ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TGTTGAAAAAAGAGGCAATTCAAAAGTTAGTGAAGTTCTTCCAAGACTGCCCAGAACAGTATTTTGTCCATATATTGGACTCTTTCTTGAAGATAATAATgtaagagtataaggcatatttcctgattagttgcaatcatgctataagacagattactgatctgtacattgtatgcatgtttcggcag

Basic information

species	Zea mays
transcript	GRMZM2G084586_T01
intron #	8
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G084586_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os04g56530.1 (Oryza sativa), 5'ss of exon 22

TGTTGAAAAAAGAGGCAATTCAAAAGTTAGTGAAGTTCTTCCAAGACTGCCCAGAACAGTATTTTGTCCATATATTGGACTCTTTCTTGAAGATAATAATgtaagagtataaggcatatttcctgattagttgcaat------------catgctataagacagattactgatctgtaca-ttgtatgcatgtttcggcag
||||||| ||||| || ||||| || ||||||||||| || ||||||||||| ||||| |||||||| |||||||||||  |||| ||||||||||| | ||||||  | |  |     |||||  ||  |  || |            ||||  |  | ||||| || |||    | || ||| ||  |  |  |  |||
TGTTGAAGAAAGATGCCATTCAGAAATTAGTGAAGTTTTTTCAAGACTGCCCTGAACAATATTTTGTTCATATATTGGATGCTTTTTTGAAGATAATCACgtaagaccaaagagttaccttcctttttgatgacattatataatatgaacatgacaggatacagaatattgagacatgcaattgcattgacttgactacag

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|60351006|gb|DN217979.1|DN217979

EST:     CCAGAACAGTATTTTGTCCATATATTGGACTCTTTCTTGAAGATAATAAT                         GAAATCTTCTAGGCTAAATACAGCAATGGCCACCAATGGCTTGACAACATT
genomic: CCAGAACAGTATTTTGTCCATATATTGGACTCTTTCTTGAAGATAATAATgtaagagtat ... gtttcggcagGAAATCTTCTAGGCTAAACACAGCAATGGCCACCAATGGCTTGACAGCATT

EST: gi|6653889|gb|AW267294.1|AW267294

EST:     TTTTGTCCATATATTGGACTCTTTCTTGAAGATAATAAT                         GAAATCTTCTAGGCTAAATACAGCAATGGCCACCAATGGCTTGACAACATT
genomic: TTTTGTCCATATATTGGACTCTTTCTTGAAGATAATAATgtaagagtat ... gtttcggcagGAAATCTTCTAGGCTAAACACAGCAATGGCCACCAATGGCTTGACAGCATT

EST: gi|18173480|gb|BM348868.1|BM348868

EST:     CCAGAACAGTATTTTGTCCATATATTGGACTCTTTCTTGAAGATAATAAT                         GAAATCTTCTAGGCTAAACACAGCAATGGCCACCAATGGCTTGACAGCATT
genomic: CCAGAACAGTATTTTGTCCATATATTGGACTCTTTCTTGAAGATAATAATgtaagagtat ... gtttcggcagGAAATCTTCTAGGCTAAACACAGCAATGGCCACCAATGGCTTGACAGCATT

EST: gi|33093532|gb|CF053526.1|CF053526

EST:     CCAGAACAGTATTTTGTCCATATATTGGACTCCTTCTTGAAGATAATAAT                         GAAATCTTCTAGGCTAAATACAGCAATGGCCACCAATGGCTTGACAACATT
genomic: CCAGAACAGTATTTTGTCCATATATTGGACTCTTTCTTGAAGATAATAATgtaagagtat ... gtttcggcagGAAATCTTCTAGGCTAAACACAGCAATGGCCACCAATGGCTTGACAGCATT

EST: gi|83278556|gb|DV942564.1|DV942564

EST:     CCAGAACAGTATTTTGTCCATATATTGGACTCTTTCTTGAAGATAATAAT                         GAAATCTTCTAGGCTAAATACAGCAATGGCCACCAATGGCTTGACAACATT
genomic: CCAGAACAGTATTTTGTCCATATATTGGACTCTTTCTTGAAGATAATAATgtaagagtat ... gtttcggcagGAAATCTTCTAGGCTAAACACAGCAATGGCCACCAATGGCTTGACAGCATT

EST: gi|31362452|gb|CD446809.1|CD446809

EST:     CCAGAACAGTATTTTGTCCATATATTGGACTCTTTCTTGAAGATAATAAT                         GAAATCTTTTAGGCTAAACACAGCAATGGCCACCAATGGCTTGACAGCATT
genomic: CCAGAACAGTATTTTGTCCATATATTGGACTCTTTCTTGAAGATAATAATgtaagagtat ... gtttcggcagGAAATCTTCTAGGCTAAACACAGCAATGGCCACCAATGGCTTGACAGCATT

EST: gi|60356264|gb|DN223237.1|DN223237

EST:     CCAGAACAGTATTTTGTCCATATATTGGACTCTTTCTTGAAGATAATAAT                         GAAATCTTCTAGGCTAAATACAGCAATGGCCACCAATGGCTTGACAACATT
genomic: CCAGAACAGTATTTTGTCCATATATTGGACTCTTTCTTGAAGATAATAATgtaagagtat ... gtttcggcagGAAATCTTCTAGGCTAAACACAGCAATGGCCACCAATGGCTTGACAGCATT

EST: gi|60337694|gb|DN204667.1|DN204667

EST:     CCAGAACAGTATTTTGTCCATATATTGGACTCTTTCTTGAAGATAATAAT                         GAAATCTTCTAGGCTAAATACAGCAATGGCCACCAATGGCTTGACAACATT
genomic: CCAGAACAGTATTTTGTCCATATATTGGACTCTTTCTTGAAGATAATAATgtaagagtat ... gtttcggcagGAAATCTTCTAGGCTAAACACAGCAATGGCCACCAATGGCTTGACAGCATT

EST: gi|78025482|gb|DV493869.1|DV493869

EST:     CCAGAACAGTATTTTGTCCATATATTGGACTCTTTCTTGAAGATAATAAT                         GAAATCTTCTAGGCTAAATACAGCAATGGCCACCAATGGCTTGACAACATT
genomic: CCAGAACAGTATTTTGTCCATATATTGGACTCTTTCTTGAAGATAATAATgtaagagtat ... gtttcggcagGAAATCTTCTAGGCTAAACACAGCAATGGCCACCAATGGCTTGACAGCATT

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: 47 (upstream exon), 48 (downstream exon)
Score: 66

TGTTGAAAAAAGAGGCAATTCAAAAGTTAGTGAAGTTCTTCCAAGACTGCCCAGAACAGTATTTTGTCCATATATTGGACTCTTTCTTGAAGATAATAATgtaagagtat ... gtttcggcagGAAATCTTCTAGGCTAAACACAGCAATGGCCACCAATGGCTTGACAGCATTGCTCATTGCAAGGCTTAACCATCGAGACGCTATTGCCCGCCTGACTCTG

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 43

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 65

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 67

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTGAAAAAAGAGGCAATTCAAAAGTTAGTGAAGTTCTTCCAAGACTGCCCAGAACAGTATTTTGTCCATATATTGGACTCTTTCTTGAAGATAATAATgtaagagtataaggcatatttcctgattagttgcaatcatgctataagacagattactgatctgtacattgtatgcatgtttcggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA