ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

AAGTCATCGAACTTCTTTGTTGAATTTGGGATGGACAGTGGATATCACAAAAAATCTACATCCAGTTCATCCAAAGTGCAGgtaactgttttattcagacatatatgattaatcatcattcatcaatatgtgaactccattgagcaagtatattgtaaagtcagaactaaaaagaggaaca...

Basic information

species	Zea mays
transcript	GRMZM2G134045_T01
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G134045_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os10g42420.1 (Oryza sativa), 5'ss of exon 4

-------------------AAGTCATCGAACTTCTTTGTTGAATTTGGGATGGACAGTGGATATCACAAAAAATCTACATCCAGTTCATCCAAAGTGCAGgtaac---tgttttattcagaca-tatatg----attaatcatcattcatcaatatgtgaactccattgagcaagtatattgtaaagtcagaactaaaaagaggaaca
                   || || || ||||||||||  |||||||||||||||||||||||||||||||||||| |  |  |  ||||||||||||||||||    | ||| || ||  |  |||||     ||  |       |  | |  |||||||||| |||     |   |  |     || ||  ||             
TGGACATGTTGCGCCCCCAAAATCTTCAAACTTCTTTGGCGAATTTGGGATGGACAGTGGATATCACAAAAAATCTGCCCCTGGCCCATCCAAAGTGCAGgtaatgtttatttaatacaatcgctatattgtatatagagtgatgattgtgagcatgtgaactcaattatattatgttggtcctctgttagt-ctgttgtc-------

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|87155179|gb|DY399968.1|DY399968

EST:     TCTTTGTTGAATTTGGGATGGACAGTGGATATCACAAAAAATCTACATCCAGTTCATCCAAAGTGCAG        
genomic: TGGACAGTGGATATCACAAAAAATCTACATCCAGTTCATCCAAAGTGCAGgtaactgttt ... tgttgttcagA

EST: gi|78082818|gb|DV511211.1|DV511211

EST:     TCTTTGTTGAATTTGGGATGGACAGTGGATATCACAAAAAATCTACATCCAGTTCATCCAAAGTGCAG        
genomic: TGGACAGTGGATATCACAAAAAATCTACATCCAGTTCATCCAAAGTGCAGgtaactgttt ... tgttgttcagA

EST: gi|86467876|gb|DY234246.1|DY234246

EST:     TGGACAGTGGATATCACAAAAAATCTACATCCAGTTCATCCAAAGTGCAG                         ATTGAGGAAAGCAGTGAAGCAAGACAGAAATTCTCGAATGCAAAATCAATT
genomic: TGGACAGTGGATATCACAAAAAATCTACATCCAGTTCATCCAAAGTGCAGgtaactgttt ... tgttgttcagATTGAGGAAAGCAGTGAAGCAAGACAGAAATTCTCGAATGCAAAATCAATT

EST: gi|87154151|gb|DY398940.1|DY398940

EST:     TCTTTGTTGAATTTGGGATGGACAGTGGATATCACAAAAAATCTACATCCAGTTCATCCAAAGTGCAG        
genomic: TGGACAGTGGATATCACAAAAAATCTACATCCAGTTCATCCAAAGTGCAGgtaactgttt ... tgttgttcagA

EST: gi|78110556|gb|DV528966.1|DV528966

EST:     TCTTTGTTGAATTTGGGATGGACAGTGGATATCACAAAAAATCTACATCCAGTTCATCCAAAGTGCAG        
genomic: TGGACAGTGGATATCACAAAAAATCTACATCCAGTTCATCCAAAGTGCAGgtaactgttt ... tgttgttcagA

EST: gi|50329244|gb|CO524370.1|CO524370

EST:     TCTTTGTTGAATTTGGGATGGACAGTGGATATCACAAAAAATCTACATCCAGTTCATCCAAAGTGCAG        
genomic: TGGACAGTGGATATCACAAAAAATCTACATCCAGTTCATCCAAAGTGCAGgtaactgttt ... tgttgttcagA

EST: gi|78027266|gb|DV495653.1|DV495653

EST:     AGTGGATATCACAAAAAATCTACATCCAGTTCATCCAAAGTGCAG                         ATTGAGGAAAGCAGTGAAGCAAGACAGAAATTCTCGAATGCAAAATCAATT
genomic: AGTGGATATCACAAAAAATCTACATCCAGTTCATCCAAAGTGCAGgtaactgttt ... tgttgttcagATTGAGGAAAGCAGTGAAGCAAGACAGAAATTCTCGAATGCAAAATCAATT

EST: gi|32909005|gb|CF013817.1|CF013817

EST:     TCTTTGTTGAATTTGGGATGGACAGTGGATATCACAAAAAATCTACATCCAGTTCATCCAAAGTGCAG        
genomic: TGGACAGTGGATATCACAAAAAATCTACATCCAGTTCATCCAAAGTGCAGgtaactgttt ... tgttgttcagA

EST: gi|26455703|gb|CA827286.1|CA827286

EST:     TCTTTGTTGAATTTGGGATGGACAGTGGATATCACAAAAAATCTACATCCAGTTCATCCAAAGTGCAG        
genomic: TGGACAGTGGATATCACAAAAAATCTACATCCAGTTCATCCAAAGTGCAGgtaactgttt ... tgttgttcagA

EST: gi|22545199|gb|BU097558.1|BU097558

EST:     TCTTTGTTGAATTTGGGATGGACAGTGGATATCACAAAAAATCTACATCCAGTTCATCCAAAGTGCAG        
genomic: TGGACAGTGGATATCACAAAAAATCTACATCCAGTTCATCCAAAGTGCAGgtaactgttt ... tgttgttcagA

EST: gi|211356763|gb|FL443096.1|FL443096

EST:     CAAAAAATCTACATCCAGTTCATCCAAAGTGCAG                         ATTGAGGAAAGCAGTGAAGCAAGMCAGAAATTCTCGAATGCAAAATCAATT
genomic: CAAAAAATCTACATCCAGTTCATCCAAAGTGCAGgtaactgttt ... tgttgttcagATTGAGGAAAGCAGTGAAGCAAGACAGAAATTCTCGAATGCAAAATCAATT

EST: gi|89759290|gb|DY688159.1|DY688159

EST:     TGGACAGTGGATATCACAAAAAATCTACATCCAGTTCATCCAAAGTGCAG                         ATTGAGGAAAGCAGTGAAGCAAGACAGAAATTCTCGAATGCAAAATCAATT
genomic: TGGACAGTGGATATCACAAAAAATCTACATCCAGTTCATCCAAAGTGCAGgtaactgttt ... tgttgttcagATTGAGGAAAGCAGTGAAGCAAGACAGAAATTCTCGAATGCAAAATCAATT

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: 43 (upstream exon), 46 (downstream exon)
Score: 29

AAGTCATCGAACTTCTTTGTTGAATTTGGGATGGACAGTGGATATCACAAAAAATCTACATCCAGTTCATCCAAAGTGCAGgtaactgttt ... tgttgttcagATTGAGGAAAGCAGTGAAGCAAGACAGAAATTCTCGAATGCAAAATCAATTTCATCCTCTCAGTTTTTTGGTGATCAGGCCAGTTTCGAAAAGGACACTC

Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 130

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 186

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 101

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGTCATCGAACTTCTTTGTTGAATTTGGGATGGACAGTGGATATCACAAAAAATCTACATCCAGTTCATCCAAAGTGCAGgtaactgttttattcagacatatatgattaatcatcattcatcaatatgtgaactccattgagcaagtatattgtaaagtcagaactaaaaagaggaaca

- - - - - - - - - - - - - - - - - - AGTGGA