ... aatcttatagGCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTG

EST: gi|18963627|gb|BM660541.1|BM660541

EST:     CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAG                         GCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTG
genomic: CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAGgtgagatccg ... aatcttatagGCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTG

EST: gi|19058178|gb|BM736845.1|BM736845

EST:     CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAG                         GCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTG
genomic: CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAGgtgagatccg ... aatcttatagGCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTG

EST: gi|87152018|gb|DY396807.1|DY396807

EST:     CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAG                         GCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTG
genomic: CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAGgtgagatccg ... aatcttatagGCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTG

EST: gi|32858467|gb|CD998148.1|CD998148

EST:     CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAG                         GCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTG
genomic: CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAGgtgagatccg ... aatcttatagGCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTG

EST: gi|67032677|gb|CO461426.1|CO461426

EST:     CTGGAAATGGTCACGCAGTGATCGGAATTCTGGAAAG                         GCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTG
genomic: CTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAGgtgagatccg ... aatcttatagGCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTG

EST: gi|87157645|gb|DY402434.1|DY402434

EST:     CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAG                         GCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTG
genomic: CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAGgtgagatccg ... aatcttatagGCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTG

EST: gi|26558945|gb|CA831180.1|CA831180

EST:     CTGTTCATCTACTCTGGAAATGGCCACGCAG-GATCGGAATTCTGGAAAG                         GCAAGCGCGAG-GTGTCTCCCACACTATGGCAACCACCAAG-GGCATTTTG
genomic: CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAGgtgagatccg ... aatcttatagGCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTG

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: 405

ATTGATTTACACAAATTCTGGTCTTGCTATCTTGGCTTTAACTTCAAGTGCTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAGgtgagatccg ... aatcttatagGCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTGATGACTAATGACACGACTGACAACAATCCTGAAGAAGCTGTTCACTGCT

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 239

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 244