ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GTGAAGCAGCTCCTTGCCGTGCTCCTCAAGTGCTGCCACATCGACCTCAAGCAGCCCAACGGCCTAGATGATCCGGAGGTGCTCGCTAGGGAGACCGTGTgtacgtccaagccgcttccccgtttccgttgtctccttcaattcttcgtccgtagtaccgtgatcgattgtcttccgtttgtcttactgcctcgtctgcgtctaaaactttacctgcag

Basic information

species	Zea mays
transcript	GRMZM2G112672_T02
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G112672_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g42840.1 (Oryza sativa), 5'ss of exon 1

GTGAAGCAGCTCCTTGCCGTGCTCCTCAAGTGCTGCCACATCGACCTCAAGCAGCCCAACGGCCTAGATGATCCGGAGGTGCTCGCTAGGGAGACCGTGTgtacgtccaagc-cgcttccccgtttcc----gttgtctccttcaatt----cttcgtccgtagtaccgtgatcgattgtcttccgtttgtcttac-tgcctcgtctgcgtctaaaact--ttacctgcag--------------
||||||||||||   | |||||| |||||||||||| || ||||||||||||||||||| || || || ||||| ||  | ||||| ||||||||||| |||||||||   | | ||  | || || |    |  || | ||| | |      |   ||  | | || |  ||  ||||| |||| ||| | || |  | | | | ||    |     |  |   ||||                
GTGAAGCAGCTCTGCGGCGTGCTACTCAAGTGCTGCGACCTCGACCTCAAGCAGCCCAAGGGGCTCGAGGATCCCGAAATCCTCGCCAGGGAGACCGTCTgtacgtcctctctctctctctcgcttgctcgtgcagtgtacttgagtgtcgattgtttcacttgaactgaaattaattgtgttccctttttgtttcgcggcgcatgtggcattgggggtggtggtctgctcgtttgtgcgtgcag

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|5846848|gb|AI999931.1|AI999931

EST:     GCTAGGGAGACCGNGT                         TTAGCGTGAGCGAGGTCGAGGCATTGTATGAGCTGTTCAAGAAGATCAGCA
genomic: GCTAGGGAGACCGTGTgtacgtccaa ... ttacctgcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCA

EST: gi|6194508|gb|AW146612.1|AW146612

EST:     GCTCGCTAGGGAGACCGNGT                         TTAGCGTGAGCGAGGTCGAGGCATTGTATGAGCTGTTCAAGAAGATCAGCA
genomic: GCTCGCTAGGGAGACCGTGTgtacgtccaa ... ttacctgcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCA

EST: gi|211071789|gb|FK958795.1|FK958795

EST:     TGCTCGCTAGGGAGACCGTGT                         TTAGCGTGAGCGAGGTCGAGGCATTGTATGAGCTGTTCAAGAAGATCAGCA
genomic: TGCTCGCTAGGGAGACCGTGTgtacgtccaa ... ttacctgcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCA

EST: gi|211071790|gb|FK958796.1|FK958796

EST:     TGCTCGCTAGGGAGACCGTGT                         TTAGCGTGAGCGAGGTCGAGGCATTGTATGAGCTGTTCAAGAAGATCAGCA
genomic: TGCTCGCTAGGGAGACCGTGTgtacgtccaa ... ttacctgcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCA

EST: gi|5325037|gb|AI783228.1|AI783228

EST:     GCTAGGGAGACCGTGT                         TTAGCGTGAGCGAGGTCGAGGCATTGTATGAGCTGTTCAAGAAGATCAGCA
genomic: GCTAGGGAGACCGTGTgtacgtccaa ... ttacctgcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCA

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: 48 (upstream exon), 49 (downstream exon)
Score: 134

GTGAAGCAGCTCCTTGCCGTGCTCCTCAAGTGCTGCCACATCGACCTCAAGCAGCCCAACGGCCTAGATGATCCGGAGGTGCTCGCTAGGGAGACCGTGTgtacgtccaa ... ttacctgcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCAGTGCTGTGATTGATGATGGGCTGATCAACAAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 147

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 223