ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GACCCTATCAACGTTAAAATCGCGGAGCTGAAGGAAGCATTAGAATCCGTTACCGCCGAGCAGAAGTACCTAAAAGCACGCGAAGCTCGTCACCGACACAgtaagctcaatggacttgggacttgcatgcgctcttattacatctctggaatgtttagcacattatgacgtttatgctagttttttttcttttgaaaaat...

Basic information

species	Zea mays
transcript	GRMZM2G147046_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G147046_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g53310.1 (Oryza sativa), 5'ss of exon 3

GACCCTATCAACGTTAAAATCGCGGAGCTGAAGGAAGCATTAGAATCCGTTACCGCCGAGCAGAAGTACCTAAAAGCACGCGAAGCTCGTCACCGACACAgtaagctcaatggacttgggacttgcatgcgctcttattacatctctggaatgtttagcacattatgacgt-ttatgctagttttttttcttttgaa-aaat-----
||||||||||| || ||||| |||||||||||||||||||||||||| || || || |||||||| ||||| ||||| || |||||||||||||||||||||||||| ||    | |     |||||   | ||  | |  | || ||| | ||||   | | |    ||| | ||   ||  |   |   |||| |  |||     
GACCCTATCAATGTGAAAATAGCGGAGCTGAAGGAAGCATTAGAATCTGTCACTGCTGAGCAGAAATACCTTAAAGCCCGTGAAGCTCGTCACCGACACAgtaagcttaacaatcct----tttgcaaatggtc--actgaagctttggca-gtttcctataatcctgcgtgtgatatgagaatgcataaatttgtatgaattttct

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|60350490|gb|DN217463.1|DN217463

EST:     TACCGCCGAGCAGAAGTACCTAAAAGCACGCGAAGCTCGTCACCGACACA                         CCAATGAGAGCACCAGAAAGCGTGTCATGTTCTATACGATGGCGGAGTACC
genomic: TACCGCCGAGCAGAAGTACCTAAAAGCACGCGAAGCTCGTCACCGACACAgtaagctcaa ... ttcaatccagCCAATGAGAGCACCAGAAAGCGTGTCATGTTCTATACGATGGCGGAGTACC

EST: gi|149097269|gb|EE183092.2|EE183092

EST:     TACCGCCGAGCAGAAGTACCTAAAAGCACGCGAAGCTCGTCACCGACACA                         CCAATGAGAGCACCAGAAAGCGTGTCATGTTTTATACGATGGCGGAGTACC
genomic: TACCGCCGAGCAGAAGTACCTAAAAGCACGCGAAGCTCGTCACCGACACAgtaagctcaa ... ttcaatccagCCAATGAGAGCACCAGAAAGCGTGTCATGTTCTATACGATGGCGGAGTACC

EST: gi|60339915|gb|DN206888.1|DN206888

EST:     TACCGCCGAGCAGAAGTACCTAAAAGCACGCGAAGCTCGTCACCGACACA                         CCAATGAGAGCACCAGAAAGCGTGTCATGTTCTATACGATGGCGGAGTACC
genomic: TACCGCCGAGCAGAAGTACCTAAAAGCACGCGAAGCTCGTCACCGACACAgtaagctcaa ... ttcaatccagCCAATGAGAGCACCAGAAAGCGTGTCATGTTCTATACGATGGCGGAGTACC

EST: gi|32859851|gb|CD999532.1|CD999532

EST:     CACCGCCGAGCAGAAGTACCTAAAAGCACGCGAAGCTCGTCACCGACACA                         CTAATGAGAGCACCAGAAAGCGTGTCATGTTCTATACGATGGCGGAGTACC
genomic: TACCGCCGAGCAGAAGTACCTAAAAGCACGCGAAGCTCGTCACCGACACAgtaagctcaa ... ttcaatccagCCAATGAGAGCACCAGAAAGCGTGTCATGTTCTATACGATGGCGGAGTACC

EST: gi|71763107|gb|DR961044.1|DR961044

EST:     TACCGCCGAGCAGAAGTACCTAAAAGCACGCGAAGCTCGTCACCGACACA                         CCAATGAGAGCACCAGAAAGCGTGTCATGTTCTATACGATGGCGGAGTACC
genomic: TACCGCCGAGCAGAAGTACCTAAAAGCACGCGAAGCTCGTCACCGACACAgtaagctcaa ... ttcaatccagCCAATGAGAGCACCAGAAAGCGTGTCATGTTCTATACGATGGCGGAGTACC

EST: gi|18178824|gb|BM380034.1|BM380034

EST:     TACCGCCGAGCAGAAGTACCTAAAAGCACGCGAAGCTCGTCACCGACACA                         CCAATGAGAGCACCAGAAAGCGTGTCATGTTCTATACGATGGCGGAGTACC
genomic: TACCGCCGAGCAGAAGTACCTAAAAGCACGCGAAGCTCGTCACCGACACAgtaagctcaa ... ttcaatccagCCAATGAGAGCACCAGAAAGCGTGTCATGTTCTATACGATGGCGGAGTACC

EST: gi|60353926|gb|DN220899.1|DN220899

EST:     TACCGCCGAGCAGAAGTACCTAAAAGCACGCGAAGCTCGTCACCGACACA                         CCAATGAGAGCACCAGAAAGCGTGTCATGTTCTATACGATGGCGGAGTACC
genomic: TACCGCCGAGCAGAAGTACCTAAAAGCACGCGAAGCTCGTCACCGACACAgtaagctcaa ... ttcaatccagCCAATGAGAGCACCAGAAAGCGTGTCATGTTCTATACGATGGCGGAGTACC

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), 48 (downstream exon)
Score: 287

GACCCTATCAACGTTAAAATCGCGGAGCTGAAGGAAGCATTAGAATCCGTTACCGCCGAGCAGAAGTACCTAAAAGCACGCGAAGCTCGTCACCGACACAgtaagctcaa ... ttcaatccagCCAATGAGAGCACCAGAAAGCGTGTCATGTTCTATACGATGGCGGAGTACCTGGCTTTCATGGCTGCTAGCGCGTTGCAGGTCCTCTACATCCGCCGCTT

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 470

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 583

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 715

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACCCTATCAACGTTAAAATCGCGGAGCTGAAGGAAGCATTAGAATCCGTTACCGCCGAGCAGAAGTACCTAAAAGCACGCGAAGCTCGTCACCGACACAgtaagctcaatggacttgggacttgcatgcgctcttattacatctctggaatgtttagcacattatgacgtttatgctagttttttttcttttgaaaaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT