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

...cagaaaaagaactgaagggactacatcataaactatatttggtcttagcctaatagcctattactaattatattttattattgttttttaattcaatcagGACAACTCTTGGCTTTTGGGCTGGCCATCGCAATTCCAAAATAAGGGTTATCCTAGCACGAGTTTGGGAGAATGACACAGAGCTTGCTATCAGCAACAAC

Basic information

species	Zea mays
transcript	GRMZM2G018962_T01
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G018962_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g09430.1 (Oryza sativa), 3'ss of exon 2

cagaaaaagaactgaagggactacatcataaactatatt-tggtcttagc--ctaatagc-ctattactaattatattttattattgttttt-taattcaatcagGACAACTCTTGGCTTTTGGGCTGGCCATCGCAATTCCAAAATAAGGGTTATCCTAGCACGAGTTTGGGAGAATGACACAGAGCTTGCTATCAGCAACAAC
     ||||   | | |    || ||     || ||  | |||| | | |  ||| | || ||  ||| || | | | || || ||| ||||   ||   | ||||||||  ||||| ||||||||||||||||||||||| |||||||| || ||  | |||| ||| ||||||||||| ||||||||||||||||| ||||| 
----gaaagttgtcatgaccataaatttgtgacgatgctatggtttgaacatctatttgcactcctacaaaatttgtctt-ttgttgcttttgccatggcaacagGACAATCCTTGGATTTTGGGCTGGCCATCGCAATTCTAAAATAAGAGTCATTTTGGCACAAGTCTGGGAGAATGATACAGAGCTTGCTATCAGTAACAAT

upper sequence: GRMZM2G018962_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA09G33330.1 (Glycine max), 3'ss of exon 3

cagaaaaagaactgaagggactaca-tcataaactatatttggtcttagcctaatagcctat--tactaattatattttattattgttttttaattcaat-------cagGACAACTCTTGGCTTTTGGGCTGGCCATCGCAATTCCAAAATAAGGGTTATCCTAGCACGAGTTTGGGAGAATGACACAGAGCTTGCTATCAGCAACAAC
          ||||| |    | || | |||     | | |  | | ||   ||||| | ||  | ||| ||||   || | |   |||  |||||  ||       |||||| |||||||| || |||||||| ||||| || || ||||| || ||||| || ||||| || ||||| ||||||||||| |||| |||    ||||| 
----------actgatgatggtgcaatgatacgtagtttgttctgtaagatcaatagacaatggttctacttattgattctgaaaatttgataattttatgcttttgcagGACTACTCTTGGATTCTGGGCTGGTCATCGGAACTCTAAAATCAGAGTTATTCTTGCACGTGTGTGGGAAAATGACACAGAACTTGATATTTCAAACAAT

upper sequence: GRMZM2G018962_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA01G02630.1 (Glycine max), 3'ss of exon 3

----cagaaaaagaactgaaggga-ctacatcataaactatatttggtcttagcctaatagcctattactaattatattttattattgttttttaattcaatcagGACAACTCTTGGCTTTTGGGCTGGCCATCGCAATTCCAAAATAAGGGTTATCCTAGCACGAGTTTGGGAGAATGACACAGAGCTTGCTATCAGCAACAAC
       || || |  |     || ||  |  || ||| | |   ||  |   | |       ||||  |  | | | |||   ||   ||| |  ||    ||| || |||||||| |||||||| || ||||| || || ||||| || ||||| || ||||| || ||||| ||||||||||| |||| |||    ||||| 
atgatgcaataatatgtagtttgatctgtaagatcaac-agacaaggattctacttgcatatttattgattctgaaaatttg--ataaatttgtgctttg--cagAACTACTCTTGGATTTTGGGCCGGTCATCGTAACTCTAAAATCAGAGTTATTCTTGCACGTGTGTGGGAAAATGACACAGAACTTGATATTTCAAACAAT

upper sequence: GRMZM2G018962_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT4G38040.1 (Arabidopsis thaliana), 3'ss of exon 2

cagaaaaagaactgaagggactacatcataaactatatttggtcttagcctaatagcctattactaattatattt-tattattgttttttaattcaatcagGACAACTCTTGGCTTTTGGGCTGGCCATCGCAATTCCAAAATAAGGGTTATCCTAGCACGAGTTTGGGAGAATGACACAGAGCTTGCTATCAGCAACAAC
   |||   |           |  || |  |||| |  | | || | |  |  ||   |      |||  || |  || | ||   |  |  |   | |||||| |||||||| ||||||||||| ||||| ||||| || ||| ||||||| || || |  || ||||| || ||||||||||||| |||    ||||||
-gtaaactaagtcctccctcttttattaggaactctggtagatcctggagttgtattgttggctcaatgttactaatactgttaaatggtggtgtta-cagGACGACTCTTGGTTTTTGGGCTGGTCATCGAAATTCTAAGATACGGGTTATACTTGCTCATGTGTGGGAAAACGACACAGAGCTTGATATTTCAAACAAC

upper sequence: GRMZM2G018962_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv00s0218g00090.t01 (Vitis vinifera), 3'ss of exon 3

---cagaaaaagaactgaagggactacatcataaactatatttggtcttagcctaatagcctattacta-attatattttattattgttttttaattcaatcagGACAACTCTTGGCTTTTGGGCTGGCCATCGCAATTCCAAAATAAGGGTTATCCTAGCACGAGTTTGGGAGAATGACACAGAGCTTGCTATCAGCAACAAC
   ||        |   || | | |  ||  |||  | ||| |||    |    |    ||  |||  | |||||    ||  ||||      |       ||||||||||||||||||||||||||| ||||| || |||||||| || ||||| |||||||| || |||||||||||||| || ||||  || |  ||||||
tagcatgtttctcatacaacgaattgaat-gtaagttttatgtggatggaa---agatcccagttatgagattattgcctaaaattgagaagcatactttgcagGACAACTCTTGGCTTTTGGGCTGGTCATCGGAACTCCAAAATTAGAGTTATACTAGCACGTGTATGGGAGAATGACACTGAACTTGACATTATGAACAAC

upper sequence: GRMZM2G018962_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv03s0038g00680.t01 (Vitis vinifera), 3'ss of exon 2

--cagaaaaagaactgaagggactacatcataaactatatttggtcttagcctaatagcctattactaattatattttattattgttttttaattcaatcagGACAACTCTTGGCTTTTGGGCTGGCCATCGCAATTCCAAAATAAGGGTTATCCTAGCACGAGTTTGGGAGAATGACACAGAGCTTGCTATCAGCAACAAC
    |  | ||   |      | |  || |     |  |  | |  |||  ||  || |     |   |||     ||  ||||      |   |    |||||| || |||||||||||||| |||||||||||||| |||||||| ||||| ||||||||  |||||||||||||||||||||||| ||| |  ||||||
gtttgctatagttttttcttaatttaataaatgcttgcaaattgagttacactgctacctc--catggattgatcattgatattaaccagtgtattctgcagGACTACACTTGGCTTTTGGGCAGGCCATCGCAATTCAAAAATAAGAGTTATACTAGCACGTATTTGGGAGAATGACACAGAGCTTGATATAAAAAACAAC

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|71761056|gb|DR958993.1|DR958993

EST:     CATTTGCCCTACCTGAAAGAGGAAATGATATTGAGAACAG                         GACAACTCTTGGC-TTTGGGCTGGCCATCGCAATTCCAAAATAAGGGTTAT
genomic: CATTTGCCCTACCTGAAGGAGGAAATGATATTGAGAACAGgttagtattt ... attcaatcagGACAACTCTTGGCTTTTGGGCTGGCCATCGCAATTCCAAAATAAGGGTTAT

EST: gi|76280814|gb|DV020382.1|DV020382

EST:     GTACTACAGCCATTTGCCCTACCTGAAGGAGGAAATGATATTGAGAACAG                         GACAACTCTTGGCTTTTGGGCTGGCCATCGCAATTCCAAAATAAGGGTTAT
genomic: GTACTACAGCCATTTGCCCTACCTGAAGGAGGAAATGATATTGAGAACAGgttagtattt ... attcaatcagGACAACTCTTGGCTTTTGGGCTGGCCATCGCAATTCCAAAATAAGGGTTAT

EST: gi|76280815|gb|DV020383.1|DV020383

EST:     GTACTACAGCCATTTGCCCTACCTGAAGGAGGAAATGATATTGAGAACAG                         GACAACTCTTGGCTTTTGGGCTGGNCATCGCAATTC
genomic: GTACTACAGCCATTTGCCCTACCTGAAGGAGGAAATGATATTGAGAACAGgttagtattt ... attcaatcagGACAACTCTTGGCTTTTGGGCTGGCCATCGCAATTC

EST: gi|76293222|gb|DV032790.1|DV032790

EST:     GTACTACAGCCATTTGCCCTACCTGAAGGAGGAAATGATATTGAGAACAG                         GACAACTCTTGGCTTTTGGGCTGGCCATCGCAATTCCAAAATAAGGGTTAT
genomic: GTACTACAGCCATTTGCCCTACCTGAAGGAGGAAATGATATTGAGAACAGgttagtattt ... attcaatcagGACAACTCTTGGCTTTTGGGCTGGCCATCGCAATTCCAAAATAAGGGTTAT

EST: gi|71430658|gb|DR811708.1|DR811708

EST:     GTACTACAGCCATTTGCCCTACCTGAAGGAGGAAATGATATTGAGAACAG                         GACAACTCTTGGCTTTTGGGCTGGCCATCGCAATTCCAAAATAAGGGTTAT
genomic: GTACTACAGCCATTTGCCCTACCTGAAGGAGGAAATGATATTGAGAACAGgttagtattt ... attcaatcagGACAACTCTTGGCTTTTGGGCTGGCCATCGCAATTCCAAAATAAGGGTTAT

EST: gi|76293223|gb|DV032791.1|DV032791

EST:     GTACTACAGCCATTTGCCCTACCTGAAGGAGGAAATGATATTGAGAACAG                         GACAACTCTTGNCTTTTGGGCTGGCCATCGCAATTCCAAA
genomic: GTACTACAGCCATTTGCCCTACCTGAAGGAGGAAATGATATTGAGAACAGgttagtattt ... attcaatcagGACAACTCTTGGCTTTTGGGCTGGCCATCGCAATTCCAAA

EST: gi|93283874|gb|EB676138.1|EB676138

EST:     GTACTACAGCCATTTGCCCTACCTGAAGGAGGAAATGATATTGAGAACAG                         GACAACTCTTGGCTTTTGGGCTGGCCATCGCAATTCCAAA
genomic: GTACTACAGCCATTTGCCCTACCTGAAGGAGGAAATGATATTGAGAACAGgttagtattt ... attcaatcagGACAACTCTTGGCTTTTGGGCTGGCCATCGCAATTCCAAA

EST: gi|71770728|gb|DR968665.1|DR968665

EST:     GTACTACAGCCATTTGCCCTACCTGAAGGAGGAAATGATATTGAGAACAG                         GACAACTCTTGGCTTTTGGGCTGGCC
genomic: GTACTACAGCCATTTGCCCTACCTGAAGGAGGAAATGATATTGAGAACAGgttagtattt ... attcaatcagGACAACTCTTGGCTTTTGGGCTGGCC

EST: gi|78114008|gb|DV532397.1|DV532397

EST:     GTACTACAGCCATTTGCCCTACCTGAAGGAGGAAATGATATTGAGAACAG                         GACAACTCTTGGCTTTTGGGCTGGCCATCGCAATTCCAAAATAAGGGTTAT
genomic: GTACTACAGCCATTTGCCCTACCTGAAGGAGGAAATGATATTGAGAACAGgttagtattt ... attcaatcagGACAACTCTTGGCTTTTGGGCTGGCCATCGCAATTCCAAAATAAGGGTTAT

EST: gi|71430659|gb|DR811709.1|DR811709

EST:     GTACTACAGCCATTTGCCCTACCTGAAGGAGGAAATGATATTGAAAACAG                         GACAACTCTTGGCTTTTGGGCTGGCCATCGCAATTCCAAA-TAAGGGTTAT
genomic: GTACTACAGCCATTTGCCCTACCTGAAGGAGGAAATGATATTGAGAACAGgttagtattt ... attcaatcagGACAACTCTTGGCTTTTGGGCTGGCCATCGCAATTCCAAAATAAGGGTTAT

EST: gi|78087916|gb|DV516309.1|DV516309

EST:     GTACTACAGCCATTTGCCCTACCTGAAGGAGGAAATGATATTGAGAACAG                         GACAACTCTTGGCTTTTGGGCTGGCCATCGCAATTCCAAAAT
genomic: GTACTACAGCCATTTGCCCTACCTGAAGGAGGAAATGATATTGAGAACAGgttagtattt ... attcaatcagGACAACTCTTGGCTTTTGGGCTGGCCATCGCAATTCCAAAAT

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: 40 (upstream exon), 42 (downstream exon)
Score: 10

CAAGCTATAATGTTGACTTTATACCACATAAGGATATTGCGCTTCCTCAAGTACTACAGCCATTTGCCCTACCTGAAGGAGGAAATGATATTGAGAACAGgttagtattt ... attcaatcagGACAACTCTTGGCTTTTGGGCTGGCCATCGCAATTCCAAAATAAGGGTTATCCTAGCACGAGTTTGGGAGAATGACACAGAGCTTGCTATCAGCAACAAC

Block sizes: 47 (upstream exon), 44 (downstream exon)
Score: 14

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 18

Block sizes: 38 (upstream exon), 49 (downstream exon)
Score: 14

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tagcctaatagcctattactaattatattttattattgttttttaattcaatcagGACAACTCTTGGCTTTTGGGCTGGCCATCGCAATTCCAAAATAAGGGTTATCCTAGCACGAGTTTGGGAGAATGACACAGAGCTTGCTATCAGCAACAAC

             tattactaattatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagaaaaagaactgaagggactacatcataaactatatttggtcttagcctaatagcctattactaattatattttattattgttttttaattcaatcagGACAACTCTTGGCTTTTGGGCTGGCCATCGCAATTCCAAAATAAGGGTTATCCTAGCACGAGTTTGGGAGAATGACACAGAGCTTGCTATCAGCAACAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
-agaaaaa
- - - - -aactgaa
- - - - - - - - - - ctacatc