ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GGTTATTTTCTTGACTGGTTTAGTGTCAATGATATTGATGAGGACACTAAGAAATGATTATGCAAAATATGCTCGTGAAGATGATGATCTGGAATCACTTgtaagttctgaacctgcaatccgtagcacatcgatatggttatatatttctcattttgtctgctaatataactcattgtttgtctttttgcgtttttaca...

Basic information

species	Zea mays
transcript	GRMZM2G087212_T01
intron #	7
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G087212_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os11g07910.1 (Oryza sativa), 5'ss of exon 7

GGTTATTTTCTTGACTGGTTTAGTGTCAATGATATTGATGAGGACACTAAGAAATGATTATGCAAAATATGCTCGTGAAGATGATGATCTGGAATCACTTgtaagttctgaacctgcaatccgtagcacatcgatatggttatatatttctcattttgtctgctaatataactcattgtttgtctttttgcgtttttaca-----
|||||||||||||||||| || || |||||||||||||||||||| || |||||||||||||| ||||||||||||||||||||||||||||| || ||||||||| |||||| || |  |    ||  |     |   || | |||| |    | ||   ||     | | |  ||||||   ||  ||   ||| | |     
GGTTATTTTCTTGACTGGATTGGTATCAATGATATTGATGAGGACGCTGAGAAATGATTATGCGAAATATGCTCGTGAAGATGATGATCTGGAGTCGCTTgtaagtactgaacgtgaagcctcacgcttacaatcac--ttgtgtattccc---tctggtagcaggagtcattttttgtttactttaatggtctttgagatgtaa

upper sequence: GRMZM2G087212_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA05G30210.1 (Glycine max), 5'ss of exon 7

GGTTATTTTCTTGACTGGTTTAGTGTCAATGATATTGATGAGGACACTAAGAAATGATTATGCAAAATATGCTCGTGAAGATGATGATCTGGAATCACTTgtaa--gttctgaacctgcaatccgtagcacatcgatatggttatatatttctcattttgtctgctaatataactc--attgtttgtctttttg-cgtttttaca----------
||| || ||| | |||||||| |||||||||||||||||| | || || |||||||| |||||||| |||||||| |||||||||||| |||||   || || |  |||  |   ||   |||   |  |  |    |   | |    ||||| | |   |     | | |   ||  ||||||     ||| | | ||| | |           
GGTCATCTTCCTTACTGGTTTGGTGTCAATGATATTGATGCGAACTCTGAGAAATGACTATGCAAAGTATGCTCGGGAAGATGATGATTTGGAAAGTCTGgtgatggtttcgtgacttttatcttaattatttgtggaatatgaatcctttcttactagataaagcattgtggttctaattgttgaatatttggtcatttcttccatgcttacag

upper sequence: GRMZM2G087212_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA12G29120.1 (Glycine max), 5'ss of exon 7

GGTTATTTTCTTGACTGGTTTAGTGTCAATGATATTGATGAGGACACTAAGAAATGATTATGCAAAATATGCTCGTGAAGATGATGATCTGGAATCACTTgtaag---ttctgaacctgcaatccgtagcac-atcgatatggttatatatttctc------------attttgtctgctaatataactcattgtttgtctttttgc--gtttttaca--------------------
||| || ||| | ||||| || |||||||||||||| ||| | ||  | |||||||| |||||||| |||||||| |||||||||||| ||||| | || || ||   ||||  |  |        ||  |  ||   |||  ||  | |||| |             ||| |   | |    | || |||||||   |||  |||    || ||                       
GGTCATCTTCCTTACTGGATTGGTGTCAATGATATTAATGCGAACGTTGAGAAATGACTATGCAAAGTATGCTCGGGAAGATGATGATTTGGAAACTCTGgtgaggctttcttgatgtttgtctgttactattattactattttttaaaatttatgtgtggaacatagattctactttcctggaaaattcattgtggttctgattgtcaattcttgttcaacccccatacatttccag

upper sequence: GRMZM2G087212_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA08G13370.1 (Glycine max), 5'ss of exon 7

GGTTATTTTCTTGACTGGTTTAGTGTCAATGATATTGATGAGGACACTAAGAAATGATTATGCAAAATATGCTCGTGAAGATGATGATCTGGAATCACTTgtaa--gttctgaacctgcaatccgtagcacatcg----atatggttatatatttct--------cattttgtctgctaatataactcattgtttgtctttttgcgtttttaca-
||| || ||| | ||||| || |||||||||||||||||| | || || |||||||| |||||||| |||||||| |||||||||||| |||||   || || |  |||      ||   |||  ||  |  | |    |||||    | | || ||        |||| ||  |   | | |     |||   |   || || | |  ||||| 
GGTCATCTTCCTTACTGGATTGGTGTCAATGATATTGATGCGAACTCTGAGAAATGACTATGCAAAGTATGCTCGGGAAGATGATGATTTGGAAAGTCTGgtgatggtttcatgacttttatctttaataatttgtggaatatgaacctttcttcctagagaaatcattgtggttctaattgtcgaatatttggtcatttcttccatgcttacag

upper sequence: GRMZM2G087212_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA08G20100.1 (Glycine max), 5'ss of exon 7

GGTTATTTTCTTGACTGGTTTAGTGTCAATGATATTGATGAGGACACTAAGAAATGATTATGCAAAATATGCTCGTGAAGATGATGATCTGGAATCACTTgtaagttctgaacctgcaatccgtagcacatcgatatggttatatatttctcattttgtctgct-aatataactcattgtttgtctttttgcgtttttaca------------------------------------------
||| || ||| | ||||| || |||||||||||||| ||| | ||| | |||||||| |||||||| ||||| || |||||||||||| ||||| | || || ||   |   | ||   |  ||     |    |||  ||||   |||   | ||| | ||   || |||  |   |||||  ||       |  ||                                             
GGTCATCTTCCTTACTGGATTGGTGTCAATGATATTAATGCGAACATTGAGAAATGACTATGCAAAGTATGCCCGGGAAGATGATGATTTGGAAACTCTGgttaggcttt--cttgatgtttgtctgttactattattattattatttttaaaatttatgtgtggaacatagatt-ctgttttcctggaaagttcattgtggttctgattgtcaattcttgttcaacccccaaatatttccag

upper sequence: GRMZM2G087212_T01 (Zea mays), 5'ss of exon 7
lower sequence: AT1G10950.1 (Arabidopsis thaliana), 5'ss of exon 7

GGTTATTTTCTTGACTGGTTTAGTGTCAATGATATTGATGAGGACACTAAGAAATGATTATGCAAAATATGCTCGTGAAGATGATGATCTGGAATCACTTgtaag---ttctgaacctgcaatccgtagcacatcgata--tggttatatatttctcatt-ttgtctgctaatataactcattgtttgtctttttgcgtttttaca--------------------------------------------
|||||||||| | || ||||| || |||||||||||||||||||| || |||||||||||||| || |||||| | |||||||||||||| ||     | || |    | || ||| |  | |    |  |  |  | |  || || | ||  | | | |  | |||   | | |    ||    || | | ||| | | |  |                                              
GGTTATTTTCCTCACCGGTTTGGTCTCAATGATATTGATGAGGACTCTCAGAAATGATTATGCGAAGTATGCTAGAGAAGATGATGATCTTGAGAGCTTGgtgatgtttcctcaacttttatttgtcattagttgcacaattgtttttttagctgttaatactctctagcagtctg-tccaacacttctttctttacttctaaatgcaaggcttcatagccatttctgacgtgagtattgatgggcacag

upper sequence: GRMZM2G087212_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv12s0035g00280.t01 (Vitis vinifera), 5'ss of exon 7

GGTTATTTTCTTGACTGGTTTAGTGTCAATGATATTGATGAGGACACTAAGAAATGATTATGCAAAATATGCTCGTGAAGATGATGATCTGGAATCACTTgtaa-gttctgaacctgca-----atccgtagcacatcgatatggttatatatttctcattttgtctgctaatataactcattgtttgtctttttgcgtttttaca
|||||| ||| | |||||||| ||||||||||| || ||| | || || |||||||| ||||| ||||||||||| |||||||||||||||||  | || || |   ||| ||| |        || | |    | |  ||  | || |    ||  |||||  | |  |  ||    |  |    |||  || |  |        
GGTTATCTTCCTCACTGGTTTGGTGTCAATGATCTTAATGCGAACCCTTAGAAATGACTATGCTAAATATGCTCGGGAAGATGATGATCTGGAGACTCTGgtgacactctcaacttttgtttatattctttttcctttaattggtttgtgggatttccatttcttttaattgtaaccattttaacatgtaattctcag--------

upper sequence: GRMZM2G087212_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv18s0041g00680.t01 (Vitis vinifera), 5'ss of exon 7

GGTTATTTTCTTGACTGGTTTAGTGTCAATGATATTGATGAGGACACTAAGAAATGATTATGCAAAATATGCTCGTGAAGATGATGATCTGGAATCACTTgtaagttctgaacctgcaatccgtagcacatcgatatggttatatatttct----cattttgtctgctaatataactcattgtttgtctttttgcgtttttaca-----
|||||||||| | ||||| || ||||| |||||||| ||| | || ||  ||||||||||||| ||||||||||| |||||||||||| ||||  | || ||||  |   |   |    ||   |     || || |  || | | ||| |     || | |||    | |  || | ||   |  | ||||    | | ||       
GGTTATTTTCCTCACTGGATTGGTGTCTATGATATTAATGCGAACTCTTCGAAATGATTATGCCAAATATGCTCGGGAAGATGATGATTTGGAGACTCTGgtaa--tgctattttaagttcttgactgtgtctatgtttttttttttttttaatatatatagtccttaagtgaaaattatgtatcttattttccactatatattgtcag

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|32933279|gb|CF038091.1|CF038091

EST:     GAAATGATTATGCAAAATATGCTCGTGAAGATGATGATCTGGAATCACTT                         GAGCGAGATGTTAATGAAGAATCCGGGTGGAAGCTTGTCCATGGTGACGTG
genomic: GAAATGATTATGCAAAATATGCTCGTGAAGATGATGATCTGGAATCACTTgtaagttctg ... cctttttcagGAGCGAGATGTTAATGAAGAATCCGGGTGGAAGCTTGTCCATGGTGATGTG

EST: gi|71428339|gb|DR809389.1|DR809389

EST:     GAAATGATTATGCAAAATATGCTCGTGAAGATGATGATCTGGAATCACTT                         GAGCGAGATGTTAATGAAGAATCCGGGTGGAAGCTTGTCCATGGTGATGTG
genomic: GAAATGATTATGCAAAATATGCTCGTGAAGATGATGATCTGGAATCACTTgtaagttctg ... cctttttcagGAGCGAGATGTTAATGAAGAATCCGGGTGGAAGCTTGTCCATGGTGATGTG

EST: gi|32932276|gb|CF037088.1|CF037088

EST:     GAAATGATTATGCAAAATATGCTCGTGAAGATGATGATCTGGAATCACTT                         GAGCGAGATGTTAATGAAGAATCCGGGTGGAAGCTTGTCCATGGTGATGTG
genomic: GAAATGATTATGCAAAATATGCTCGTGAAGATGATGATCTGGAATCACTTgtaagttctg ... cctttttcagGAGCGAGATGTTAATGAAGAATCCGGGTGGAAGCTTGTCCATGGTGATGTG

EST: gi|211036620|gb|FL478462.1|FL478462

EST:     GAAATGATTATGCAAAATATGCTCGTGAAGATGATGATCTGGAATCACTT                         GAGCGAGATGTTAATGAAGAATCCGGGTGGAAGCTTGTCCATGGTGATGTG
genomic: GAAATGATTATGCAAAATATGCTCGTGAAGATGATGATCTGGAATCACTTgtaagttctg ... cctttttcagGAGCGAGATGTTAATGAAGAATCCGGGTGGAAGCTTGTCCATGGTGATGTG

EST: gi|71764885|gb|DR962822.1|DR962822

EST:     GAAATGATTATGCAAAATATGCTCGTGAAGATGATGATCTGGAATCACTT                         GAGCGAGATGTTAATGAAGAATCCGGGTGGAAGCTTGTCCATGGTGATGTG
genomic: GAAATGATTATGCAAAATATGCTCGTGAAGATGATGATCTGGAATCACTTgtaagttctg ... cctttttcagGAGCGAGATGTTAATGAAGAATCCGGGTGGAAGCTTGTCCATGGTGATGTG

EST: gi|15199064|gb|BI423636.1|BI423636

EST:     GAAATGATTATGCAAAATATGCTCGTGAAGATGATGATCTGGAATCACTT                         GAGCGAGATGTTAATGAAGAATCCGGGTGGAAGCTTGTCCATGGTGATGTG
genomic: GAAATGATTATGCAAAATATGCTCGTGAAGATGATGATCTGGAATCACTTgtaagttctg ... cctttttcagGAGCGAGATGTTAATGAAGAATCCGGGTGGAAGCTTGTCCATGGTGATGTG

EST: gi|87153936|gb|DY398725.1|DY398725

EST:     GAAATGATTATGCAAAATATGCTCGTGAAGATGATGATCTGGAATCACTT                         GAGCGAGATGTTAATGAAGAATCCGGGTGGAAGCTTGTCCATGGTGATGTG
genomic: GAAATGATTATGCAAAATATGCTCGTGAAGATGATGATCTGGAATCACTTgtaagttctg ... cctttttcagGAGCGAGATGTTAATGAAGAATCCGGGTGGAAGCTTGTCCATGGTGATGTG

EST: gi|19350701|gb|BM895233.1|BM895233

EST:     GAAATGATTATGCAAAATATGCTCGTGAAGATGATGATCTGGAATCACTT                         GAGCGAGATGTTAATGAAGAATCCGGGTGGAAGCTTGTCCATGGTGATGTG
genomic: GAAATGATTATGCAAAATATGCTCGTGAAGATGATGATCTGGAATCACTTgtaagttctg ... cctttttcagGAGCGAGATGTTAATGAAGAATCCGGGTGGAAGCTTGTCCATGGTGATGTG

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: 141

GGTTATTTTCTTGACTGGTTTAGTGTCAATGATATTGATGAGGACACTAAGAAATGATTATGCAAAATATGCTCGTGAAGATGATGATCTGGAATCACTTgtaagttctg ... cctttttcagGAGCGAGATGTTAATGAAGAATCCGGGTGGAAGCTTGTCCATGGTGATGTGTTCCGGCCTCCTCGTGGCCAGGTGTTTCTTTCTGCCCTAGTTGGTATTG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 111

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 110

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 177

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTTATTTTCTTGACTGGTTTAGTGTCAATGATATTGATGAGGACACTAAGAAATGATTATGCAAAATATGCTCGTGAAGATGATGATCTGGAATCACTTgtaagttctgaacctgcaatccgtagcacatcgatatggttatatatttctcattttgtctgctaatataactcattgtttgtctttttgcgtttttaca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG