ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GGCCGCGAAGAGTCAGTGGAGGAGTTCGTGCGCCGCAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAGgtgcttattgcagtgtgttattgttgtttgttctggcctgctacttgcagcggttagccgattaccataagaatttaacaactttgtaaacctaag

Basic information

species	Zea mays
transcript	GRMZM2G039396_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G039396_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g18320.1 (Oryza sativa), 5'ss of exon 3

GGCCGCGAAGAGTCAGTGGAGGAGTTCGTGCGCCGCAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAGgtgcttattgcagtgtgttattgttgtttgttctggcctgctacttgcagcggttagccgattaccataagaatttaacaactttgtaaacctaag
|| || || ||||| |||||||| |||||||| ||||||||||| || |||||||||||||||||||||||||||||||||||||||| |||||| ||||||  |||| |||||  | |    || | |    |    |  |  |||| |  |      |||                   
GGGCGTGAGGAGTCGGTGGAGGACTTCGTGCGGCGCAACCTCGGCGCGGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAGgtgtttattgtagtgtgcaattgctgttttgtttttgatgattcagataagaatacggtgatttcggtg----cttag------------------

upper sequence: GRMZM2G039396_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT4G01690.1 (Arabidopsis thaliana), 5'ss of exon 3

GGCCGCGAAGAGTCAGTGGAGGAGTTCGTGCGCCGCAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAGgtgc--ttattg--------cagtgtgttattgttgtttgttctg--gcctgctacttgcagcggttagccgattaccataagaatttaaca-actttgtaaacctaag---------------
|| || ||||| || ||||||||||| || || || |||||||||| |||||| ||||||||||| ||||| || || || ||||||    |||| |           ||||      || ||  ||  |  | | || | |   |     |||| | || |  |     | ||    ||  |  |  | | ||               
GGTCGTGAAGAATCTGTGGAGGAGTTTGTACGGCGTAACCTCGGTGATGAGGTTTTTGAGCGCCTGATTGAACCGTTTTGTTCAGgtagagttatagataaaacttcatgtgaaccatttattcatttagatgtcagcgaatctgattatctagcagttttcatttttgttctagtgcacccttaatgctttagattttatgcttttag

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|149005349|gb|EE039900.2|EE039900

EST:     CAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAG                         GTGTCTATGCTGGTGATCCTTCTAAGCTCAGCATGAANGCTGCATTTGGGA
genomic: CAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAGgtgcttattg ... taaacctaagGTGTCTATGCTGGTGATCCTTCTAAGCTCAGCATGAAGGCTGCATTTGGGA

EST: gi|149071120|gb|EE159520.2|EE159520

EST:     CAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAG                         GTGTCTATGCTGGTGATCCTTCTAAGCTCAGCATGAAGGCTGCATTTGGGA
genomic: CAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAGgtgcttattg ... taaacctaagGTGTCTATGCTGGTGATCCTTCTAAGCTCAGCATGAAGGCTGCATTTGGGA

EST: gi|78079002|gb|DV507414.1|DV507414

EST:     CAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAG                         GTGTCTATGCTGGTGATCCTTCTAAGCTCAGCATGAAGGCTGCATTTGGGA
genomic: CAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAGgtgcttattg ... taaacctaagGTGTCTATGCTGGTGATCCTTCTAAGCTCAGCATGAAGGCTGCATTTGGGA

EST: gi|211265727|gb|FL016769.1|FL016769

EST:     CAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAG                         GTGTCTATGCTGGTGATCCNTCTA-GCTCAGCATGAAGGCTGCATTT
genomic: CAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAGgtgcttattg ... taaacctaagGTGTCTATGCTGGTGATCCTTCTAAGCTCAGCATGAAGGCTGCATTT

EST: gi|211265725|gb|FL016767.1|FL016767

EST:     CAACCTCGGTGCTGAAGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAG                         GTGTCTATGCTGG
genomic: CAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAGgtgcttattg ... taaacctaagGTGTCTATGCTGG

EST: gi|78087541|gb|DV515934.1|DV515934

EST:     CAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAG                         GTGTCTATGCTGGTGATCCTTCTAAGCTCAGCATGAAGGCTGCATTTGGGA
genomic: CAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAGgtgcttattg ... taaacctaagGTGTCTATGCTGGTGATCCTTCTAAGCTCAGCATGAAGGCTGCATTTGGGA

EST: gi|211265728|gb|FL016770.1|FL016770

EST:     CAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAG                         GTGTCTATGCTGGTGATCCNTCTA-GCTCAGCATGAAG-CTGC
genomic: CAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAGgtgcttattg ... taaacctaagGTGTCTATGCTGGTGATCCTTCTAAGCTCAGCATGAAGGCTGC

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: 77

GGCCGCGAAGAGTCAGTGGAGGAGTTCGTGCGCCGCAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAGgtgcttattg ... taaacctaagGTGTCTATGCTGGTGATCCTTCTAAGCTCAGCATGAAGGCTGCATTTGGGAAGGTTTGGCGGTTGGAAGAAACTGGAGGTAGTATTATTGGTGGAACCAT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 170

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 51