ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

...ttgtaaatgaatgatcattcatacataaaaaatatggcaagtaatggaatgaagcaagtttcagctgttgctaacacacattattgattcattattgcagGCGTACCTCGAATACCACCAGATGCCTCAACTTGGGCTCCTACAACTACCTTGGCTTTGCTGCAGCAGATGAGTATTGCACACCACGTGTTATTGAGTCT

Basic information

species	Zea mays
transcript	GRMZM2G152888_T01
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G152888_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os11g31640.1 (Oryza sativa), 3'ss of exon 3

ttgtaaatgaatgatcatt-catacataaaaaatatggcaagtaatggaatgaag--------caagtttcagctgttgctaacacacattattgattcattattgcagGCGTACCTCGAATACCACCAGATGCCTCAACTTGGGCTCCTACAACTACCTTGGCTTTGCTGCAGCAGATGAGTATTGCACACCACGTGTTATTGAGTCT
    | ||  ||||| ||   | | ||| |  ||     ||  |||| ||||||         ||||||||| |||||| | | || |   ||      ||| || ||||||||| || |||||||| |||||||||||| | || |||||||| |||||||| ||||| |||||||||||||| ||||| |||| ||| || ||||||
---catatagatgattatgataaaaatatatgatccaaaaataaatgaaatgaaaaacacgcacaagtttcaactgttgtttaaactccaaat------attgtttcagGCGTACTTCAAATACCACAAGATGCCTCAACCTAGGATCCTACAATTACCTTGGATTTGCAGCAGCAGATGAGTACTGCACTCCACTTGTGATCGAGTCT

upper sequence: GRMZM2G152888_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G07250.1 (Glycine max), 3'ss of exon 3

ttgtaaatgaatgatcattcatacataaaaaatatggca-agtaatggaatgaagcaagtttcagctgttgctaacacacattattgattcatt-attgcagGCGTACCTCGAATACCACCAGATGCCTCAACTTGGGCTCCTACAACTACCTTGGCTTTGCTGCAGCAGATGAGTATTGCACACCACGTGTTATTGAGTCT
||| ||||  ||    |||  |   ||||   ||    | ||     | ||||   |  | || | ||    |    || | ||||  | |    | ||||| || ||    || |  |  |||||||| || ||||| || |||||||| ||||| ||||| ||||||||||| || ||||| || || ||  ||||  | 
ttg-aaatatatatatatttgt-tgtaaattttaatttagagcttcagcatgagaaatatatctgatgcctatttttcatactatttctcctcccaatgcagACGGACTGATAAAATAAGTAGATGCCTTAATTTGGGATCATACAACTATCTTGGTTTTGCGGCAGCAGATGAATACTGCACGCCTCGAGTAGTTGATACG

upper sequence: GRMZM2G152888_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA16G26210.1 (Glycine max), 3'ss of exon 3

ttgtaaat-gaatgatcattcatacataaaaaatatggc--aagtaatggaatgaagcaagtttcagctgttgctaacacacattattgattcattattgcagGCGTACCTCGAATACCACCAGATGCCTCAACTTGGGCTCCTACAACTACCTTGGCTTTGCTGCAGCAGATGAGTATTGCACACCACGTGTTATTGAGTCT
 |||  || |||| || |||  |  ||  ||  |   |    ||   | | ||||   |  | || | ||    |    || | ||||  |    || ||||| || ||    || |  |  |||||||| || ||||| || |||||||| ||||| ||||| ||||||||||| || ||||||||  | ||  ||||  | 
-tgtggattgaattattattattttatttaattttaagttagagctttagcatgagatatttatccgatgcctatttttcatactatt--tctcctaatgcagACGGACTGATAAAATAAGTAGATGCCTTAATTTGGGATCATACAACTATCTTGGTTTTGCGGCAGCAGATGAATACTGCACACCTAGAGTAGTTGATACG

upper sequence: GRMZM2G152888_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 3

ttgtaaatgaatgatcattcatacataaaaaatatggcaagtaatggaatgaagcaagtttcagctgttgctaacacacatta-ttgattcattat-tgcagGCGTACCTCGAATACCACCAGATGCCTCAACTTGGGCTCCTACAACTACCTTGGCTTTGCTGCAGCAGATGAGTATTGCACACCACGTGTTATTGAGTCT
 | |   || |  || ||| ||   |        |  ||       |  | |   ||   |||    ||  ||  |   || |  | ||  |||   ||||| || ||    |||| ||   ||||||| |||||||| || |||||||||||||||||||||||| | ||||| || ||||| |||||||| ||||| || 
-tatgg-tgcacaatgatttatggttgccctgatttacattctccagtgtaagctaaaactcataaatttttagtatctatcaactaatcgatttcatgcagACGAACTAGCAATATCAGTCGATGCCTTAACTTGGGATCATACAACTACCTTGGCTTTGCTGCATCGGATGAATACTGCACGCCACGTGTAATTGAATCA

upper sequence: GRMZM2G152888_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 3

ttgtaaatgaatgatcattcatacataaaaaatatggcaagtaatggaat--gaagcaagtttcagctgttgctaacacacattatt-gattcattat--tgcagGCGTACCTCGAATACCACCAGATGCCTCAACTTGGGCTCCTACAACTACCTTGGCTTTGCTGCAGCAGATGAGTATTGCACACCACGTGTTATTGAGTCT
   | ||| || | |  |  ||   |      |  ||    |  |||| |  ||  |||  |  |    ||| |    ||  | ||| | |||| | |  ||||| || ||| | || |  |  |  || || |||||||| || ||||| |||||||| ||||| ||| ||||||| |  |||||||||||||| || ||||||
---ttaataaa-gtttttgtatg-gttgcttgttgggagtctcttggattttgactcaacctgaaatatttggtggatcaattgatttggttcaatctcatgcagACGAACCACAAAGATAAGTAAGTGTCTTAACTTGGGGTCATACAATTACCTTGGATTTGCCGCATCAGATGAATTCTGCACACCACGTGTAATCGAGTCT

upper sequence: GRMZM2G152888_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ20689 (Selaginella moellendorffii), 3'ss of exon 3

ttgtaaatgaatgatcattcatacataaaaaatatgg--caagtaatggaatgaagcaagtttcagctgttgc--taacacacattattgattcattattgcagGCGTACCTCGAATACCACCAGATGCCTCAACTTGGGCTCCTACAACTACCTTGGCTTTGCTGCAGCAGATGAGTATTGCACACCACGTGTTATTGAGTCT
  |||  ||| | |   ||  |   |   |  ||     |  ||  |      |      |||| |  | | |  | |  |      || |||  || |   || ||  |||  || ||    ||||| |||||| | ||||| |||||||||||||| |||||||| || || ||||| ||||| || || || || ||||||
--gtaggtga-taactttttgtgtttggtacttagaattctcgtgcttttggaagtttcttttcgggagcttccctgatccttggattttattttttttgatagTCGGCCCTTCAAGACACGGAGATGTCTCAACCTTGGCTCTTACAACTACCTTGGATTTGCTGCCGCTGACGAGTACTGCACGCCCCGGGTGATCGAGTCT

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|211452250|gb|FK947270.1|FK947270

EST:     TGGTTTGATGTTGTTGAGCGGACCTCANAGGACAATAACAAGACACTACA                         GCGTACCTCGAATACCACCAGATGCCTCAACCTGGGCTCCTACAACT
genomic: TGGTTTGATGTTGTTGAGCGGACCTCAAAGGACAATAACAAGACACTACAgtaagtattt ... attattgcagGCGTACCTCGAATACCACCAGATGCCTCAACTTGGGCTCCTACAACT

EST: gi|211452245|gb|FK947265.1|FK947265

EST:     TGGTTTGATGTTGTTGAGCGGACCTCAAAGGACAATAACAAGACACTACA                         GCGTACCTCGAATACCACCAGATGCCTCAACCTGGGCTCCTACAACTACCT
genomic: TGGTTTGATGTTGTTGAGCGGACCTCAAAGGACAATAACAAGACACTACAgtaagtattt ... attattgcagGCGTACCTCGAATACCACCAGATGCCTCAACTTGGGCTCCTACAACTACCT

EST: gi|211527655|gb|FL070682.1|FL070682

EST:     TGGTTTGATGTTGTTGAGCGGACCTCAAAGGACAATAACAAGACACTACA                         GCGTACCTCGAATACCACCAGATGCCTCAACTTGGGCTCCTACAACTACCT
genomic: TGGTTTGATGTTGTTGAGCGGACCTCAAAGGACAATAACAAGACACTACAgtaagtattt ... attattgcagGCGTACCTCGAATACCACCAGATGCCTCAACTTGGGCTCCTACAACTACCT

EST: gi|211452252|gb|FK947272.1|FK947272

EST:     GGNTTTGATGTTGTTGAGCGGACCTCAAAGGACAATAACAAGACACTACA                         GCGTACCTCGAATACCACCAGATGCCTNCACCT-GGGCTCCCTACA-CTAC
genomic: GG-TTTGATGTTGTTGAGCGGACCTCAAAGGACAATAACAAGACACTACAgtaagtattt ... attattgcagGCGTACCTCGAATACCACCAGATGCCT-CAACTTGGGCTCC-TACAACTAC

EST: gi|76014233|gb|DT941403.1|DT941403

EST:     TGGTTTGATGTTGTTGAGCGGACCTCAAAGGACAATAACAAGACACTACA                         GCGTACCTCGAATACCACCAGATGCCTCAACTTGGGCTCCTACAACTACCT
genomic: TGGTTTGATGTTGTTGAGCGGACCTCAAAGGACAATAACAAGACACTACAgtaagtattt ... attattgcagGCGTACCTCGAATACCACCAGATGCCTCAACTTGGGCTCCTACAACTACCT

EST: gi|211452244|gb|FK947264.1|FK947264

EST:     TGGTTTGATGTTGTTGAGCGGACCTCAAAGGACAATAACAAGACACTACA                         GCGTACCTCGAATACCACCAGATGCCTCACCCTGGGCTCCCTACA-CTACC
genomic: TGGTTTGATGTTGTTGAGCGGACCTCAAAGGACAATAACAAGACACTACAgtaagtattt ... attattgcagGCGTACCTCGAATACCACCAGATGCCTCAACTTGGGCTCC-TACAACTACC

EST: gi|211452248|gb|FK947268.1|FK947268

EST:     TGGTTTGATGTTGTTGAGCGGACCTCAAAGGACAATAACAAGACACTACA                         GCGTACCTCGAATACCACCAGATGCCTCAACCTGGGCTCCTACAACTACCT
genomic: TGGTTTGATGTTGTTGAGCGGACCTCAAAGGACAATAACAAGACACTACAgtaagtattt ... attattgcagGCGTACCTCGAATACCACCAGATGCCTCAACTTGGGCTCCTACAACTACCT

EST: gi|78083290|gb|DV511683.1|DV511683

EST:     TGGTTTGATGTTGTTGAGCGGACCTCAAAGGACAATAACAAGACACTACA                         GCGTACCTCGAATACCACCAGATGCCTCAACTTGGGCTCCTACAACTACCT
genomic: TGGTTTGATGTTGTTGAGCGGACCTCAAAGGACAATAACAAGACACTACAgtaagtattt ... attattgcagGCGTACCTCGAATACCACCAGATGCCTCAACTTGGGCTCCTACAACTACCT

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), 49 (downstream exon)
Score: 115

GATTGCTTTGGTAGGCCGATCGCAAGTGCGCCAGATTCATGGTTTGATGTTGTTGAGCGGACCTCAAAGGACAATAACAAGACACTACAgtaagtattt ... attattgcagGCGTACCTCGAATACCACCAGATGCCTCAACTTGGGCTCCTACAACTACCTTGGCTTTGCTGCAGCAGATGAGTATTGCACACCACGTGTTATTGAGTCT

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 103

Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 67

Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 103

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ggaatgaagcaagtttcagctgttgctaacacacattattgattcattattgcagGCGTACCTCGAATACCACCAGATGCCTCAACTTGGGCTCCTACAACTACCTTGGCTTTGCTGCAGCAGATGAGTATTGCACACCACGTGTTATTGAGTCT

                                  attattgattcattat  TA-rich tract

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtaaatgaatgatcattcatacataaaaaatatggcaagtaatggaatgaagcaagtttcagctgttgctaacacacattattgattcattattgcagGCGTACCTCGAATACCACCAGATGCCTCAACTTGGGCTCCTACAACTACCTTGGCTTTGCTGCAGCAGATGAGTATTGCACACCACGTGTTATTGAGTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - atgaatg
- - - - - - - -cattcat
- - - - - - - - - - - - - aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - -tgaagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acacaca