ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GTGGTGCATCTGCAATGTCTCCTATGCAGTTTGTAGGAACTCCAGGCACTAATATGCCGAAGAATGACATGAGAAATGCTATGGACAATAGAAAAAGGAAgtatgcaccacctcccttgcaatcatccaacagtcattttatgaagttatttgtccatgcattgttttctttccttgctattttgtctgtgctatgaaat...

Basic information

species	Zea mays
transcript	GRMZM2G139683_T02
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G139683_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os07g07020.1 (Oryza sativa), 5'ss of exon 4

GTGGTGCATCTGCAATGTCTCCTATGCAGTTTGTAGGAACTCCAGGCACTAATATGCCGAAGAATGACATGAGAAATGCTATGGACA---------ATAGAAAAAGGAAgtatgcaccacctcccttgcaatcatccaacagtcattttatgaagttatttgtccatgcattgttttctttccttgctattttgtctgtg-ctatgaaat--
         |||| ||||||||||||||||||| ||||||||| ||||| ||||| || ||||| |||||||||||||  ||||             |||||| || ||||||||||    |||||| ||||| | ||    || | | | |   ||| || ||  |||| || | | || |||||| | ||  | | || ||| |  |   
---------CTGCCATGTCTCCTATGCAGTTTGCAGGAACTCCTGGCACCAATATCCCAAAGAACGACATGAGAAATGTCATGGGTGGACAGGGTGGTAGAAAGAGAAAgtatgcact---tcccttacaatcgttcatatctcttatgaagttattagttctctgtgcagtgatattttgccttgcgagttgttttctgtctaggcgaaca

upper sequence: GRMZM2G139683_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os10g41450.1 (Oryza sativa), 5'ss of exon 5

GTGGTGCATCTGCAATGTCTCCTATGCAGTTTGTAGGAACTCCAGGCACTAATATGCCGAAGAATGACATGAGAAATGCTATGGACA---------ATAGAAAAAGGAAgtatgcaccacctcccttgcaatcatccaacagtcattttatgaagttatttg---tccatgcattgttttctttccttgctattttgtctgtg-ctatgaaat--
         |||||||||||||||||||||||| |||||| || ||||| ||||| || ||||| |||||||||||||  ||||             |||||| || ||||||||||    |||||| ||||||||||    || | |||||||||| ||||   ||  |||| || | | || |||||| | ||  | |  | ||||| ||   
---------CTGCAATGTCTCCTATGCAGTTTGCAGGAACCCCTGGCACCAATATCCCAAAGAACGACATGAGAAATGTCATGGGTGGACAGGGTGGTAGAAAGAGAAAgtatgcact---tcccttacaatcatccat--atc-tcttatgaagttgtttgttttctttgcagtgatgttttgccttgcgagttgttttccgtctatgcaaaca

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|44900865|gb|CK827410.1|CK827410

EST:     AATATGCCGAAGAATGACATGAGAAATGCTATGGACAATAGAAAAAGGAA                         GATGGGCTAATTGAAGTTCTTGCGCAACTTTTCAACGGACACTGCCGGATT
genomic: AATATGCCGAAGAATGACATGAGAAATGCTATGGACAATAGAAAAAGGAAgtatgcacca ... ttcatcgcagGATGGGCTAATTGAAGTTCTTGCGCAACTTTTCAACGGACACTGCCGGATT

EST: gi|78021237|gb|DV489624.1|DV489624

EST:     AATATGCCGAAGAATGACATGAGAAATGCTATGGACAATAGAAAAAGGAA                         GATGGGCTAATTGAAGTTCTTGCGCAACTTTTCAACGGACACTGCCGGATT
genomic: AATATGCCGAAGAATGACATGAGAAATGCTATGGACAATAGAAAAAGGAAgtatgcacca ... ttcatcgcagGATGGGCTAATTGAAGTTCTTGCGCAACTTTTCAACGGACACTGCCGGATT

EST: gi|5650062|gb|AI920422.1|AI920422

EST:     AATATGCCGAAGAATGACATGAGAAATGCTATGGACAATAGAAAAAGGAA                         GATGGGCTAATTGAAGTTCTTGCGCAACTTTTCAACGGACACTGCCGGATT
genomic: AATATGCCGAAGAATGACATGAGAAATGCTATGGACAATAGAAAAAGGAAgtatgcacca ... ttcatcgcagGATGGGCTAATTGAAGTTCTTGCGCAACTTTTCAACGGACACTGCCGGATT

EST: gi|28911118|gb|CB331779.1|CB331779

EST:     AATATGCCGAAGAATGACATGAGAAATGCTATGGACAATAGAAAAAGGAA                         GATGGGCTAATTGAAGTTCTTGCGCAACTTTTCAACGGACACTGCCGGATT
genomic: AATATGCCGAAGAATGACATGAGAAATGCTATGGACAATAGAAAAAGGAAgtatgcacca ... ttcatcgcagGATGGGCTAATTGAAGTTCTTGCGCAACTTTTCAACGGACACTGCCGGATT

EST: gi|101390996|gb|EB817434.1|EB817434

EST:     AATATGCCGAAGAATGACATGAGAAATGCTATGGACAATAGAAAAAGGAA                         GATGGGCTAATTGAAGTTCTTGCGCAACTTTTCAACGGACACTGCCGGATT
genomic: AATATGCCGAAGAATGACATGAGAAATGCTATGGACAATAGAAAAAGGAAgtatgcacca ... ttcatcgcagGATGGGCTAATTGAAGTTCTTGCGCAACTTTTCAACGGACACTGCCGGATT

EST: gi|211398948|gb|FL436156.1|FL436156

EST:     AATATGCCGAAGAATGACATGAGAAATGCTATGGACAATAGAAAAAGGAA                         GATGGGCTAATTGAAGTTCTTGCGCAACTTTTCAACGGACACTGCCGGATT
genomic: AATATGCCGAAGAATGACATGAGAAATGCTATGGACAATAGAAAAAGGAAgtatgcacca ... ttcatcgcagGATGGGCTAATTGAAGTTCTTGCGCAACTTTTCAACGGACACTGCCGGATT

EST: gi|17932478|gb|BM269438.1|BM269438

EST:     AATATGCCGAAGAATGACATGAGAAATGCTATGGACAATAGAAAAAGGAA                         GATGGGCTAATTGAAGTTCTTGCGCAACTTTTCAACGGACACTGCCGGATT
genomic: AATATGCCGAAGAATGACATGAGAAATGCTATGGACAATAGAAAAAGGAAgtatgcacca ... ttcatcgcagGATGGGCTAATTGAAGTTCTTGCGCAACTTTTCAACGGACACTGCCGGATT

EST: gi|18163991|gb|BM333830.1|BM333830

EST:     AATATGCCGAAGAATGACATGAGAAATGCTATGGACAATAGAAAAAGGAA                         GATGGGCTAATTGAAGTTCTTGCGCAACTTTTCAACGGACACTGCCGGATT
genomic: AATATGCCGAAGAATGACATGAGAAATGCTATGGACAATAGAAAAAGGAAgtatgcacca ... ttcatcgcagGATGGGCTAATTGAAGTTCTTGCGCAACTTTTCAACGGACACTGCCGGATT

EST: gi|93016786|gb|EB642306.1|EB642306

EST:     AATATGCCGAAGAATGACATGAGAAATGCTATGGACAATAGAAAAAGGAA                         GATGGGCTAATTGAAGTTCTTGCGCAACTTTTCAACGGACACTGCCGGATT
genomic: AATATGCCGAAGAATGACATGAGAAATGCTATGGACAATAGAAAAAGGAAgtatgcacca ... ttcatcgcagGATGGGCTAATTGAAGTTCTTGCGCAACTTTTCAACGGACACTGCCGGATT

EST: gi|94479606|gb|EB708564.1|EB708564

EST:     AATATGCCGAAGAATGACATGAGAAATGCTATGGACAATAGAAAAAGGAA                         GATGGGCTAATTGAAGTTCTTGCGCAACTTTTCAACGGACACTGCCGGATT
genomic: AATATGCCGAAGAATGACATGAGAAATGCTATGGACAATAGAAAAAGGAAgtatgcacca ... ttcatcgcagGATGGGCTAATTGAAGTTCTTGCGCAACTTTTCAACGGACACTGCCGGATT

EST: gi|93016785|gb|EB642305.1|EB642305

EST:     AATATGCCGAAGAATGACATGAGAAATGCTATGGACAATAGAAAAAGGAA                         GATGGGCTAATTGAAGTTCTTGCGCAACTTTTCAACGGACACTGCCGGATT
genomic: AATATGCCGAAGAATGACATGAGAAATGCTATGGACAATAGAAAAAGGAAgtatgcacca ... ttcatcgcagGATGGGCTAATTGAAGTTCTTGCGCAACTTTTCAACGGACACTGCCGGATT

EST: gi|18165240|gb|BM335079.1|BM335079

EST:     AATATGCCGAAGAATGACATGAGAAATGCTATGGACAATAGAAAAAGGAA                         GATGGGCTAATTGAAGTTCTTGCGCAACTTTTCAACGGACACTGCCGGATT
genomic: AATATGCCGAAGAATGACATGAGAAATGCTATGGACAATAGAAAAAGGAAgtatgcacca ... ttcatcgcagGATGGGCTAATTGAAGTTCTTGCGCAACTTTTCAACGGACACTGCCGGATT

EST: gi|6695598|gb|AW288706.1|AW288706

EST:     AATATGCCGAAGAATGACATGAGAAATGCTATGGACAATAGAAAAAGGAA                         GATGGGCTAATTGAAGTTCTTGCGCAACTTTTCAACGGACACTGCCGGATT
genomic: AATATGCCGAAGAATGACATGAGAAATGCTATGGACAATAGAAAAAGGAAgtatgcacca ... ttcatcgcagGATGGGCTAATTGAAGTTCTTGCGCAACTTTTCAACGGACACTGCCGGATT

EST: gi|32837416|gb|CD977094.1|CD977094

EST:     AATATGCCGAAGAATGACATGAGAAATGCTATGGACAATAGAAAAAGGAA                         GATGGGCTAATTGAAGTTCTTGCGCAACTTTTCAACGGACACTGCCGGATT
genomic: AATATGCCGAAGAATGACATGAGAAATGCTATGGACAATAGAAAAAGGAAgtatgcacca ... ttcatcgcagGATGGGCTAATTGAAGTTCTTGCGCAACTTTTCAACGGACACTGCCGGATT

EST: gi|37382055|gb|CF627949.1|CF627949

EST:     AATATGCCGAAGAATGACATGAGAAATGCTATGGACAATAGAAAAAGGAA                         GATGGGCTAATTGAAGTTCTTGCGCAACTTTTCAACGGACACTGCCGGATT
genomic: AATATGCCGAAGAATGACATGAGAAATGCTATGGACAATAGAAAAAGGAAgtatgcacca ... ttcatcgcagGATGGGCTAATTGAAGTTCTTGCGCAACTTTTCAACGGACACTGCCGGATT

EST: gi|17929753|gb|BM266713.1|BM266713

EST:     AATATGCCGAAGAATGACATGAGAAATGCTATGGACAATAGAAAAAGGAA                         GATGGGCTAATTGAAGTTCTTGCGCAACTTTTCAACGGACACTGCCGGATT
genomic: AATATGCCGAAGAATGACATGAGAAATGCTATGGACAATAGAAAAAGGAAgtatgcacca ... ttcatcgcagGATGGGCTAATTGAAGTTCTTGCGCAACTTTTCAACGGACACTGCCGGATT

EST: gi|5901084|gb|AW042184.1|AW042184

EST:     AATATGCCGAAGAATGACATGAGAAATGCTATGGACAATAGAAAAAGGAA                         GATGGGCTAATTGAAGTTCTTGCGCAACTTTTCAACGGACACTGNCGGATT
genomic: AATATGCCGAAGAATGACATGAGAAATGCTATGGACAATAGAAAAAGGAAgtatgcacca ... ttcatcgcagGATGGGCTAATTGAAGTTCTTGCGCAACTTTTCAACGGACACTGCCGGATT

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), 48 (downstream exon)
Score: 53

GTGGTGCATCTGCAATGTCTCCTATGCAGTTTGTAGGAACTCCAGGCACTAATATGCCGAAGAATGACATGAGAAATGCTATGGACAATAGAAAAAGGAAgtatgcacca ... ttcatcgcagGATGGGCTAATTGAAGTTCTTGCGCAACTTTTCAACGGACACTGCCGGATTCGAGCACAGTTGCTGCCTCAGGAGCCTTATTATTTCCTTTTGTTTTAGT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 52

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 100

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 58

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGTGCATCTGCAATGTCTCCTATGCAGTTTGTAGGAACTCCAGGCACTAATATGCCGAAGAATGACATGAGAAATGCTATGGACAATAGAAAAAGGAAgtatgcaccacctcccttgcaatcatccaacagtcattttatgaagttatttgtccatgcattgttttctttccttgctattttgtctgtgctatgaaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccacctcc