ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TGATATTGGTCAGTTCCATCCTGATGGGTGCCTTGAGATTATTGACAGGAAAAAAGATATAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAGgtttgtttgttagttttttttaaaaaaaattcctactgtgaatattttgttgaacgagtgatttaccgtctctctttgcag

Basic information

species	Zea mays
transcript	GRMZM5G840955_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G840955_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g25310.1 (Oryza sativa), 5'ss of exon 10

TGATATTGGTCAGTTCCATCCTGATGGGTGCCTTGAGATTATTGACAGGAAAAAAGATATAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAGgtttgtttgttagttttttttaaaaaaaattcctactgtgaatattttgttgaacgagtgatttaccgtctctctttgcag-------------------
 |||||||| ||||||||||||||||||||||| ||||| ||||| || ||||| ||||||||||| |||||||||||||||||||||||||||||||||||||| ||   |   |   | ||  |  ||   || | |   | || | ||  |    |  |  |||  |||||| |   |                   
AGATATTGGCCAGTTCCATCCTGATGGGTGCCTCGAGATCATTGATAGAAAAAAGGATATAGTAAAACTTCAGCATGGAGAATATGTGTCTCTTGGCAAGgtttggttacaatagtgcctcaaccattatgggtattct---ttttgtattataattatattaaaccccctctctctctcgttctctctggcctttacag

upper sequence: GRMZM5G840955_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA20G07280.1 (Glycine max), 5'ss of exon 9

TGATATTGGTCAGTTCCATCCTGATGGGTGCCTTGAGATTATTGACAGGAAAAAAGATATAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAGgt-----------ttgtttgttagttttt---tttaaaaaaaattcctactgtgaata---------ttttgttgaacg------agtgattta-ccgtctctc-tttgcag
||||||||| || ||||| |||||||| || ||||| || || || ||||| |||||||| || || ||||| |||||||||||| | ||||| || |||||           |   ||||| |||||    | |  | ||| | | |||     ||          ||||  ||  |       |||| ||||    |  ||   ||||||
TGATATTGGGCAATTCCACCCTGATGGATGTCTTGAAATCATAGATAGGAAGAAAGATATTGTCAAACTTCAACATGGAGAATATATCTCTCTCGGAAAGgtaactcaaaccataccttgttcgttttggagtctggataaagtacttacaccagatccacagtaactttttctgggccttacgtagtgttttaattatgacttacttgcag

upper sequence: GRMZM5G840955_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA13G11700.1 (Glycine max), 5'ss of exon 10

TGATATTGGTCAGTTCCATCCTGATGGGTGCCTTGAGATTATTGACAGGAAAAAAGATATAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAGgt-------ttgtttgttagttttt---tttaaaaaaaattcctactgtgaatattttgttgaa----cgagtgatt-taccgt-ctctctttgcag-----------
 |||||||| || |||||||||||||| || ||||| || || || ||||| |||||||| || || ||||| |||||||||||| | |||||||| |||||       |   |||||  || |    | |  |  || | |  ||     || |   ||   |    | || | ||  | | |  | || ||               
CGATATTGGGCAATTCCATCCTGATGGATGTCTTGAAATCATAGATAGGAAGAAAGATATTGTCAAACTTCAACATGGAGAATATATATCTCTTGGAAAGgtaaagcaataccttgttcattctggaatctggatgaagtgctgacacaagatctgcagtaacattttctagggcttacatcatgttttcattatgacttgcttgcag

upper sequence: GRMZM5G840955_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA20G07060.1 (Glycine max), 5'ss of exon 9

TGATATTGGTCAGTTCCATCCTGATGGGTGCCTTGAGATTATTGACAGGAAAAAAGATATAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAGgtttgtttgttagttttttttaaaaaaaattcctactgtgaatattttgttgaa---cgagtgatttaccgtctctctttgcag-----------------------------
 ||||| || || |||||||||||||| || ||||| || || || ||||| || ||||| || || |||||||||||||||||||| ||||| || ||||||  |    ||    || | |    | | ||  | ||  |||| |      |    | ||||| ||      |  ||    ||                             
GGATATCGGACAATTCCATCCTGATGGATGTCTTGAAATCATAGATAGGAAGAAGGATATTGTCAAACTTCAGCATGGAGAATATGTCTCTCTCGGAAAGgttactcaaatataccttgtcattttagaatctgaatg-aaatactgccacaagtttctagtgaatttttcaattcctacatagtgatttcattttttttctcttaattgcag

upper sequence: GRMZM5G840955_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv12s0057g01270.t01 (Vitis vinifera), 5'ss of exon 10

TGATATTGGTCAGTTCCATCCTGATGGGTGCCTTGAGATTATTGACAGGAAAAAAGATATAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAGgtttgt--------ttgttagttttttttaa---aaaaaattcctactgt---gaatattttgttgaacgagtgatttaccgtctctctttgcag-----------------
||| ||||| ||||| || ||| |||| |||||||| || ||||||||||| || ||||| || || || ||||||||||||||| | || ||||| |||||||||        |   ||||  || || |   |  | |  ||| ||     |||    | | || |   ||  ||    ||| ||||||                     
TGACATTGGACAGTTTCAACCTAATGGTTGCCTTGAAATAATTGACAGGAAGAAGGATATTGTTAAACTACAGCATGGAGAATATATCTCCCTTGGGAAGgtttgtactggatttgactagtacttcttgattgaggataccccttctcatcagaagggatagctgtaatcgtttttggaagtcactctttatgtttgtccatgctttgcag

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|32868300|gb|CF007982.1|CF007982

EST:     AAAAAGATATAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAG                         GTTGAATCGGCTCTAGCAACAAGCAACTATGTGGAGAACATCATGGTTTAT
genomic: AAAAAGATATAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAGgtttgtttgt ... ctctttgcagGTTGAATCGGCTCTAGCAACAAGCAACTATGTGGAGAACATCATGGTTTAT

EST: gi|67018930|gb|CO447679.1|CO447679

EST:     AAAAAGATATAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAG                         GTTGAATCGGCTCTAGCAACAAGCAACTATGTGGAGAACATCATGGTTTAT
genomic: AAAAAGATATAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAGgtttgtttgt ... ctctttgcagGTTGAATCGGCTCTAGCAACAAGCAACTATGTGGAGAACATCATGGTTTAT

EST: gi|22715395|gb|BU197739.1|BU197739

EST:     AAAAAGATATAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAG                         GTTGAATCGGCTCTAGCAACAAGCAACTATGTGGAGAACATCATGGTTTAT
genomic: AAAAAGATATAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAGgtttgtttgt ... ctctttgcagGTTGAATCGGCTCTAGCAACAAGCAACTATGTGGAGAACATCATGGTTTAT

EST: gi|211013565|gb|FL361178.1|FL361178

EST:     AAAAAGATATAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAG                         GTTGAATCGGCTCTAGCAACAAGCAACTATGTGGAGAACATCATGGTTTAT
genomic: AAAAAGATATAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAGgtttgtttgt ... ctctttgcagGTTGAATCGGCTCTAGCAACAAGCAACTATGTGGAGAACATCATGGTTTAT

EST: gi|38229819|gb|CF920132.1|CF920132

EST:     AAAAAGATACAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAG                         GTTGAATCGGCTCTAGCAACAAGCAACTATGTGGAGAACATCATGGTTTAT
genomic: AAAAAGATATAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAGgtttgtttgt ... ctctttgcagGTTGAATCGGCTCTAGCAACAAGCAACTATGTGGAGAACATCATGGTTTAT

EST: gi|60358827|gb|DN225800.1|DN225800

EST:     AAAAAGATATAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAG                         GTTGAATCGGCTCTAGCAACAAGCAACTATGTGGAGAACATCATGGTTTAT
genomic: AAAAAGATATAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAGgtttgtttgt ... ctctttgcagGTTGAATCGGCTCTAGCAACAAGCAACTATGTGGAGAACATCATGGTTTAT

EST: gi|5761807|gb|AI966960.1|AI966960

EST:     AAAAAGATATAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAG                         GTTGAATCGGCTCTAGCAACAAGCAACTATGTGGAGAACATCATGGTTTAT
genomic: AAAAAGATATAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAGgtttgtttgt ... ctctttgcagGTTGAATCGGCTCTAGCAACAAGCAACTATGTGGAGAACATCATGGTTTAT

EST: gi|87156299|gb|DY401088.1|DY401088

EST:     AAAAAGATATAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAG                         GTTGAATCGGCTCTAGCAACAAGCAACTATGTGGAGAACATCATGGTTTAT
genomic: AAAAAGATATAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAGgtttgtttgt ... ctctttgcagGTTGAATCGGCTCTAGCAACAAGCAACTATGTGGAGAACATCATGGTTTAT

EST: gi|26559525|gb|CA831760.1|CA831760

EST:     AAAAAGATATAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAG                         GTTGAATCGGCTCTAGCAACAAGCAACTATGTGGAGAACATCATGGTTTAT
genomic: AAAAAGATATAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAGgtttgtttgt ... ctctttgcagGTTGAATCGGCTCTAGCAACAAGCAACTATGTGGAGAACATCATGGTTTAT

EST: gi|211176149|gb|FL381702.1|FL381702

EST:     AAAAAGATATAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAG                         GTTGAATCGGCTCTAGCAACAAGCAACTATGTGGAGAACATCATGGTTTAT
genomic: AAAAAGATATAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAGgtttgtttgt ... ctctttgcagGTTGAATCGGCTCTAGCAACAAGCAACTATGTGGAGAACATCATGGTTTAT

EST: gi|71764388|gb|DR962325.1|DR962325

EST:     AAAAAGATATAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAG                         GTTGAATCGGCTCTAGCAACAAGCAACTATGTGGAGAACATCATGGTTTAT
genomic: AAAAAGATATAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAGgtttgtttgt ... ctctttgcagGTTGAATCGGCTCTAGCAACAAGCAACTATGTGGAGAACATCATGGTTTAT

EST: gi|40335028|gb|CK369098.1|CK369098

EST:     AAAAAGATATAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAG                         GTTGAATCGGCTCTAGCAACAAGCAACTATGTGGAGAACATCATGGTTTAT
genomic: AAAAAGATATAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAGgtttgtttgt ... ctctttgcagGTTGAATCGGCTCTAGCAACAAGCAACTATGTGGAGAACATCATGGTTTAT

EST: gi|21809634|gb|BQ667952.1|BQ667952

EST:     AAAAAGATATAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAG                         GTTGAATCGGCTCTAGCAACAAGCAACTATGTGGAGAACATCATGGTTTAT
genomic: AAAAAGATATAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAGgtttgtttgt ... ctctttgcagGTTGAATCGGCTCTAGCAACAAGCAACTATGTGGAGAACATCATGGTTTAT

EST: gi|211524614|gb|FL412500.1|FL412500

EST:     AAAAAGATATAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAG                         GTTGAATCGGCTCTAGCAACAAGCAACTATGTGGAGAACATCATGGTTTAT
genomic: AAAAAGATATAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAGgtttgtttgt ... ctctttgcagGTTGAATCGGCTCTAGCAACAAGCAACTATGTGGAGAACATCATGGTTTAT

EST: gi|56382586|gb|CV985255.1|CV985255

EST:     AAAAAGATATAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAG                         GTTGAATCGGCTCTAGCAACAAGCAACTATGTGGAGAACATCATGGTTTAT
genomic: AAAAAGATATAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAGgtttgtttgt ... ctctttgcagGTTGAATCGGCTCTAGCAACAAGCAACTATGTGGAGAACATCATGGTTTAT

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: 514

TGATATTGGTCAGTTCCATCCTGATGGGTGCCTTGAGATTATTGACAGGAAAAAAGATATAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAGgtttgtttgt ... ctctttgcagGTTGAATCGGCTCTAGCAACAAGCAACTATGTGGAGAACATCATGGTTTATGCCGATCCATTTCATAACTACTGTGTTGCCCTGGTTGTTCCAGCGCACC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 589

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 731

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 944

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATATTGGTCAGTTCCATCCTGATGGGTGCCTTGAGATTATTGACAGGAAAAAAGATATAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAGgtttgtttgttagttttttttaaaaaaaattcctactgtgaatattttgttgaacgagtgatttaccgtctctctttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA