ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TGCTTCTGCAGTCAATCATTACCTACACATCGCGCATGAAAACACTTATACATAGAGAAACAGACAAGATTGACATACGTGCTGATGCAGAATTACTGAGgtattacatgccttgtcttcagttttattattactgtgttcaggaatagacattaaaaggagttctgtgtatttttggtttgtcacacctagtgctgatt...

Basic information

species	Zea mays
transcript	GRMZM2G055917_T02
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G055917_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os09g21780.1 (Oryza sativa), 5'ss of exon 2

TGCTTCTGCAGTCAATCATTACCTACACATCGCGCATGAAAACACTTATACATAGAGAAACAGACAAGATTGACATACGTGCTGATGCAGAATTACTGAGgtattacatgcct-----tgtcttcagttttattattactgtgttcaggaatagacattaaaaggagttctgtgtatttttggtttgtcacacctagtgctgatt
| || ||||| ||||||||||| |||||||| |||||||||| ||| ||||||| ||||||||||||||||||||||||||||||||||||| |  ||||||| |||    ||     | | ||||||| |   ||| |||| |||| ||||| |||| ||||  | ||     |         |  | |       | |   | 
TACTGCTGCAATCAATCATTACATACACATCACGCATGAAAATACTCATACATAAAGAAACAGACAAGATTGACATACGTGCTGATGCAGAACTTTTGAGgtactaccattctatatctattttcagttgttgcatt-ctgt-ttcatgaatacacatgaaaaataatttgactttccacca--tcatgatgatggttacgtgt-

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|71446872|gb|DR827922.1|DR827922

EST:     CATAGAGAAACAGACAAGATTGACATACGTGCTGATGCAGAATTACTGAG                         GTATAAATATGAAAATGAGCAGGTTATTGATGCTGCTTCAACTGATGCAAG
genomic: CATAGAGAAACAGACAAGATTGACATACGTGCTGATGCAGAATTACTGAGgtattacatg ... tctttcctagGTATAAATATGAAAATGAGCAGGTTATTGATGCTGCTTCAACTGATGCAAG

EST: gi|60358142|gb|DN225115.1|DN225115

EST:     CATAGAGAAACAGACAAGATTGACATACGTGTTGATGCAGAATTAGTGAG                         GTATAAATATGAAAATGAGCATGTTATTGATGCTGCTTCAACTGATGCAAG
genomic: CATAGAGAAACAGACAAGATTGACATACGTGCTGATGCAGAATTACTGAGgtattacatg ... tctttcctagGTATAAATATGAAAATGAGCAGGTTATTGATGCTGCTTCAACTGATGCAAG

EST: gi|211258413|gb|FL016731.1|FL016731

EST:     CATAGAGAAACAGACAAGATTGACATACGTGCTGATGCAGAATTACTGAG                         GTATAAATATGAAAATGAGCAGGTTATTGATGCTGCTTCAACTGATGC
genomic: CATAGAGAAACAGACAAGATTGACATACGTGCTGATGCAGAATTACTGAGgtattacatg ... tctttcctagGTATAAATATGAAAATGAGCAGGTTATTGATGCTGCTTCAACTGATGC

EST: gi|211258417|gb|FL016735.1|FL016735

EST:     CATAGAGAAACAGACAAGATTGACATACGTGCTGATGCAGAATTACTGAG                         GTATAAATATGAAAATGAGCAGGTTATTGATGCTGCTTCAACTGATGCAAG
genomic: CATAGAGAAACAGACAAGATTGACATACGTGCTGATGCAGAATTACTGAGgtattacatg ... tctttcctagGTATAAATATGAAAATGAGCAGGTTATTGATGCTGCTTCAACTGATGCAAG

EST: gi|211255978|gb|FL016719.1|FL016719

EST:     CATAGAGAAACAGACNAGATTGACATACGTGCTGATGCAGAATTACTGAG                         GTATAAATATGAAAATGAGCAGGTTATTGA
genomic: CATAGAGAAACAGACAAGATTGACATACGTGCTGATGCAGAATTACTGAGgtattacatg ... tctttcctagGTATAAATATGAAAATGAGCAGGTTATTGA

EST: gi|211258406|gb|FL016724.1|FL016724

EST:     CATAGAGAAACAGACAAGATTGACATACGTGCTGATGCAGAATTACTGAG                         GTATAAATATGAAAATGAGCAGGTTATTGATGCTG
genomic: CATAGAGAAACAGACAAGATTGACATACGTGCTGATGCAGAATTACTGAGgtattacatg ... tctttcctagGTATAAATATGAAAATGAGCAGGTTATTGATGCTG

EST: gi|211258410|gb|FL016728.1|FL016728

EST:     TAGAGAAACAGACNAGATTGACATACGTGCTGATGGCAGAAATTACTGAG                         GTATAAATATGAAAAATGAGCAGGGTTAT
genomic: TAGAGAAACAGACAAGATTGACATACGTGCTGATG-CAGAA-TTACTGAGgtattacatg ... tctttcctagGTATAAATATGAAAA-TGAGCAGG-TTAT

EST: gi|211258408|gb|FL016726.1|FL016726

EST:     CATAGAGAAACAGACAAGATTGACATACGTGCTGATGCAGAATTACTGAG                         GTATAAATATGAAAATGAGCA
genomic: CATAGAGAAACAGACAAGATTGACATACGTGCTGATGCAGAATTACTGAGgtattacatg ... tctttcctagGTATAAATATGAAAATGAGCA

EST: gi|211255965|gb|FL016706.1|FL016706

EST:     CCTAGAGAAACAGACAAGATTGACATACGTGCTGATGCAGAATTACTGAG                         GGATAAATATGAAAATGAGCAGGTTATTGATGCTGC
genomic: CATAGAGAAACAGACAAGATTGACATACGTGCTGATGCAGAATTACTGAGgtattacatg ... tctttcctagGTATAAATATGAAAATGAGCAGGTTATTGATGCTGC

EST: gi|211258416|gb|FL016734.1|FL016734

EST:     CATAGAGAAACAGACAAGATTGACATACGTGCTGATGCAGAATTACTGAG                         GTATAAATATGAAAATGAGCAGGTTATTGATGCTGCTTCA
genomic: CATAGAGAAACAGACAAGATTGACATACGTGCTGATGCAGAATTACTGAGgtattacatg ... tctttcctagGTATAAATATGAAAATGAGCAGGTTATTGATGCTGCTTCA

EST: gi|31357593|gb|CD441950.1|CD441950

EST:     CATAGAGAAACAGACAAGATTGACATACGTGCTGATGCAGAATTACTGAG                         GTATAAATATGAAAATGAGCAGGTTATTGATGCTGCTTCAACTGATGCAAG
genomic: CATAGAGAAACAGACAAGATTGACATACGTGCTGATGCAGAATTACTGAGgtattacatg ... tctttcctagGTATAAATATGAAAATGAGCAGGTTATTGATGCTGCTTCAACTGATGCAAG

EST: gi|211255966|gb|FL016707.1|FL016707

EST:     CATAGAGAAACAGACAAGATTGACATACGTGCTGATGCAGAATTACTGAG                         GTATAAATATGAAAATGAGCAGGTTATTGATGCTGCTTCAACTGATGCAA
genomic: CATAGAGAAACAGACAAGATTGACATACGTGCTGATGCAGAATTACTGAGgtattacatg ... tctttcctagGTATAAATATGAAAATGAGCAGGTTATTGATGCTGCTTCAACTGATGCAA

EST: gi|211255974|gb|FL016715.1|FL016715

EST:     CATAGAGAAACAGACAAGATTGACATACGTGCTGATGCAGAATTACTGAG                         GTATAAATATGAAAATGAGCAGGTTATTGATG
genomic: CATAGAGAAACAGACAAGATTGACATACGTGCTGATGCAGAATTACTGAGgtattacatg ... tctttcctagGTATAAATATGAAAATGAGCAGGTTATTGATG

EST: gi|24462472|gb|BM660003.1|BM660003

EST:     CATAGAGAAACAGACAAGATTGACATACGTGCTGATGCAGAATTACTGAG                         GTATAAATATGAAAATGAGCAGGTTATTGATGCTGCTTCAACTGATGCAAG
genomic: CATAGAGAAACAGACAAGATTGACATACGTGCTGATGCAGAATTACTGAGgtattacatg ... tctttcctagGTATAAATATGAAAATGAGCAGGTTATTGATGCTGCTTCAACTGATGCAAG

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: 48 (upstream exon), 48 (downstream exon)
Score: 142

TGCTTCTGCAGTCAATCATTACCTACACATCGCGCATGAAAACACTTATACATAGAGAAACAGACAAGATTGACATACGTGCTGATGCAGAATTACTGAGgtattacatg ... tctttcctagGTATAAATATGAAAATGAGCAGGTTATTGATGCTGCTTCAACTGATGCAAGCTCACCCTTACCGTATCAGGTGTATGGCAATGGGAAGATTGGATCTCAG

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

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

Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 47

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTTCTGCAGTCAATCATTACCTACACATCGCGCATGAAAACACTTATACATAGAGAAACAGACAAGATTGACATACGTGCTGATGCAGAATTACTGAGgtattacatgccttgtcttcagttttattattactgtgttcaggaatagacattaaaaggagttctgtgtatttttggtttgtcacacctagtgctgatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaggag