ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

ACCAGGGCACCACAAGCACCCGGTTCATCGTCTACGACCGCCACGCCAAACCCGTCGCATCGCACCAGCTCGAGTTCAAGCAACACTACCCGGAGGCAGGgtgagtgcgggcgggtttcatgttcttctcgggccagagatcggttgggtagcgggtttgtttgcttttggattgcgcgaattctggaccggtggttgta...

Basic information

species	Zea mays
transcript	GRMZM2G023163_T01
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G023163_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os04g55410.1 (Oryza sativa), 5'ss of exon 1

ACCAGGGCACCACAAGCACCCGGTTCATCGTCTACGACCGCCACGCCAAACCCGTCGCATCGCACCAGCTCGAGTTCAAGCAACACTACCCGGAGGCAGGgtgagtgcgg-gcgggtttcat--gttcttctcgggccagagatcggttgggtagcgggtttgtttgcttttggattgcgcgaattctggaccggtggttgta
|||||||||| || ||||| ||||||||||||||||||||||||||||| |||||||| ||||| ||||||||||||||||| |||||||||||||| |||| |||| |  ||     | ||  ||  | |||    ||  |||  | |   | | | |    || || || | || |    | |    || | |||      
ACCAGGGCACGACGAGCACGCGGTTCATCGTCTACGACCGCCACGCCAAGCCCGTCGCGTCGCATCAGCTCGAGTTCAAGCAGCACTACCCGGAGGCTGGgtaagtgtgctgcactgctaattagtgatgctctttacaacgatgtgatatttcgggtggagattggcattagcatgggattattatgtgatctgtgtga---

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|71766456|gb|DR964393.1|DR964393

EST:     CCCGTCGCATCGCACCAGCTCGAGTTCAAGCAACACTACCCGGAGGCAGG                         GTGGGTTGAGCATGATCCTATGGAGATTATAGAGACTGTTAAGGTGTGTAT
genomic: CCCGTCGCATCGCACCAGCTCGAGTTCAAGCAACACTACCCGGAGGCAGGgtgagtgcgg ... gaactaaaagGTGGGTTGAGCATGATCCTATGGAGATTATAGAGACTGTTAAGGTGTGTAT

EST: gi|88753132|gb|DY537273.1|DY537273

EST:     CCCGTCGCATCGCACCAGCTCGAGTTCAAGCAACACTACCCGGAGGCAGG                         GTGGGTTGAGCATGATCCTATGGAGATTATAGAGACTGTTAAGGTGTGTAT
genomic: CCCGTCGCATCGCACCAGCTCGAGTTCAAGCAACACTACCCGGAGGCAGGgtgagtgcgg ... gaactaaaagGTGGGTTGAGCATGATCCTATGGAGATTATAGAGACTGTTAAGGTGTGTAT

EST: gi|20300207|gb|BQ163150.1|BQ163150

EST:     CCCGTCGCAT-GCACCAGCTCGAGTTCAAGCAACACTACCCGGAGGCAGG                         GTGGGTTGAGCATGATCCTATGGAGATTATAGAGACTGTTAAGGTGTGTAT
genomic: CCCGTCGCATCGCACCAGCTCGAGTTCAAGCAACACTACCCGGAGGCAGGgtgagtgcgg ... gaactaaaagGTGGGTTGAGCATGATCCTATGGAGATTATAGAGACTGTTAAGGTGTGTAT

EST: gi|94475699|gb|EB704657.1|EB704657

EST:     CCCGTCGCATCGCACCAGCTCGAGTTCAAGCAACACTACCCGGAGGCAGG                         GTGGGTTGAGCATGATCCTATGGAGATTATAGAGACTGTTAAGGTGTGTAT
genomic: CCCGTCGCATCGCACCAGCTCGAGTTCAAGCAACACTACCCGGAGGCAGGgtgagtgcgg ... gaactaaaagGTGGGTTGAGCATGATCCTATGGAGATTATAGAGACTGTTAAGGTGTGTAT

EST: gi|211053229|gb|FL127755.1|FL127755

EST:     CCCGTCGCATCGCACCAGCTCGAGTTCAAGCAACACTACCCGGAGGCAGG                         GTGGGTTGAGCATGATCCTATGGAGATTATAGAGACTGTTAAGGTGTGTAT
genomic: CCCGTCGCATCGCACCAGCTCGAGTTCAAGCAACACTACCCGGAGGCAGGgtgagtgcgg ... gaactaaaagGTGGGTTGAGCATGATCCTATGGAGATTATAGAGACTGTTAAGGTGTGTAT

EST: gi|28187593|gb|CB179203.1|CB179203

EST:     CCCGTCGCATCGCACCAGCTCGAGTTCAAGCAACACTACCCGGAGGCAGG                         GTGGGTTGAGCATGATCCTATGGAGATTATAGAGACTGTTAAGGTGTGTAT
genomic: CCCGTCGCATCGCACCAGCTCGAGTTCAAGCAACACTACCCGGAGGCAGGgtgagtgcgg ... gaactaaaagGTGGGTTGAGCATGATCCTATGGAGATTATAGAGACTGTTAAGGTGTGTAT

EST: gi|211457298|gb|FK983860.1|FK983860

EST:     CCCGTCGCATCGCACCAGCTCGAGTTCAAGCAACACTACCCGGAGGCAGG                         GTGGGTTGAGCATGATCCTATGGAGATTATAGAGACTGTTAAGGTGTGTAT
genomic: CCCGTCGCATCGCACCAGCTCGAGTTCAAGCAACACTACCCGGAGGCAGGgtgagtgcgg ... gaactaaaagGTGGGTTGAGCATGATCCTATGGAGATTATAGAGACTGTTAAGGTGTGTAT

EST: gi|211457295|gb|FK983857.1|FK983857

EST:     CCCGTCGCATCGCACCAGCTCGAGTTCAAGCAACACTACCCGGAG-CAGG                         GTGGGTTGAGCATGATCCTATGGAGATTATAGAGACTGTTAAGGTGTGTAT
genomic: CCCGTCGCATCGCACCAGCTCGAGTTCAAGCAACACTACCCGGAGGCAGGgtgagtgcgg ... gaactaaaagGTGGGTTGAGCATGATCCTATGGAGATTATAGAGACTGTTAAGGTGTGTAT

EST: gi|101392646|gb|EB818253.1|EB818253

EST:     CCCGTCGCATCGCACCAGCTCGAGTTCAAGCAACACTACCCGGAGGCAGG                         GTGGGTTGAGCATGATCCTATGGAGATTATAGAGACTGTTAAGGTGTGTAT
genomic: CCCGTCGCATCGCACCAGCTCGAGTTCAAGCAACACTACCCGGAGGCAGGgtgagtgcgg ... gaactaaaagGTGGGTTGAGCATGATCCTATGGAGATTATAGAGACTGTTAAGGTGTGTAT

EST: gi|22490347|gb|BU050270.1|BU050270

EST:     CCCGTCGCATCGCACCAGCTCGAGTTCAAGCAACACTACCCGGAGGCAGG                         GTGGGTTGAGCATGATCCTATGGAGATTATAGAGACTGTTAAGGTGTGTAT
genomic: CCCGTCGCATCGCACCAGCTCGAGTTCAAGCAACACTACCCGGAGGCAGGgtgagtgcgg ... gaactaaaagGTGGGTTGAGCATGATCCTATGGAGATTATAGAGACTGTTAAGGTGTGTAT

EST: gi|211457288|gb|FK983850.1|FK983850

EST:     CCCGTCGCATCGCACCAGCTCGAGTTCAAGCAACACTACCCGGAGGCAGG                         GTGGGTTGAGCATGATCCTATGGAGATTATAGAGACTGTTAAGGTGTGTAT
genomic: CCCGTCGCATCGCACCAGCTCGAGTTCAAGCAACACTACCCGGAGGCAGGgtgagtgcgg ... gaactaaaagGTGGGTTGAGCATGATCCTATGGAGATTATAGAGACTGTTAAGGTGTGTAT

EST: gi|19057965|gb|BM736632.1|BM736632

EST:     CCCGTCGCAT-GCACCAGCTCG-GTTCAAGCAACACTACCCGGAGGCAGG                         GTGGGTTGAGCATGATCCTATGGAGATTATAGAGACTGTTAAGGTGTGTAT
genomic: CCCGTCGCATCGCACCAGCTCGAGTTCAAGCAACACTACCCGGAGGCAGGgtgagtgcgg ... gaactaaaagGTGGGTTGAGCATGATCCTATGGAGATTATAGAGACTGTTAAGGTGTGTAT

EST: gi|211457291|gb|FK983853.1|FK983853

EST:     CCCGTCGCATCGCACCAGCTCGAGTTCAAGCAACACTACCCGGAGGCAGG                         GTGGGTTGAGCATGATCCTATGGAGATTATAGAGACTGTYAAGGTGTGTAT
genomic: CCCGTCGCATCGCACCAGCTCGAGTTCAAGCAACACTACCCGGAGGCAGGgtgagtgcgg ... gaactaaaagGTGGGTTGAGCATGATCCTATGGAGATTATAGAGACTGTTAAGGTGTGTAT

EST: gi|211457293|gb|FK983855.1|FK983855

EST:     CCCGTCGCATCGCACCAGCTCGAGTTCAAGCAACACTACCCGGAGGCAGG                         GTGGGTTGAGCATGATCCTATGGAGATTATAGAGACTGTTAAGGTGTGTAT
genomic: CCCGTCGCATCGCACCAGCTCGAGTTCAAGCAACACTACCCGGAGGCAGGgtgagtgcgg ... gaactaaaagGTGGGTTGAGCATGATCCTATGGAGATTATAGAGACTGTTAAGGTGTGTAT

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: 58

ACCAGGGCACCACAAGCACCCGGTTCATCGTCTACGACCGCCACGCCAAACCCGTCGCATCGCACCAGCTCGAGTTCAAGCAACACTACCCGGAGGCAGGgtgagtgcgg ... gaactaaaagGTGGGTTGAGCATGATCCTATGGAGATTATAGAGACTGTTAAGGTGTGTATGAAAGAGGCAGTTGGCAAAGCCAAAGATGGTAAACACAATGTGGTTGCT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 139

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 123

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 223

Putative cis-regulatory sequences

atgc	intron	ATGC	exonic elements by Pertea et al.
ATGC	exon	atgc	putative intronic elements
		ATGC	putative exonic elements identified for retained introns

        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCAGGGCACCACAAGCACCCGGTTCATCGTCTACGACCGCCACGCCAAACCCGTCGCATCGCACCAGCTCGAGTTCAAGCAACACTACCCGGAGGCAGGgtgagtgcgggcgggtttcatgttcttctcgggccagagatcggttgggtagcgggtttgtttgcttttggattgcgcgaattctggaccggtggttgta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA