ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GTTTGGACCATACTTCTGCCAACCAGTTATTGCTGGCCTAGGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAAgtatgtatcaactaatcttcagtttatctttcttgattttttccacactgctgttattttcttgtttgaaatttcttttaaaaaattatacaacctagga...

Basic information

species	Zea mays
transcript	GRMZM2G117544_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G117544_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g08520.1 (Oryza sativa), 5'ss of exon 4

GTTTGGACCATACTTCTGCCAACCAGTTATTGCTGGCCTAGGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAAgtatgtatcaactaatcttcagtttatctttcttgattttttccacact-gctgtt---atttt--cttgtttgaaatttcttttaaaaaattatacaacctagga
|||||| || ||||||||||||||||||||||||||  ||||||| || |||||||| ||||||||||||||||| ||||||||||||||||||||||||  ||   |      | || || | |   ||| | | | |   |||    | ||   ||  | |||| ||         |   || ||||       
GTTTGGGCCGTACTTCTGCCAACCAGTTATTGCTGGATTAGGAGATAATGATGAGCCATTTATATGTACCATGGATTGCATTGGTGCCAAgtatgtatcacttatattctctcgtctcattttagtcgtttactaaatttattgtccaaaattcaactgatctgaagttctcaacggtaccataaacaat------

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|89247888|gb|DY619674.1|DY619674

EST:     GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAA                         GGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA
genomic: GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAAgtatgtatca ... ttttattcagGGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA

EST: gi|60356716|gb|DN223689.1|DN223689

EST:     GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAA                         GGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA
genomic: GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAAgtatgtatca ... ttttattcagGGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA

EST: gi|71429028|gb|DR810078.1|DR810078

EST:     GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAA                         GGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA
genomic: GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAAgtatgtatca ... ttttattcagGGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA

EST: gi|148995894|gb|EE035134.2|EE035134

EST:     GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAA                         GGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA
genomic: GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAAgtatgtatca ... ttttattcagGGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA

EST: gi|76288304|gb|DV027872.1|DV027872

EST:     GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAA                         GGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA
genomic: GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAAgtatgtatca ... ttttattcagGGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA

EST: gi|76288303|gb|DV027871.1|DV027871

EST:     GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAA                         GGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA
genomic: GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAAgtatgtatca ... ttttattcagGGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA

EST: gi|37379861|gb|CF626698.1|CF626698

EST:     GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAA                         GGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA
genomic: GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAAgtatgtatca ... ttttattcagGGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA

EST: gi|89758446|gb|DY687621.1|DY687621

EST:     GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAA                         GGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA
genomic: GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAAgtatgtatca ... ttttattcagGGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA

EST: gi|71429029|gb|DR810079.1|DR810079

EST:     GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAA                         GGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA
genomic: GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAAgtatgtatca ... ttttattcagGGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA

EST: gi|88758274|gb|DY542415.1|DY542415

EST:     GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAA                         GGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA
genomic: GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAAgtatgtatca ... ttttattcagGGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA

EST: gi|94476825|gb|EB705783.1|EB705783

EST:     AGACAACGATCGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAA                         GGAACTAGCAAAAGATTTTGTGGCCTCCCGGTACTGCTTCAGAGTCACTTT
genomic: AGACAACGAT-GAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAAgtatgtatca ... ttttattcagGGAACTAGCAAAAGATTTTGTGGTCT-CCGGTACTGCTTCAGAGTCACTTT

EST: gi|60395143|gb|DN228012.1|DN228012

EST:     GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAA                         GGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA
genomic: GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAAgtatgtatca ... ttttattcagGGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA

EST: gi|88754192|gb|DY538333.1|DY538333

EST:     GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAA                         GGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA
genomic: GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAAgtatgtatca ... ttttattcagGGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA

EST: gi|60398269|gb|DN231085.1|DN231085

EST:     GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAA                         GGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA
genomic: GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAAgtatgtatca ... ttttattcagGGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA

EST: gi|148987000|gb|EE030820.2|EE030820

EST:     GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAA                         GGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA
genomic: GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAAgtatgtatca ... ttttattcagGGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA

EST: gi|67012342|gb|CO441091.1|CO441091

EST:     GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAA                         GGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA
genomic: GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAAgtatgtatca ... ttttattcagGGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA

EST: gi|211034562|gb|FL157508.1|FL157508

EST:     GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAA                         GGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA
genomic: GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAAgtatgtatca ... ttttattcagGGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA

EST: gi|89247887|gb|DY619673.1|DY619673

EST:     GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAA                         GGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA
genomic: GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAAgtatgtatca ... ttttattcagGGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA

EST: gi|211263410|gb|FL474910.1|FL474910

EST:     GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAA                         GGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA
genomic: GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAAgtatgtatca ... ttttattcagGGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA

EST: gi|60337320|gb|DN204293.1|DN204293

EST:     GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAA                         GGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA
genomic: GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAAgtatgtatca ... ttttattcagGGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA

EST: gi|88758273|gb|DY542414.1|DY542414

EST:     GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAA                         GGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA
genomic: GGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAAgtatgtatca ... ttttattcagGGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTA

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), 47 (downstream exon)
Score: 118

GTTTGGACCATACTTCTGCCAACCAGTTATTGCTGGCCTAGGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAAgtatgtatca ... ttttattcagGGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTATGGTGCTTGTGAGTCCATGTATAAGCCAAACATG

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 81

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 107

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 107

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTGGACCATACTTCTGCCAACCAGTTATTGCTGGCCTAGGAGACAACGATGAGCCGTTTATATGTACCATGGACTGCATTGGTGCCAAgtatgtatcaactaatcttcagtttatctttcttgattttttccacactgctgttattttcttgtttgaaatttcttttaaaaaattatacaacctagga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA