ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TTGGTGCAGAAATCTCATTTGATTCTGCCACTGGGAACTTCACCAAATACAATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagttttctaagttagcaatcttatatatttaggcactgtatgcgactgttgtttgacaacccttaagcttatttgatacctgtaatatctttattga...

Basic information

species	Zea mays
transcript	GRMZM2G146670_T01
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G146670_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA08G40800.1 (Glycine max), 5'ss of exon 5

TTGGTGCAGAAATCTCATTTGATTCTGCCACTGGGAACTTCACCAAATACAATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagt-----tttctaagttagcaatcttatata--tttaggcactgtatgcgac-tgttgtttgacaaccc---ttaagcttatttgatacctgtaatatctttattga----
||||  ||||  | ||||||||| ||||| |||| ||||| |||||||||||||| ||  |||   | |||||||  |||||||| ||||| || | | ||| |||     |  | | | ||   || |     |  |||||  |  ||  || |  | ||| |   ||||     || | ||  |    || |||   | | ||| ||      
TTGGGACAGATCTTTCATTTGATACTGCCTCTGGCAACTTTACCAAATACAATGCAGGGCTGAACATTACTCATGCTGACCTTATTGCATCTCTAACTCTgtaagtagttatcccaaggctatatatgtccatcaattttagagaaggttagccatatattgctattcaacttgagttgatctcctaatttatctgctctttttttcttatgtag

upper sequence: GRMZM2G146670_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv01s0026g01650.t01 (Vitis vinifera), 5'ss of exon 5

TTGGTGCAGAAATCTCATTTGATTCTGCCACTGGGAACTTCACCAAATACAATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagt-----tttctaagttagca-----atcttatatatttaggcactgtatgcgactgttgtttgacaacccttaagcttatttgatacctgtaatatctttattga
||||  | ||  |||| |||||  |||||||||||||||||||||||| |||||| ||  ||   ||| |  |||  ||||| || ||  || | | | |||||||      ||||     |        || |||| | || |   |   ||| |     ||| ||  |   |||    ||   || |||| | | || |         
TTGGGACTGATCTCTCGTTTGACACTGCCACTGGGAACTTCACCAAATGCAATGCAGGCCTGGGTTTCTCCAATGCTGACCTCATTGCTGCCTTGACTTTgtgagtagttccttctggaaaaatgtttttattttattttttaatttatcttattcattcattgctt--ccttcctagccctcgcttaatactttttatttg--------

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|32919820|gb|CF024632.1|CF024632

EST:     AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATAT                         GAACAACAAGGGA
genomic: AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagttttc ... tctcttgcagGAACAACAAGGGA

EST: gi|31354274|gb|CD438631.1|CD438631

EST:     AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATAT                         GAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA
genomic: AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagttttc ... tctcttgcagGAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA

EST: gi|60394030|gb|DN226900.1|DN226900

EST:     AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATAT                         GAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA
genomic: AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagttttc ... tctcttgcagGAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA

EST: gi|211283575|gb|FL005708.1|FL005708

EST:     AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATAT                         GAACAACAAGGGAGA
genomic: AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagttttc ... tctcttgcagGAACAACAAGGGAGA

EST: gi|211272931|gb|FL017958.1|FL017958

EST:     AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATAT                         GAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA
genomic: AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagttttc ... tctcttgcagGAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA

EST: gi|30307134|gb|CD001807.1|CD001807

EST:     AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATAT                         GAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA
genomic: AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagttttc ... tctcttgcagGAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA

EST: gi|24769940|gb|CA405069.1|CA405069

EST:     AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATAT                         GAACAACAAGGGAGACACCCTTACTGGAGCTTACTACCACAAGGTGAGCGA
genomic: AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagttttc ... tctcttgcagGAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA

EST: gi|32945222|gb|CF050041.1|CF050041

EST:     AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATAT                         GAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA
genomic: AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagttttc ... tctcttgcagGAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA

EST: gi|33093487|gb|CF053481.1|CF053481

EST:     AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATAT                         GAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA
genomic: AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagttttc ... tctcttgcagGAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA

EST: gi|60344080|gb|DN211053.1|DN211053

EST:     AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATAT                         GAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA
genomic: AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagttttc ... tctcttgcagGAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA

EST: gi|60345112|gb|DN212085.1|DN212085

EST:     AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATAT                         GAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA
genomic: AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagttttc ... tctcttgcagGAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA

EST: gi|32917034|gb|CF021846.1|CF021846

EST:     AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATAT                         GAACAACAAGGGAGA
genomic: AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagttttc ... tctcttgcagGAACAACAAGGGAGA

EST: gi|50322855|gb|CO517981.1|CO517981

EST:     AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATAT                         GAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA
genomic: AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagttttc ... tctcttgcagGAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA

EST: gi|20802437|gb|BQ293487.1|BQ293487

EST:     AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATAT                         GAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA
genomic: AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagttttc ... tctcttgcagGAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA

EST: gi|166423475|gb|EG200146.1|EG200146

EST:     CTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATAT                         GAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA
genomic: CTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagttttc ... tctcttgcagGAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA

EST: gi|166537316|gb|EG318259.1|EG318259

EST:     AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATAT                         GAACAACAAGGGAGACAACCTTAC
genomic: AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagttttc ... tctcttgcagGAACAACAAGGGAGACAACCTTAC

EST: gi|60400177|gb|DN232984.1|DN232984

EST:     AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATAT                         GAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA
genomic: AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagttttc ... tctcttgcagGAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA

EST: gi|33092306|gb|CF052300.1|CF052300

EST:     AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATAT                         GAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA
genomic: AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagttttc ... tctcttgcagGAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA

EST: gi|16380087|gb|BI993308.1|BI993308

EST:     AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATAT                         GAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA
genomic: AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagttttc ... tctcttgcagGAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA

EST: gi|31354722|gb|CD439079.1|CD439079

EST:     AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATAT                         GAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA
genomic: AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagttttc ... tctcttgcagGAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA

EST: gi|33094802|gb|CF054796.1|CF054796

EST:     CATGAAGACCTTATCGCATCCCTTAATAT                         GAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA
genomic: CATGAAGACCTTATCGCATCCCTTAATATgtgagttttc ... tctcttgcagGAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA

EST: gi|67022240|gb|CO450989.1|CO450989

EST:     AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATAT                         GAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA
genomic: AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagttttc ... tctcttgcagGAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA

EST: gi|32937145|gb|CF041964.1|CF041964

EST:     ATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATAT                         GAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA
genomic: ATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagttttc ... tctcttgcagGAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA

EST: gi|20208350|gb|BQ134439.1|BQ134439

EST:     GCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATAT                         GAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA
genomic: GCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagttttc ... tctcttgcagGAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA

EST: gi|15208686|gb|BI430570.1|BI430570

EST:     AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATAT                         GAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA
genomic: AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagttttc ... tctcttgcagGAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA

EST: gi|74243487|gb|DT651401.1|DT651401

EST:     AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATAT                         GAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA
genomic: AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagttttc ... tctcttgcagGAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA

EST: gi|5030719|gb|AI714913.1|AI714913

EST:     AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATAT                         GAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA
genomic: AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagttttc ... tctcttgcagGAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA

EST: gi|30307135|gb|CD001808.1|CD001808

EST:     AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATAT                         GAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA
genomic: AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagttttc ... tctcttgcagGAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA

EST: gi|6538860|gb|AW224999.1|AW224999

EST:     AATGCTGGATTGATGTTCACTCAT-AAGGCCTTATCGCATCCCTTAATAT                         GAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA
genomic: AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagttttc ... tctcttgcagGAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA

EST: gi|33094138|gb|CF054132.1|CF054132

EST:     AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATAT                         GAACAACAAGGGA
genomic: AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagttttc ... tctcttgcagGAACAACAAGGGA

EST: gi|61118574|gb|DN559535.1|DN559535

EST:     AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATAT                         GAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGGGAGCGA
genomic: AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagttttc ... tctcttgcagGAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA

EST: gi|61118573|gb|DN559534.1|DN559534

EST:     AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATAT                         GAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA
genomic: AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagttttc ... tctcttgcagGAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA

EST: gi|32912387|gb|CF017199.1|CF017199

EST:     AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATAT                         GAACAACAAGGGA
genomic: AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagttttc ... tctcttgcagGAACAACAAGGGA

EST: gi|31355357|gb|CD439714.1|CD439714

EST:     AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATAT                         GAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA
genomic: AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagttttc ... tctcttgcagGAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA

EST: gi|24769460|gb|CA404589.1|CA404589

EST:     AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATAT                         GAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA
genomic: AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagttttc ... tctcttgcagGAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA

EST: gi|21331617|gb|BQ486998.1|BQ486998

EST:     AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATAT                         GAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA
genomic: AATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagttttc ... tctcttgcagGAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGA

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: 226

TTGGTGCAGAAATCTCATTTGATTCTGCCACTGGGAACTTCACCAAATACAATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagttttc ... tctcttgcagGAACAACAAGGGAGACAACCTTACTGGAGCTTACTACCACAAGGTGAGCGAATTGACAAACACAGCTGTTGGGGCAGAGCTTACCCACAGTTTCTCGACC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 226

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 171

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 236

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGGTGCAGAAATCTCATTTGATTCTGCCACTGGGAACTTCACCAAATACAATGCTGGATTGATGTTCACTCATGAAGACCTTATCGCATCCCTTAATATgtgagttttctaagttagcaatcttatatatttaggcactgtatgcgactgttgtttgacaacccttaagcttatttgatacctgtaatatctttattga

- - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA