ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TGCCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGGTTGAACAGGAAATGCCAAAATGCATATTTCTGACATCCCCAAATAATCCAGATGGCAGgtatatctctgtcattcataagtgcaggaactattctattcgctgctgtccagattaccatattttactgaattactttgattctatttgttcag

Basic information

species	Zea mays
transcript	GRMZM2G170595_T01
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G170595_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g47940.1 (Oryza sativa), 5'ss of exon 5

TGCCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGGTTGAACAGGAAATGCCAAAATGCATATTTCTGACATCCCCAAATAATCCAGATGGCAGgtatatctctgtcattcataagtgcaggaactattctattcgc-tgctgtccagatt----acc---atattttactgaattactttgattctatttgttcag
| || |||||||| ||||| ||||  |  |||||| |||||||||||||||||| |||||||| ||||||||||||||| || || || |||||||||||||| | || | |||| |   | ||   |  || || |  | |  || ||||||||||    | |    |||||  ||||||||| |  ||||||||| |||||
TTCCTGATTTTTCTCTAGACGTTGCACAGATTGTCAAAGTGGTTGAACAGGAAAAGCCAAAATCCATATTTCTGACATCTCCGAACAACCCAGATGGCAGgtacacctttctcatgcgagaatg---gggctgttttggttgtatgttgtccagattctgtatcttagtatttcgctgaattacctcaattctattt-ttcag

upper sequence: GRMZM2G170595_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA16G27220.1 (Glycine max), 5'ss of exon 6

TGCCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGGTTGAACAGGAAATGCCAAAATGCATATTTCTGACATCCCCAAATAATCCAGATGGCAGgtatatctc---tgtcattcataagtgcaggaactattctattcgctgctgtccagattaccatattt-tactgaattactttgattcta-tttgttcag
 ||| |||||   | |  ||||||| |  ||||  ||||| ||| |||| || | ||| |||||||||||| | ||||| ||||||||||||||||| |||||  | ||   | || ||  | | |  ||     ||  |       | |  |  || |   || ||| || ||  ||  |||    ||| ||||||   
GGCCAGATTTCAGCTTGAATGTTGAACAAATTGCTGAAGTTGTTAAACAAGAGAAGCCCAAATGCATATTTTTAACATCTCCAAATAATCCAGATGGAAGgtaactgtcaattatcctttcttactctagagtgaatagttagaaagggtacctggagttgtatgtttgtagtgttttctttttcaactaatttgttttt

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|71437833|gb|DR818883.1|DR818883

EST:     GAAATGCCAAAATGCATATTTCTGACATCCCCAAATAATCCAGATGGCAG                         TGTAATCAATGATGAGGATCTTTTAAAGATACTTGATCT
genomic: GAAATGCCAAAATGCATATTTCTGACATCCCCAAATAATCCAGATGGCAGgtatatctct ... atttgttcagTGTAATCAATGATGAGGATCTTTTAAAGATACTTGATCT

EST: gi|78078617|gb|DV507029.1|DV507029

EST:     GAAATGCCAAAATGCATATTTCTGACATCCCCAAATAATCCAGATGGCAG                         TGTAATCAATGATGAGGATCCTTTAAAGATACTTGATCTCCCAATACTTGT
genomic: GAAATGCCAAAATGCATATTTCTGACATCCCCAAATAATCCAGATGGCAGgtatatctct ... atttgttcagTGTAATCAATGATGAGGATCTTTTAAAGATACTTGATCTCCCAATACTTGT

EST: gi|32930096|gb|CF034908.1|CF034908

EST:     GAAAGGCCAAAATGCATATTTCTGACATCCCCAAATAATCCAGATGGCAG                         TGTAATCAATGATGAGGATCTTTTAAAGATACTTGATCTCCCAATACTTGT
genomic: GAAATGCCAAAATGCATATTTCTGACATCCCCAAATAATCCAGATGGCAGgtatatctct ... atttgttcagTGTAATCAATGATGAGGATCTTTTAAAGATACTTGATCTCCCAATACTTGT

EST: gi|91048897|gb|EB159315.1|EB159315

EST:     GAAATGCCAAAATGCATATTTCTGACATCCCCCAATAATCCAGATGGCAG                         TGTAATCAATGATGAGGATCTTTTAAAGATACTTGATCTCCCAATAC
genomic: GAAATGCCAAAATGCATATTTCTGACATCCCCAAATAATCCAGATGGCAGgtatatctct ... atttgttcagTGTAATCAATGATGAGGATCTTTTAAAGATACTTGATCTCCCAATAC

EST: gi|148963664|gb|EE014723.2|EE014723

EST:     GAAATGCCAAAATGCATATTTCTGACATCCCCAAATAATCCAGATGGCAG                         TGTAATCAATGATGAGGATCTTTTAAAGATACTTGATCTC
genomic: GAAATGCCAAAATGCATATTTCTGACATCCCCAAATAATCCAGATGGCAGgtatatctct ... atttgttcagTGTAATCAATGATGAGGATCTTTTAAAGATACTTGATCTC

EST: gi|148932895|gb|EE285676.2|EE285676

EST:     GAAATGCCAAAATGCATATTTCTGACATCCCCAAATAATCCAGATGGCAG                         TGTAATCAATGATGAGGATCTTTTAAAGATACTTGATCTCCCCATACTTGT
genomic: GAAATGCCAAAATGCATATTTCTGACATCCCCAAATAATCCAGATGGCAGgtatatctct ... atttgttcagTGTAATCAATGATGAGGATCTTTTAAAGATACTTGATCTCCCAATACTTGT

EST: gi|78079657|gb|DV508069.1|DV508069

EST:     GAAATGCCAAAATGCATATTTCTGACATCCCCAAATAATCCAGATGGCAG                         TGTAATCAATGATGAGGATCTTTTAAAGATACTTGATCTCCCCATACTTGT
genomic: GAAATGCCAAAATGCATATTTCTGACATCCCCAAATAATCCAGATGGCAGgtatatctct ... atttgttcagTGTAATCAATGATGAGGATCTTTTAAAGATACTTGATCTCCCAATACTTGT

EST: gi|148932277|gb|EC875831.2|EC875831

EST:     GAAATGCCAAAATGCATATTTCTGACATCCCCAAATAATCCAGATGGCAG                         TGTAATCAATGATGAGGATCTTTTAAAGATACTTGATCTCCCCATACTTGT
genomic: GAAATGCCAAAATGCATATTTCTGACATCCCCAAATAATCCAGATGGCAGgtatatctct ... atttgttcagTGTAATCAATGATGAGGATCTTTTAAAGATACTTGATCTCCCAATACTTGT

EST: gi|76289509|gb|DV029077.1|DV029077

EST:     GAAATGCCAAAATGCATATTTCTGACATCCCCAAATAATCCAGATGGCAG                         TGTAATCAATGATGAGGATCTTTTAAAGATACTTGATCTCCCAATACTTGT
genomic: GAAATGCCAAAATGCATATTTCTGACATCCCCAAATAATCCAGATGGCAGgtatatctct ... atttgttcagTGTAATCAATGATGAGGATCTTTTAAAGATACTTGATCTCCCAATACTTGT

EST: gi|149109171|gb|EE190055.2|EE190055

EST:     GAAATGCCAAAATGCATATTTCTGACATCCCCAAATAATCCAGATGGCAG                         TGTAATCAATGATGAGGATCTTTTAAAGATACTTGATCTCCCA
genomic: GAAATGCCAAAATGCATATTTCTGACATCCCCAAATAATCCAGATGGCAGgtatatctct ... atttgttcagTGTAATCAATGATGAGGATCTTTTAAAGATACTTGATCTCCCA

EST: gi|71328633|gb|DR800987.1|DR800987

EST:     GAAATGCCAAAATGCATATTTCTGACATCCCCAAATAATCCAGATGGCAG                         TGTAATCAATGATGAGGATCTTTTTAAGATACTTGATCTCTCAATACTTGT
genomic: GAAATGCCAAAATGCATATTTCTGACATCCCCAAATAATCCAGATGGCAGgtatatctct ... atttgttcagTGTAATCAATGATGAGGATCTTTTAAAGATACTTGATCTCCCAATACTTGT

EST: gi|149111871|gb|EE191026.2|EE191026

EST:     GAAATGCCAAAATGCATATTTCTGACATCCCCAAATAATCCAGATGGCAG                         TGTAATCAATGATGAGGATCTTTTAAAGATACTTGATCTCCCAATACTTGT
genomic: GAAATGCCAAAATGCATATTTCTGACATCCCCAAATAATCCAGATGGCAGgtatatctct ... atttgttcagTGTAATCAATGATGAGGATCTTTTAAAGATACTTGATCTCCCAATACTTGT

EST: gi|6020568|gb|AW065601.1|AW065601

EST:     GAAAGGCCAAAATGCATATTTCTGACATCCCCAAATAATCCAGATGGCAG                         TGTAATCAATGATGAGGATCTTTTAAAGATACTTGATCTCCCAATACTTGT
genomic: GAAATGCCAAAATGCATATTTCTGACATCCCCAAATAATCCAGATGGCAGgtatatctct ... atttgttcagTGTAATCAATGATGAGGATCTTTTAAAGATACTTGATCTCCCAATACTTGT

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: 47 (upstream exon), 48 (downstream exon)
Score: 87

TGCCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGGTTGAACAGGAAATGCCAAAATGCATATTTCTGACATCCCCAAATAATCCAGATGGCAGgtatatctct ... atttgttcagTGTAATCAATGATGAGGATCTTTTAAAGATACTTGATCTCCCAATACTTGTAGTGCTGGATGAAGCTTATATTGAGTTTTCAAGCCTTCAGTCAAGAATG

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 141

Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 134

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 115

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGGTTGAACAGGAAATGCCAAAATGCATATTTCTGACATCCCCAAATAATCCAGATGGCAGgtatatctctgtcattcataagtgcaggaactattctattcgctgctgtccagattaccatattttactgaattactttgattctatttgttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG