ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gtccgtcgttgttccctcccttttctcagatctgccaccccacctccctgaaggcgaagcagctagcggtcctcccactgataaaccaaggatttctctctccctctctttgttgttcgtcccgccccgcagATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTGGGCCTGCCCTGCATCGAGAAGGCCGGCGTCGCCCACAAGATCGACTTCCGCGAGGGTCCCG

Basic information

species	Zea mays
transcript	GRMZM2G127948_T04
intron #	5
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G127948_T04 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os06g06980.3 (Oryza sativa), 3'ss of exon 2

gtccgtcgttgttccctcccttttctcagatctgccaccccacctccctgaaggcgaagcagctagcggtcctcccactgataaaccaaggatttctctctccctc--tctttgttgttcgtcccgccc-cgcagATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTGGGCCTGCCCTGCATCGAGAAGGCCGGCGTCGCCCACAAGATCGACTTCCGCGAGGGTCCCG
                                               |   | || || |  | | |  | |   | | |||    |||| | | | |  ||  |     |   |   ||  |   |    |||||||||||| |||||||||||||| ||||||||||||||||| || || |  ||||||||||| || || || ||||||||||||||||| ||||| ||||
------------------------------------------gtcagcaacacgcaaatcccccatctcttccatcgcagatctggcaagaaatccccaatcgattgacgtccatccctctgctaactaatgcagATCTTGGCGATGGACATCAACCGGGAGAACTACGAGCTGGGGCTCCCGTCGATCGAGAAGGCGGGAGTGGCGCACAAGATCGACTTCCGGGAGGGACCCG

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|50324343|gb|CO519469.1|CO519469

EST:     CCGGCTACTCCCTCCTCGCCACGGCGCTCGCCCTCCCGGAGGACGGCACG                         ATCTTGGCCATGGACATCAACCGCGAGAACTA
genomic: CCGGCTACTCCCTCCTCGCCACGGCGCTCGCCCTCCCGGAGGACGGCACGgtccgtcgtt ... cgccccgcagATCTTGGCCATGGACATCAACCGCGAGAACTA

EST: gi|29544906|gb|CB605514.1|CB605514

EST:     CCGGCTACTCCCTCCTCGCCACGGCGCTCGCCCTCCCGGAGGACGGCACG                         ATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTGGGCCTGCCCTGC
genomic: CCGGCTACTCCCTCCTCGCCACGGCGCTCGCCCTCCCGGAGGACGGCACGgtccgtcgtt ... cgccccgcagATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTGGGCCTGCCCTGC

EST: gi|9952456|gb|BE639039.1|BE639039

EST:     CCGGCTACTCCCTNCTCGCCACGGCGCTCGCCCTCCCGGAGGACGGCACG                         ATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTGGGCCTGCCCTGC
genomic: CCGGCTACTCCCTCCTCGCCACGGCGCTCGCCCTCCCGGAGGACGGCACGgtccgtcgtt ... cgccccgcagATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTGGGCCTGCCCTGC

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: 44 (upstream exon), 48 (downstream exon)
Score: 96

GCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGCTACTCCCTCCTCGCCACGGCGCTCGCCCTCCCGGAGGACGGCACGgtccgtcgtt ... cgccccgcagATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTGGGCCTGCCCTGCATCGAGAAGGCCGGCGTCGCCCACAAGATCGACTTCCGCGAGGGTCCCG

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 394

Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 342

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 617

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ctgataaaccaaggatttctctctccctctctttgttgttcgtcccgccccgcagATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTGGGCCTGCCCTGCATCGAGAAGGCCGGCGTCGCCCACAAGATCGACTTCCGCGAGGGTCCCG