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

...tgcagatggatttgctggaattcactttctttagccaatcagtatttgctgtttaaaatgtgtctcaaatctcaatccaagtacctttccttttgagcagCTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTCTACCTGGGAAGTTCCTGAAGCTCCTTGGTTTTTTGGCCTTGTCTCGGCT

Basic information

species	Zea mays
transcript	GRMZM5G809546_T01
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G809546_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g15460.2 (Oryza sativa), 3'ss of exon 2

----tgcagatggatttgctggaattcacttt-----ctttagccaatcagtatttgctgtttaaaatgtgtctcaaatctcaatccaagtacctttccttttgagcagCTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTCTACCTGGGAAGTTCCTGAAGCTCCTTGGTTTTTTGGCCTTGTCTCGGCT
    | |  |        |  |||  ||   |      |||| ||||  || |||  || |||||||||||||| ||        |||||||  || |||||||||||||||||||||| ||||| ||||||||||||||||||||||||||||| |||||||||||||||||| ||||||||||||||| ||||||||||||||| ||
aggttcccaaccctcactcctgaacgcagcctaataagtttaaccaactagaattc-ctatttaaaatgtgtcttaa-------cccaagtag-ttcccttttgagcagCTGCAATTGAAGATAGTTCCATTGACATTGGTGACTTCTTCAAGGGTCCTCTACCTGGGAAGTTCTTGAAGCTCCTTGGTTATTTGGCCTTGTCTCGACT

upper sequence: GRMZM5G809546_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA06G30020.1 (Glycine max), 3'ss of exon 2

------------tgcagatggatttgctggaattcactttctttagccaatcagtatttgctgtttaaaatgtgtctcaaatctcaatccaagtacctttccttttgagcagCTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTCTACCTGGGAAGTTCCTGAAGCTCCTTGGTTTTTTGGCCTTGTCTCGGCT
            |    ||  || |  ||||        |  | ||    |  |||| | ||    | |  |  |     | || | |   | |   |||   | |  ||||||||||| |||||||| || || ||  |||||||||| || |||||||| || || |||||||| || |||||  | || ||| | ||||||||  ||||
gtatcattcttctctttatttatcttatggagcctgaaattatgagt---tttgtatctcctagcaatagaggattgttcaactgatt---attgtattttggtgttggcagCTGCAATAGAGGATAGTTCAATAGATTTTGGTGACTTTTTTAAGGGCCCACTGCCAGGGAAGTTTCTCAAGCTTTTAGGGTTTCTTGCCTTGTCAAGGCT

upper sequence: GRMZM5G809546_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv11s0065g00940.t01 (Vitis vinifera), 3'ss of exon 2

---tgcagatggatttgctggaattcactttctttagccaatcagtatttgctgtttaaaatgtgtctcaaatctcaatccaagtacctttccttttgagcagCTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTCTACCTGGGAAGTTCCTGAAGCTCCTTGGTTTTTTGGCCTTGTCTCGGCT
   ||    | || |||    |  | ||          |  ||        ||   |      ||  |  | || |     | |    | |    |||| ||||||||||||||||||| ||||||||| |||| ||||||||||| || ||  |||| || || || || |||||  | || || |||||||| || || ||
gtttgtttttagacttgtaatatgttacccataaagatctttcgtc--ccactacatgcttgttgcttttagtccctgattatgatagtgtgacattga-cagCTGCAATTGAGGATAGTTCCATTGACTTTGGGGACTTCTTCAAAGGGCCATTACCAGGAAAATTTCTAAAGCTTTTGGGGTTATTGGCCTTATCCCGCCT

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|91055592|gb|EB166010.1|EB166010

EST:     CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAG                         CTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC
genomic: CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAGgttgccaatt ... ttttgagcagCTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC

EST: gi|37419824|gb|CF647597.1|CF647597

EST:     CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCACCAG                         CTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC
genomic: CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAGgttgccaatt ... ttttgagcagCTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC

EST: gi|211153530|gb|FL067383.1|FL067383

EST:     CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAG                         CTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC
genomic: CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAGgttgccaatt ... ttttgagcagCTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC

EST: gi|71426547|gb|DR807597.1|DR807597

EST:     CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAG                         CTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC
genomic: CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAGgttgccaatt ... ttttgagcagCTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC

EST: gi|149098782|gb|EE184793.2|EE184793

EST:     CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAG                         CTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC
genomic: CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAGgttgccaatt ... ttttgagcagCTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC

EST: gi|211085341|gb|FL067379.1|FL067379

EST:     CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAG                         CTGCAATTGAGGATAGCTCCATTGACATTGGTGATTTCTTCAAGGGCCCTC
genomic: CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAGgttgccaatt ... ttttgagcagCTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC

EST: gi|148963941|gb|EE015062.2|EE015062

EST:     CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAG                         CTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC
genomic: CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAGgttgccaatt ... ttttgagcagCTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC

EST: gi|50329513|gb|CO524639.1|CO524639

EST:     CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAG                         CTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC
genomic: CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAGgttgccaatt ... ttttgagcagCTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC

EST: gi|211153529|gb|FL067382.1|FL067382

EST:     CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAG                         CTGCAATTGAGGATAGCTCCATTGACATTGGTGATTTCTTCAAGGGCCCTC
genomic: CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAGgttgccaatt ... ttttgagcagCTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC

EST: gi|149099086|gb|EE185106.2|EE185106

EST:     CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAG                         CTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC
genomic: CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAGgttgccaatt ... ttttgagcagCTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC

EST: gi|148960438|gb|EE153702.2|EE153702

EST:     CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAG                         CTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC
genomic: CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAGgttgccaatt ... ttttgagcagCTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC

EST: gi|211085340|gb|FL067378.1|FL067378

EST:     CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAG                         CTGCAATTGAGGATAGCTCCATTGACATTGGTGATTTCTTCAAGGGCCCTC
genomic: CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAGgttgccaatt ... ttttgagcagCTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC

EST: gi|148936040|gb|EC880098.2|EC880098

EST:     CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAG                         CTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC
genomic: CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAGgttgccaatt ... ttttgagcagCTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC

EST: gi|149101791|gb|EE287390.2|EE287390

EST:     CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAG                         CTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC
genomic: CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAGgttgccaatt ... ttttgagcagCTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC

EST: gi|74244984|gb|DT652898.1|DT652898

EST:     CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAG                         CTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC
genomic: CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAGgttgccaatt ... ttttgagcagCTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC

EST: gi|211153533|gb|FL067386.1|FL067386

EST:     CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAG                         CTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC
genomic: CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAGgttgccaatt ... ttttgagcagCTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC

EST: gi|78106673|gb|DV525091.1|DV525091

EST:     CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAG                         CTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC
genomic: CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAGgttgccaatt ... ttttgagcagCTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC

EST: gi|71435836|gb|DR816886.1|DR816886

EST:     CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAG                         CTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC
genomic: CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAGgttgccaatt ... ttttgagcagCTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC

EST: gi|37421532|gb|CF648466.1|CF648466

EST:     CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAG                         CTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC
genomic: CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAGgttgccaatt ... ttttgagcagCTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC

EST: gi|71315713|gb|DR794488.1|DR794488

EST:     CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAG                         CTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC
genomic: CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAGgttgccaatt ... ttttgagcagCTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC

EST: gi|148980501|gb|EE027162.2|EE027162

EST:     CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAG                         CTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC
genomic: CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAGgttgccaatt ... ttttgagcagCTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC

EST: gi|148951012|gb|EC896664.2|EC896664

EST:     CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAG                         CTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC
genomic: CAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAGgttgccaatt ... ttttgagcagCTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTC

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: 75

TCTCCCCTGTCTACCTTCTTTGGTATCATGGCGCCGGTATTTGGGAGCTCCAGCGGCGGTGGTGCAAGTAGGGAGAAGGCGTCCGGGCGAGGAGCAGCAGgttgccaatt ... ttttgagcagCTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTCTACCTGGGAAGTTCCTGAAGCTCCTTGGTTTTTTGGCCTTGTCTCGGCT

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 154

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 45

Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 54

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttgctgtttaaaatgtgtctcaaatctcaatccaagtacctttccttttgagcagCTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTCTACCTGGGAAGTTCCTGAAGCTCCTTGGTTTTTTGGCCTTGTCTCGGCT

                                    tacctttcctttt  CT-rich tract
      tttaaaatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcagatggatttgctggaattcactttctttagccaatcagtatttgctgtttaaaatgtgtctcaaatctcaatccaagtacctttccttttgagcagCTGCAATTGAGGATAGCTCCATTGACATTGGTGACTTCTTCAAGGGCCCTCTACCTGGGAAGTTCCTGAAGCTCCTTGGTTTTTTGGCCTTGTCTCGGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
-gcagatg
- - - - - tttgctg
- - - - - - - - - - - - - - - - - ccaatca
- - - - - - - - - - - - - - - - - - - - - - - tgctgtt