ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CATTTACAACAGAGAAACAGATCAAAGTCGTGGGTTTGGGTTTGTCACTATGAGCACTGTCGAGGAGGCTGAGAAGGCTGTGGAGATGTTCCATCGCTATgtgagtttattgatgactatcagctattaatttttttgacagattttgggtatagttatggttaatatggcctgtttgcttatgccatttgcaactcatt...

Basic information

species	Zea mays
transcript	GRMZM2G011129_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G011129_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os09g39180.1 (Oryza sativa), 5'ss of exon 2

CATTTACAACAGAGAAACAGATCAAAGTCGTGGGTTTGGGTTTGTCACTATGAGCACTGTCGAGGAGGCTGAGAAGGCTGTGGAGATGTTCCATCGCTATgtgagtttattgatgactat-cagctattaatttttttgacagattttgggtatagttatgg-ttaatatggcctgtttgcttatgccatttgcaactcatt
||| |||||||||||||||||||  |||||||| ||||| |||||||| |||||||| || |||||||||||||||||||||||||||||||||||||| |||||| | |   |  |||    ||  |   |    |  |||  || |   | | |||   | | || ||  |||| || | ||||  | || || ||||  
CATCTACAACAGAGAAACAGATCGGAGTCGTGGATTTGGATTTGTCACCATGAGCACCGTTGAGGAGGCTGAGAAGGCTGTGGAGATGTTCCATCGCTACgtgagtctctctctatctaaattgccctatttcccctcaacattttcttcattttgttgaagctcaagataacctgatttcctatgttagttacagctca--

upper sequence: GRMZM2G011129_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA06G18470.1 (Glycine max), 5'ss of exon 2

CATTTACAACAGAGAAACAGATCAAAGTCGTGGGTTTGGGTTTGTCACTATGAGCACTGTCGAGGAGGCTGAGAAGGCTGTGGAGATGTTCCATCGCTATgtgagtttattgatgactatcagctattaatttttttgacagattttgggtatagttatggttaatatggcctg-tttgcttatgccatttgcaactcatt---
 ||||| ||||| ||||| || || ||||| |||||||||||||| || ||||| ||||| || || ||||| |  ||||||||||  ||| | |||||||| |||| ||  || |||      | ||  |||         |||| |||    |   ||   |||  ||  || ||| | |||   ||||     |  ||   
TATTTATAACAGGGAAACTGACCAGAGTCGCGGGTTTGGGTTTGTGACGATGAGTACTGTTGAAGAAGCTGAAAGCGCTGTGGAGAAATTCAACCGCTATgtaagttgatatataacttg----ttttgttttcaaatgtgaatttggggggaggggttgaaaaattcggtttgattttcgtattgaatttatgtgtggttatg

upper sequence: GRMZM2G011129_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT4G24770.1 (Arabidopsis thaliana), 5'ss of exon 2

CATTTACAACAGAGAAACAGATCAAAGTCGTGGGTTTGGGTTTGTCACTATGAGCACTGTCGAGGAGGCTGAGAAGGCTGTGGAGATGTTCCATCGCTATgtgagtttat-tgat---gactatcagctattaatttttttgacagattt-tgggtatagttatggttaatatggcctgtttgcttatgccatttgcaactcatt
 || ||||| || ||||| || || |||||||||||||| ||||| || |||||  |||| || || |||||||  |||||||||| |||| | || ||||| ||||||| || |    ||| |||   |||  | ||| |||   |||     |||| || ||||   |||| ||   |||| ||  | | ||| |  |||   
TATATACAATAGGGAAACTGACCAGAGTCGTGGGTTTGGATTTGTGACAATGAGTTCTGTGGACGAAGCTGAGACAGCTGTGGAGAAGTTCAACCGTTATgtaagtttatatggttcaaactttcaatcatttctgtttctgagttattagcatgtattgtgatgg--gatattgctcctttgatttcgtccttt-ctgctct--

upper sequence: GRMZM2G011129_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv14s0066g00140.t01 (Vitis vinifera), 5'ss of exon 2

CATTTACAACAGAGAAACAGATCAAAGTCGTGGGTTTGGGTTTGTCACTATGAGCACTGTCGAGGAGGCTGAGAAGGCTGTGGAGATGTTCCATCGCTATgtgagtttattgatgactatcagctattaatttttttgacagattttgggtatagtta--tggttaatatggcctgtttgcttatgccatttgcaactcatt
 |||||||| |||||||||||||| |||||||||||||||||| | || ||||||||||| || ||||| || |||||||||||||||||| | || ||||| ||||  ||| |  ||||||   ||   ||  ||||     || ||| |     |   ||| |  |  ||        |  |           |  | ||
AATTTACAATAGAGAAACAGATCAGAGTCGTGGGTTTGGGTTTATAACAATGAGCACTGTTGAAGAGGCCGAAAAGGCTGTGGAGATGTTCAACCGATATgtaagttgcttgttttctatcaatcat--gttactttgttgttttctggtttcctgtgggtgggtggtggggaagtgaaacaaagaatgaagatgatacttt

upper sequence: GRMZM2G011129_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv17s0000g09680.t01 (Vitis vinifera), 5'ss of exon 2

CATTTACAACAGAGAAACAGATCAAAGTCGTGGGTTTGGGTTTGTCACTATGAGCACTGTCGAGGAGGCTGAGAAGGCTGTGGAGATGTTCCATCGCTATgtgagtttattgat--gactatcagctattaatttttttgacagattttgggtata-gttatggttaatatggcctgtttgcttatgccatttgcaactcatt
 |||||||| || || || |||  |||||||||||| ||||||||  | ||||| ||||| || || || || ||||||||||| ||||| ||||| |||||||||| | | ||  |  ||||    ||  |||||| ||   |||| |   |||  |  || ||| || |    | | ||  | |   |   | |      |
TATTTACAATAGGGAGACTGATAGAAGTCGTGGGTTCGGGTTTGTGTCAATGAGTACTGTTGAAGAAGCCGAAAAGGCTGTGGATATGTTTCATCGTTATgtgagttcacttatttgtttatct-tcatgcatttttgtgtttgattctctctatttggaatagttgat-taatttctgtgtatctagtaaa-gtattgtggt

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|71421598|gb|DR805510.1|DR805510

EST:     GAGATGTTCCATCGCTAT                         GATGTCAATGGAAGGCTTCTGACTGTAAATAAAGCAGCTCCTAGAGGCTCT
genomic: GAGATGTTCCATCGCTATgtgagtttat ... atgtggacagGATGTCAATGGAAGGCTTCTGACTGTAAATAAAGCAGCTCCTAGAGGCTCT

EST: gi|37394214|gb|CF634378.1|CF634378

EST:     TGAGAAGGCTGTGGAGATGTTCCATCGCTAT                         GATGTCAATGGAAGGCTTCTGACTGTAAATAAAGCAGCTCCTAGAGGCTCT
genomic: TGAGAAGGCTGTGGAGATGTTCCATCGCTATgtgagtttat ... atgtggacagGATGTCAATGGAAGGCTTCTGACTGTAAATAAAGCAGCTCCTAGAGGCTCT

EST: gi|5649975|gb|AI920335.1|AI920335

EST:     GCTGTGGAGATGTTCCATCGCTAT                         GATGTCAATGGAAGGCTTCTGACTGTAAATAAAGCAGCTCCTAGAGGCTCT
genomic: GCTGTGGAGATGTTCCATCGCTATgtgagtttat ... atgtggacagGATGTCAATGGAAGGCTTCTGACTGTAAATAAAGCAGCTCCTAGAGGCTCT

EST: gi|13382019|gb|BG458694.1|BG458694

EST:     GAGATGTTCCATCGCTAT                         GATGTCAATGGAAGGCTTCTGACTGTAAATAAAGCAGCTCCTA-AGGCTCT
genomic: GAGATGTTCCATCGCTATgtgagtttat ... atgtggacagGATGTCAATGGAAGGCTTCTGACTGTAAATAAAGCAGCTCCTAGAGGCTCT

EST: gi|45846769|gb|CN070712.1|CN070712

EST:     AGATGTTCCATCGCTAT                         GATGTCAATGGAAGGCTTCTGCCTGTAAATAAAGCAGCTCCTAGAGGCTCT
genomic: AGATGTTCCATCGCTATgtgagtttat ... atgtggacagGATGTCAATGGAAGGCTTCTGACTGTAAATAAAGCAGCTCCTAGAGGCTCT

EST: gi|18179590|gb|BM380800.1|BM380800

EST:     TGAGCACTGTCGAGCAGGCTGAGAAGGCTGTGGAGATGTTCCATCGCTAT                         GATGTCAATGGAAGGCTTCTGACTGTAAATAAAGCAGCTCCTAGAGGCTCT
genomic: TGAGCACTGTCGAGGAGGCTGAGAAGGCTGTGGAGATGTTCCATCGCTATgtgagtttat ... atgtggacagGATGTCAATGGAAGGCTTCTGACTGTAAATAAAGCAGCTCCTAGAGGCTCT

EST: gi|50337197|gb|CO532323.1|CO532323

EST:     GTGGAGATGTTCCATCGCTAT                         GATGTCAATGGAAGGCTTCTGACTGTAAATAAAGCAGCTCCTAGAGGCTCT
genomic: GTGGAGATGTTCCATCGCTATgtgagtttat ... atgtggacagGATGTCAATGGAAGGCTTCTGACTGTAAATAAAGCAGCTCCTAGAGGCTCT

EST: gi|148934224|gb|EC878245.2|EC878245

EST:     TGAGCACTGTCGAGGAGGCTGAGAAGGCTGTGGAGATGTTCCATCGCTAT                         GATGTCAATGGAAGGCTTCTGACTGTAAATAAAGCAGCTCCTAGAGGCTCT
genomic: TGAGCACTGTCGAGGAGGCTGAGAAGGCTGTGGAGATGTTCCATCGCTATgtgagtttat ... atgtggacagGATGTCAATGGAAGGCTTCTGACTGTAAATAAAGCAGCTCCTAGAGGCTCT

EST: gi|71761890|gb|DR959827.1|DR959827

EST:     TGAGCACTGTCGAGGAGGCTGAGAAGGCTGTGGAGATGTTCCATCGCTAT                         GATGTCAATGGAAGGCTTCTGACTGTAAATAAAGCAGCTCCTAGAGGCTCT
genomic: TGAGCACTGTCGAGGAGGCTGAGAAGGCTGTGGAGATGTTCCATCGCTATgtgagtttat ... atgtggacagGATGTCAATGGAAGGCTTCTGACTGTAAATAAAGCAGCTCCTAGAGGCTCT

EST: gi|40335533|gb|CK369603.1|CK369603

EST:     TGAGCACTGTTGAGGAGGCTGAGAAGGCTGTGGAGATGTTCCATCGCTAT                         GATGTCAATGGAAGGCTTCTGACTGTAAATAAAGCAGCTCCTAGAGGCTCT
genomic: TGAGCACTGTCGAGGAGGCTGAGAAGGCTGTGGAGATGTTCCATCGCTATgtgagtttat ... atgtggacagGATGTCAATGGAAGGCTTCTGACTGTAAATAAAGCAGCTCCTAGAGGCTCT

EST: gi|76017245|gb|DT944415.1|DT944415

EST:     TGAGCACTGTCGAGGAGGCTGAGAAGGCTGTGGAGATGTTCCATCGCTAT                         GATGTCAATGGAAGGCTTCTGACTGTAAATAAAGCAGCTCCTAGAGGCTCT
genomic: TGAGCACTGTCGAGGAGGCTGAGAAGGCTGTGGAGATGTTCCATCGCTATgtgagtttat ... atgtggacagGATGTCAATGGAAGGCTTCTGACTGTAAATAAAGCAGCTCCTAGAGGCTCT

EST: gi|93017347|gb|EB642867.1|EB642867

EST:     TGAGCACTGTCGAGGAGGCTGAGAAGGCTGTGGAGATGTTCCATCGCTAT                         GATGTCAATGGAAGGCTTCTGACTGTAAATAAAGCAGCTCCTAGAGGCTCT
genomic: TGAGCACTGTCGAGGAGGCTGAGAAGGCTGTGGAGATGTTCCATCGCTATgtgagtttat ... atgtggacagGATGTCAATGGAAGGCTTCTGACTGTAAATAAAGCAGCTCCTAGAGGCTCT

EST: gi|37385171|gb|CF629707.1|CF629707

EST:     TGAGCACTGTTGAGGAGGCTGAGAAGGCTGTGGAGATGTTCCATCGCTAT                         GATGTCAATGGAAGGCTTCTGACTGTAAATAAAGCAGCTCCTAGAGGCTCT
genomic: TGAGCACTGTCGAGGAGGCTGAGAAGGCTGTGGAGATGTTCCATCGCTATgtgagtttat ... atgtggacagGATGTCAATGGAAGGCTTCTGACTGTAAATAAAGCAGCTCCTAGAGGCTCT

EST: gi|71756576|gb|DR954513.1|DR954513

EST:     TGAGCACTGTCGAGGAGGCTGAGAAGGCTGTGGAGATGTTCCATCGCTAT                         GATGTCAATGGAAGGCTTCTGACTGTAAATAAAGCAGCTCCTAGAGGCTCT
genomic: TGAGCACTGTCGAGGAGGCTGAGAAGGCTGTGGAGATGTTCCATCGCTATgtgagtttat ... atgtggacagGATGTCAATGGAAGGCTTCTGACTGTAAATAAAGCAGCTCCTAGAGGCTCT

EST: gi|3157158|gb|AA979780.1|AA979780

EST:     GAGAANGCTGTGGAGATGTTCCATCGCTAT                         GATGTCAATGGAAGGCTTCTGACTGTAAATAAAGCAGCTCCTAGAGGCTCT
genomic: GAGAAGGCTGTGGAGATGTTCCATCGCTATgtgagtttat ... atgtggacagGATGTCAATGGAAGGCTTCTGACTGTAAATAAAGCAGCTCCTAGAGGCTCT

EST: gi|44900775|gb|CK827320.1|CK827320

EST:     TGAGCACTGTTGAGGAGGCTGAGAAGGCTGTGGAGATGTTCCATCGCTAT                         GATGTCAATGGAAGGCTTCTGACTGTAAATAAAGCAGCTCCTAGAGGCTCT
genomic: TGAGCACTGTCGAGGAGGCTGAGAAGGCTGTGGAGATGTTCCATCGCTATgtgagtttat ... atgtggacagGATGTCAATGGAAGGCTTCTGACTGTAAATAAAGCAGCTCCTAGAGGCTCT

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), 49 (downstream exon)
Score: 75

CATTTACAACAGAGAAACAGATCAAAGTCGTGGGTTTGGGTTTGTCACTATGAGCACTGTCGAGGAGGCTGAGAAGGCTGTGGAGATGTTCCATCGCTATgtgagtttat ... atgtggacagGATGTCAATGGAAGGCTTCTGACTGTAAATAAAGCAGCTCCTAGAGGCTCTCGTGTGGACAGACCTCCCAGACAATCTGGGCCTTCTCTCAGAATTTATG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 439

Block sizes: 43 (upstream exon), 46 (downstream exon)
Score: 43

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 118

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATTTACAACAGAGAAACAGATCAAAGTCGTGGGTTTGGGTTTGTCACTATGAGCACTGTCGAGGAGGCTGAGAAGGCTGTGGAGATGTTCCATCGCTATgtgagtttattgatgactatcagctattaatttttttgacagattttgggtatagttatggttaatatggcctgtttgcttatgccatttgcaactcatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG