ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GGTTTCAATGGGGCTGATCTTCGGAACGTGTGCACCGAAGCTGGCATGGCTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAGgtgcactatctcgcactccaatcttgtgtaccttcgaatagttgtggttaaacattgacactcaaaatccctgcaacttttatttcag

Basic information

species	Zea mays
transcript	GRMZM2G165817_T01
intron #	9
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G165817_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os02g10640.1 (Oryza sativa), 5'ss of exon 9

GGTTTCAATGGGGCTGATCTTCGGAACGTGTGCACCGAAGCTGGCATGGCTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAGgtgcactatctcgcactccaatcttgtgtaccttcgaatagttgtggttaaacattgacactcaaaatccctgcaacttttatttcag
|| |||||||||||||||||||| ||||| ||||| ||||| || ||||||||||||||||| ||  | || ||||| ||||| || |||||||||||||||| |    |   ||||   |||| | |        | |   |  |||| |||||  | | ||   | | ||| | || || |||||
GGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCTGCAATTCGTGCTGAACGGGACTACGTTGTCCATGAGGACTTCATGAAGgtgcgccgcattatactc---tcttctatctaccaacacaccagctgttagacattatctcacagtttacatgcgaattgtacttcag

upper sequence: GRMZM2G165817_T01 (Zea mays), 5'ss of exon 9
lower sequence: PP1S47_46V6.3 (Physcomitrella patens), 5'ss of exon 8

GGTTTCAATGGGGCTGATCTTCGGAACGTGTGCACCGAAGCTGGCATGGCTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAGgtgcactatctcgcactccaatcttgt-gtaccttcgaatagttgtggttaaacattgacactcaaaatccctgcaacttttatttcag-----------------
|| ||||| || ||||||||||| ||||||||||| ||||| ||||||  ||| || || || ||  | || || || || || |||||||| ||||||||      |||| || |  | |  | | |    ||  |||| ||||  || |  |   | | |  ||     | ||   || ||  ||                  
GGCTTCAACGGAGCTGATCTTCGCAACGTGTGCACTGAAGCGGGCATGTTTGCTATCCGGGCTGATCGGGACTATGTTGTACAAGAAGACTTTATGAAGgtat----tctctcagttgatttgtttagggggttgaaataattgtaatttattagacagattttaaggttgttcag--ttgatcgcaagtggaatttcatagaga

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|21432323|gb|BQ547813.1|BQ547813

EST:     CTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAG                         GCTGTGAGGAAACTAAATGATGCAAAAAAGCTGGAATCGAGTGCGCATTAC
genomic: CTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAGgtgcactatc ... tttatttcagGCTGTGAGGAAGCTAAATGATGCAAAAAAGCTGGAATCGAGTGCGCATTAC

EST: gi|211064360|gb|FL103106.1|FL103106

EST:     AGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAG                         GCTGTGAGGAAGCTAAATGATGCAAAAAAGCTGGAATCGAGTGCGCATTAC
genomic: AGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAGgtgcactatc ... tttatttcagGCTGTGAGGAAGCTAAATGATGCAAAAAAGCTGGAATCGAGTGCGCATTAC

EST: gi|211472647|gb|FL103084.1|FL103084

EST:     CTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAG                         GCTGTGAGGAAGCTAAATGATGCAAAAAAGCTGGAATCGAGTGCGCATTAC
genomic: CTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAGgtgcactatc ... tttatttcagGCTGTGAGGAAGCTAAATGATGCAAAAAAGCTGGAATCGAGTGCGCATTAC

EST: gi|37374242|gb|CF623465.1|CF623465

EST:     CTGCAATTCGTTCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAG                         GCTGTGAGGAAGCTAAATGATGCAAAAAAGCTGGAATCGAGTGCGCATTAC
genomic: CTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAGgtgcactatc ... tttatttcagGCTGTGAGGAAGCTAAATGATGCAAAAAAGCTGGAATCGAGTGCGCATTAC

EST: gi|113702338|gb|EE679842.1|EE679842

EST:     CTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAG                         GCTGTGAGGAAGCTAAATGATGCAAAAAAGCTGGAATCGAGTGCGCATTAC
genomic: CTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAGgtgcactatc ... tttatttcagGCTGTGAGGAAGCTAAATGATGCAAAAAAGCTGGAATCGAGTGCGCATTAC

EST: gi|7145297|gb|AW506778.1|AW506778

EST:     CTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAG                         GCTGTGAGGAAACTAAATGATGCAAAAAAGCTGGAATCGAGTGCGCATTAC
genomic: CTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAGgtgcactatc ... tttatttcagGCTGTGAGGAAGCTAAATGATGCAAAAAAGCTGGAATCGAGTGCGCATTAC

EST: gi|19770067|gb|BQ034788.1|BQ034788

EST:     CTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAG                         GCTGTGAGGAAACTAAATGATGCAAAAAAGCTGGAATCGAGTGCGCATTAC
genomic: CTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAGgtgcactatc ... tttatttcagGCTGTGAGGAAGCTAAATGATGCAAAAAAGCTGGAATCGAGTGCGCATTAC

EST: gi|6445587|gb|AW179550.1|AW179550

EST:     CTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAG                         GCTGTGAGGAAACTAAATGATGCAAAAAAGCTGGAATCGAGTGCGCATTAC
genomic: CTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAGgtgcactatc ... tttatttcagGCTGTGAGGAAGCTAAATGATGCAAAAAAGCTGGAATCGAGTGCGCATTAC

EST: gi|5871417|gb|AW017888.1|AW017888

EST:     CTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAG                         GCTGTGAGGAAGCTAAATGATGCAAAAAAGCTGGAATCGAGTGCGCATTAC
genomic: CTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAGgtgcactatc ... tttatttcagGCTGTGAGGAAGCTAAATGATGCAAAAAAGCTGGAATCGAGTGCGCATTAC

EST: gi|211475158|gb|FL103091.1|FL103091

EST:     CTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAG                         GCTGTGAGGAAGCTAAATGATGCAAAADAGCTGGAATCGAGTGCGCATTAC
genomic: CTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAGgtgcactatc ... tttatttcagGCTGTGAGGAAGCTAAATGATGCAAAAAAGCTGGAATCGAGTGCGCATTAC

EST: gi|21432254|gb|BQ547744.1|BQ547744

EST:     CTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAG                         GCTGTGAGGAAACTAAATGATGCAAAAAAGCTGGAATCGAGTGCGCATTAC
genomic: CTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAGgtgcactatc ... tttatttcagGCTGTGAGGAAGCTAAATGATGCAAAAAAGCTGGAATCGAGTGCGCATTAC

EST: gi|15427178|gb|BI543000.1|BI543000

EST:     CTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAG                         GCTGTGAGGAAGCTAAATGATGCAAAAAAGCTGGAATCGAGTGCGCATTAC
genomic: CTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAGgtgcactatc ... tttatttcagGCTGTGAGGAAGCTAAATGATGCAAAAAAGCTGGAATCGAGTGCGCATTAC

EST: gi|4966712|gb|AI691568.1|AI691568

EST:     CTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAG                         GCTGTGAGGAAACTAAATGATGCAAAAAAGCTGGAATCGAGTGCGCATTAC
genomic: CTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAGgtgcactatc ... tttatttcagGCTGTGAGGAAGCTAAATGATGCAAAAAAGCTGGAATCGAGTGCGCATTAC

EST: gi|30087282|gb|CB885490.1|CB885490

EST:     CTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAG                         GCTGTGAGGAAGCTAAATGATGCAAAAAAGCTGGAATCGAGTGCGCATTAC
genomic: CTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAGgtgcactatc ... tttatttcagGCTGTGAGGAAGCTAAATGATGCAAAAAAGCTGGAATCGAGTGCGCATTAC

EST: gi|7145298|gb|AW506779.1|AW506779

EST:     CTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAG                         GCTGTGAGGAAACTAAATGATGCAAAAAAGCTGGAATCGAGTGCGCAT
genomic: CTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAGgtgcactatc ... tttatttcagGCTGTGAGGAAGCTAAATGATGCAAAAAAGCTGGAATCGAGTGCGCAT

EST: gi|71449604|gb|DR830654.1|DR830654

EST:     CTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAG                         GCTGTGAGGAAGCTAAATGATGCAAAAAAGCTGGAATCGAGTGCGCATTAC
genomic: CTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAGgtgcactatc ... tttatttcagGCTGTGAGGAAGCTAAATGATGCAAAAAAGCTGGAATCGAGTGCGCATTAC

EST: gi|37400602|gb|CF637657.1|CF637657

EST:     CTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAG                         GCTGTGAGGAAGCTAAATGATGCAAAAAAGCTGGAATCGAGTGCGCATTAC
genomic: CTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAGgtgcactatc ... tttatttcagGCTGTGAGGAAGCTAAATGATGCAAAAAAGCTGGAATCGAGTGCGCATTAC

EST: gi|60340244|gb|DN207217.1|DN207217

EST:     CTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAG                         GCTGTGAGGAAGCTAAATGATGCAAAAAAGCTGGAATCGAGTGCGCATTAC
genomic: CTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAGgtgcactatc ... tttatttcagGCTGTGAGGAAGCTAAATGATGCAAAAAAGCTGGAATCGAGTGCGCATTAC

EST: gi|45847148|gb|CN071091.1|CN071091

EST:     CTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAG                         GCTGTGAGGAAGCTAAATGATGCAAAAAAGCTGGAATCGAGTGCGCATTAC
genomic: CTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAGgtgcactatc ... tttatttcagGCTGTGAGGAAGCTAAATGATGCAAAAAAGCTGGAATCGAGTGCGCATTAC

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), 47 (downstream exon)
Score: 299

GGTTTCAATGGGGCTGATCTTCGGAACGTGTGCACCGAAGCTGGCATGGCTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAGgtgcactatc ... tttatttcagGCTGTGAGGAAGCTAAATGATGCAAAAAAGCTGGAATCGAGTGCGCATTACAGTGCAGATTTTGGCAAAGAGTAATGATGCTAATGCCGATGCAACGGAC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 238

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 367

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 188

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTTTCAATGGGGCTGATCTTCGGAACGTGTGCACCGAAGCTGGCATGGCTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAGgtgcactatctcgcactccaatcttgtgtaccttcgaatagttgtggttaaacattgacactcaaaatccctgcaacttttatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA