ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TGCCAAGTCAAATTATATGTCAGCTGGTCAGATATCTGTTCCTATTGTTTTTAGAGGACCAAACGGAGCTGCTGCTGGAGTTGGTGCTCAACACTCACAGgtttgtcagatggaattgctcatgtagttatgtaattatgtgtctgattatcatccttctacttcctaatttttcatctttatgttattgccatcctttt...

Basic information

species	Zea mays
transcript	GRMZM2G097226_T01
intron #	7
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G097226_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os09g33500.1 (Oryza sativa), 5'ss of exon 7

TGCCAAGTCAAATTATATGTCAGCTGGTCAGATATCTGTTCCTATTGTTTTTAGAGGACCAAACGGAGCTGCTGCTGGAGTTGGTGCTCAACACTCACAGgtttgtcag-atggaattgctcatgtagttatgtaattat----gtgtctgatt-atcatccttctacttcctaatttttcatctttatgttattgccatcctttt
|||||||||||| || |||||||| |||||||||||||| ||||||||||| |||||||| || |||||||||||||||||||| ||||||||||| ||||||||| |  | ||||| ||| ||| | |||  | || ||    |   |  ||| | | |  |   | ||| |  |||    |  || |||| || | | ||    
TGCCAAGTCAAACTACATGTCAGCGGGTCAGATATCTGTCCCTATTGTTTTCAGAGGACCTAATGGAGCTGCTGCTGGAGTTGGCGCTCAACACTCGCAGgtttgtgatcagggaatggcttatg-aattagtttatcatcctaggaccccattgaactttgtaaaagttcattgtttccttttgttgtgttgtt-ctaccc----

upper sequence: GRMZM2G097226_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA02G46380.2 (Glycine max), 5'ss of exon 7

TGCCAAGTCAAATTATATGTCAGCTGGTCAGATATCTGTTCCTATTGTTTTTAGAGGACCAAACGGAGCTGCTGCTGGAGTTGGTGCTCAACACTCACAGgtttgtcagatggaattgctcatgtagttatgtaa---ttatgtgtctgattatcatccttctacttcctaatttttcatctttatgttattgccatcctttt----------
 || || ||||| || ||||| ||||| || |||||||| |||||||| ||||||||||| || || || |||||||||||||||||||| || || || || ||        |  ||||    |    |   ||   |||| |  ||  ||   | |     | |   | |  |||| ||||| | |      || | ||            
CGCAAAATCAAACTACATGTCTGCTGGGCAAATATCTGTGCCTATTGTCTTTAGAGGACCCAATGGTGCCGCTGCTGGAGTTGGTGCTCAGCATTCTCAAgtatggttctcctagctgctttcttttaaagacaaactttatttaactatttgagaactgataaataattcaggtttcgtctttgtatgcccaacaactttgcctttatgcag

upper sequence: GRMZM2G097226_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA14G36540.3 (Glycine max), 5'ss of exon 7

TGCCAAGTCAAATTATATGTCAGCTGGTCAGATATCTGTTCCTATTGTTTTTAGAGGACCAAACGGAGCTGCTGCTGGAGTTGGTGCTCAACACTCACAGgtttgtcagatggaattgctcatgtagttatgtaattatgtgtctgattatcatccttctacttcctaatt----tttcatctttatgttattgccatcctttt----------
 || || ||||| || ||||| ||||| || |||||||| |||||||| ||||||||||| || || ||||||||||| ||||||||||| || || || ||  |           ||||    |  | | |  |   | | | | | |||       ||  |   |||||    |||  ||||| | |      || | ||            
CGCAAAATCAAACTACATGTCTGCTGGGCAAATATCTGTACCTATTGTCTTTAGAGGACCCAATGGTGCTGCTGCTGGGGTTGGTGCTCAGCATTCTCAAgtacggttctccttgctgctttctttttaaagacaaactttatttaactatttgagaactgataaataattcaggttttgtctttgtatgcccaacaactttgcctttatgcag

upper sequence: GRMZM2G097226_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA14G02380.2 (Glycine max), 5'ss of exon 7

TGCCAAGTCAAATTATATGTCAGCTGGTCAGATATCTGTTCCTATTGTTTTTAGAGGACCAAACGGAGCTGCTGCTGGAGTTGGTGCTCAACACTCACAGgtttgtcagatggaattgctcatgtagttatgtaa---ttatgtgtctgattatcatccttctacttcctaatttttcatctttatgttattgccatcctttt----------
 || || ||||| || ||||| ||||| || ||||| || |||||||| ||||||||||| || || ||||||||||| ||||||||||| || || || ||  |        |  ||||    |    |   ||   |||| |  |   ||   | |     | |   | |  |||| ||||| | |      || | |||           
CGCAAAATCAAACTACATGTCTGCTGGGCAAATATCGGTACCTATTGTCTTTAGAGGACCCAATGGTGCTGCTGCTGGGGTTGGTGCTCAGCATTCTCAAgtacggttctcctagctgctttcttttaaagacaaactttatttaaccatttgagaactgataaataattcaggtttcgtctttgtatgcccaacaacttttcctttatgcag

upper sequence: GRMZM2G097226_T02 (Zea mays), 5'ss of exon 7
lower sequence: AT5G50850.1 (Arabidopsis thaliana), 5'ss of exon 8

TGCCAAGTCAAATTATATGTCAGCTGGTCAGATATCTGTTCCTATTGTTTTTAGAGGACCAAACGGAGCTGCTGCTGGAGTTGGTGCTCAACACTCACAGgtttg---tcagatggaattgctcatgtagttatgtaattatgtgtctgattatcat---ccttctacttcctaatttttcatctttatgttattgccatcctttt
||| ||||||||||| ||||| ||||| ||||||  ||| || || || ||||||||||| || || ||||||||||| ||||| |||||||| || |||||      |||     ||    |    || || ||| | | ||  |    | |  |    |||||  || |  || |  | |   |  |  ||| |  ||      
TGCAAAGTCAAATTACATGTCTGCTGGACAGATAAATGTACCCATCGTCTTTAGAGGACCCAATGGTGCTGCTGCTGGTGTTGGAGCTCAACATTCTCAGgtaaacgctcacccaaaaaaaattgaataatt-tgttactttgcattctttcaaaagagaccttcagctactaaactgataaagatattcatatagg-atga----

upper sequence: GRMZM2G097226_T02 (Zea mays), 5'ss of exon 7
lower sequence: Vv17s0000g00690.t01 (Vitis vinifera), 5'ss of exon 7

TGCCAAGTCAAATTATATGTCAGCTGGTCAGATATCTGTTCCTATTGTTTTTAGAGGACCAAACGGAGCTGCTGCTGGAGTTGGTGCTCAACACTCACAGgtttgtcagatggaattgctcatgtagttatgtaattatgtg-tctgattatcatcctt--ctacttcctaatttttcatctttatgttattgccatcctttt
||| |||||||| |||||||| ||||||||||||||||| || |||||||| ||||| ||||| || |||||||| ||||||||||| || || || ||||  |||       | |   ||   || |||| |  ||||| | | |    |||||   |   || |  |    |   | |||  ||| | |    ||  |   
TGCAAAGTCAAACTATATGTCTGCTGGTCAGATATCTGTGCCAATTGTTTTCAGAGGGCCAAATGGGGCTGCTGCAGGAGTTGGTGCCCAGCATTCTCAGg--tgtagtccaaattctgtctgatacttat-tgtttatgcgattttgccatcatatatggttagtctccttctaaccttctagatgctctgcttattttccc

upper sequence: GRMZM2G097226_T02 (Zea mays), 5'ss of exon 7
lower sequence: Vv01s0146g00310.t01 (Vitis vinifera), 5'ss of exon 8

TGCCAAGTCAAATTATATGTCAGCTGGTCAGATATCTGTTCCTATTGTTTTTAGAGGACCAAACGGAGCTGCTGCTGGAGTTGGTGCTCAACACTCACAGgtttgtcagatggaattg-ctcatgtagttatgtaattatgtgtctgattatcatccttctacttcctaatttttcatctttatgttattgccatcctttt--
||| || ||||| || ||||| |||||||||||||| || ||||||||||||||||||||||| || ||||| |||||||||||||| || ||||| |||||        ||   ||  ||| || |  |    | || | ||||  |  | | |   ||||  |  |      |  |  | || |   |   | | |  |  
TGCAAAATCAAACTACATGTCCGCTGGTCAGATATCCGTACCTATTGTTTTTAGAGGACCAAATGGTGCTGCCGCTGGAGTTGGTGCCCAGCACTCCCAGgtacactccctgaggttttctcttgcacctggtgacttgtttgtc--accagcttttctctatatgatg-cccgtggtgctgatctggatcataacataatga

upper sequence: GRMZM2G097226_T02 (Zea mays), 5'ss of exon 7
lower sequence: EFJ19158 (Selaginella moellendorffii), 5'ss of exon 5

TGCCAAGTCAAATTATATGTCAGCTGGTCAGATATCTGTTCCTATTGTTTTTAGAGGACCAAACGGAGCTGCTGCTGGAGTTGGTGCTCAACACTCACAGgtttgtcagatggaattgctcatgtagttatgtaattatgtgtctgattatcatccttctacttcctaatttttcatctttatgttattgccatcctttt
 || ||| || | |||||||| |  || || ||||||||||| ||||| ||| | || || || || || ||||| || |||||||||||||||||||||||      ||  |   || || ||      | |   |   | | | ||| ||||||||  |                                       
AGCAAAGACATACTATATGTCCGGAGGGCAAATATCTGTTCCCATTGTATTTCGGGGTCCCAATGGTGCAGCTGCCGGTGTTGGTGCTCAACACTCACAGgt------gagcgctctgttc-tgcgagagt-tggctccat-ttttattttcatcctttcag--------------------------------------

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|78122124|gb|DV540508.1|DV540508

EST:     TTAGAGGACCAAACGGAGCTGCTGCTGGAGTTGGTGCTCAACACTCACAG                         TGTTATGCAGCTTGGTTTGCACATGTTCCAGGACTTAAGGTTCTCACACCA
genomic: TTAGAGGACCAAACGGAGCTGCTGCTGGAGTTGGTGCTCAACACTCACAGgtttgtcaga ... ttgtatgcagTGTTATGCAGCTTGGTTTGCACATGTTCCAGGACTTAAGGTTCTCACACCA

EST: gi|211317947|gb|FL318710.1|FL318710

EST:     TTAGAGGACCAAACGGAGCTGCTGCTGGAGTTGGTGCTCAACACTCACAG                         TGTTATGCAGCTTGGTTTGCACATGTTCCAGGACTTAAGGTTCTCACACCA
genomic: TTAGAGGACCAAACGGAGCTGCTGCTGGAGTTGGTGCTCAACACTCACAGgtttgtcaga ... ttgtatgcagTGTTATGCAGCTTGGTTTGCACATGTTCCAGGACTTAAGGTTCTCACACCA

EST: gi|32940983|gb|CF045802.1|CF045802

EST:     TTAGAGGACCAAACGGAGCTGCTGCTGGAGTTGGTGCTCAACACTCACAG                         TGTTATGCAGCTTGGTTTGCACATGTTCCAGGACTTAAGGTTCTCACACCA
genomic: TTAGAGGACCAAACGGAGCTGCTGCTGGAGTTGGTGCTCAACACTCACAGgtttgtcaga ... ttgtatgcagTGTTATGCAGCTTGGTTTGCACATGTTCCAGGACTTAAGGTTCTCACACCA

EST: gi|211088145|gb|FL307530.1|FL307530

EST:     TTAGAGGACCAAACGGAGCTGCTGCTGGAGTTGGTGCTCAACACTCACAG                         TGTTATGCAGCTTGGTTTGCACATGTTCCAGGACTTAAGGTTCTCACACCA
genomic: TTAGAGGACCAAACGGAGCTGCTGCTGGAGTTGGTGCTCAACACTCACAGgtttgtcaga ... ttgtatgcagTGTTATGCAGCTTGGTTTGCACATGTTCCAGGACTTAAGGTTCTCACACCA

EST: gi|32829636|gb|CD969314.1|CD969314

EST:     TGCTGCTGGAGTTGGTGCTCAACACTCACAG                         TGTTATGCAGCTTGGTTTGCACATGTTCCAGGACTTAAGGTTCTCACACCA
genomic: TGCTGCTGGAGTTGGTGCTCAACACTCACAGgtttgtcaga ... ttgtatgcagTGTTATGCAGCTTGGTTTGCACATGTTCCAGGACTTAAGGTTCTCACACCA

EST: gi|91057168|gb|EB167586.1|EB167586

EST:     TTAGAGGACCAAACGGAGCTGCTGCTGGAGTTGGTGCTCAACACTCACAG                         TGTTATGCAGCTTGGTTTGCACATGTTCCAGGACTTAAGGTTCTCACACCA
genomic: TTAGAGGACCAAACGGAGCTGCTGCTGGAGTTGGTGCTCAACACTCACAGgtttgtcaga ... ttgtatgcagTGTTATGCAGCTTGGTTTGCACATGTTCCAGGACTTAAGGTTCTCACACCA

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: 44 (upstream exon), 49 (downstream exon)
Score: 305

TGCCAAGTCAAATTATATGTCAGCTGGTCAGATATCTGTTCCTATTGTTTTTAGAGGACCAAACGGAGCTGCTGCTGGAGTTGGTGCTCAACACTCACAGgtttgtcaga ... ttgtatgcagTGTTATGCAGCTTGGTTTGCACATGTTCCAGGACTTAAGGTTCTCACACCATACTCTTCAGAAGATGCCCGAGGCTTGCTCAAAGCTGCTATCAGGGACC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 212

Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 210

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 504

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCCAAGTCAAATTATATGTCAGCTGGTCAGATATCTGTTCCTATTGTTTTTAGAGGACCAAACGGAGCTGCTGCTGGAGTTGGTGCTCAACACTCACAGgtttgtcagatggaattgctcatgtagttatgtaattatgtgtctgattatcatccttctacttcctaatttttcatctttatgttattgccatcctttt

- - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA