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

...ctcctgtttccaccaaatagaattcgttattaagctgatgtagtctttattttctatttggccaagtgctaatatttttgtgttgcctgctccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCT

Basic information

species	Zea mays
transcript	GRMZM2G152775_T02
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G152775_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os06g04800.1 (Oryza sativa), 3'ss of exon 1

ctcctgtttccaccaaatagaattcgttattaagctgatgtagtcttta---ttttctatttggcca----agtgctaatatttttgtgttgcc-tgctccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCT
        |  | | ||| ||| ||  ||||||| || |||  ||| |    || |||||||   |     | |   | |   |||||  ||   || |    || |||||||||||| || |||||||| || ||||| |||||||||||||| ||||||||||| ||||| ||||||||||||
--------ttgatccaatcgaaatcaatattaagttggtgtgctctgtctgcttgtctattttttccctttaatttaattgcctttgttatgtggtgttaattcttagGAATGTATGTGGCGAACCGTGCATCTGACAAAATTACTCAACTGACTGACAATGTGTACGTCTGCCGCTCTGGATCT

upper sequence: GRMZM2G152775_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g53060.2 (Oryza sativa), 3'ss of exon 1

ctcctgtttccaccaaatagaattcgttattaagctgatgtagtct-ttattttctatttggccaagtgctaatat-ttttgtgttgcctgctccaa---ctcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCT
    ||||   | | ||  ||| ||| | ||| | ||| ||| | | ||  ||| | ||   |       ||||||    | ||||| ||| |   |   || |||||||||||| || |||||||| || |||||||||||||| || || |||||||||||  |||| ||||||||||||
---atgttctgaaccaactgaaatcgatgttatgttgacgtactatgttggtttttgtt--actttcctttaatataccctttgttgtctggtattaattcttagGAATGTATGTGGCAAACCGTGCGTCGGACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCT

upper sequence: GRMZM2G152775_T04 (Zea mays), 3'ss of exon 1
lower sequence: AT4G31300.1 (Arabidopsis thaliana), 3'ss of exon 1

-----------------------------------------------------------------------ctcctgtttccacca-aatagaattcgttattaagctgatgtagtctttattttctatttggccaagtgctaatatttt--tgtgttgcctgct-ccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCT
                                                                        |   ||||| | |  || | |      |  ||| |   |||  | |||   |  | |   |  |  || |||  ||    | |||||     | |   | |||| ||||| ||||| || || ||||| || |||||||| ||||||||||| ||||| || ||||| ||||||||||| 
gtgagatttccccccttctctacttttctagggttttagttcctcttcgttgggtttgtatttgagttttgttttcgtttcaatcggaacaaagaataatcctaatcgattgttctatttgggtaatttagagaaagctgttaaatttgggatctgttgtaaattactcgcgcagGTATGTACGTAGCGAATCGAGCTTCTGATAAGATTACACAACTGACAGATAATGTCTACGTCTGCCGCTCTGGATCG

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|211427386|gb|FK988649.1|FK988649

EST:     CTGCTACGAGGGCGGCGTCGTCCTGGGCGCCGATTCCAGGACCAGCACTG                         GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTNCA-CTGACAGAC
genomic: CTGCTACGAGGGCGGCGTCGTCCTGGGCGCCGATTCCAGGACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACT-CAACTGACAGAC

EST: gi|89252178|gb|DY623964.1|DY623964

EST:     CTGCTACGAGGGCGGCGTCGTCCTGGGCGCCGATTCCAGGACCAGCACTG                         GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACA
genomic: CTGCTACGAGGGCGGCGTCGTCCTGGGCGCCGATTCCAGGACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACA

EST: gi|211424798|gb|FK988647.1|FK988647

EST:     CTGCTACGAGGGCGGCGTCGTCCTGGGCGCCGATTCCAGGACCAGCACTG                         GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACA
genomic: CTGCTACGAGGGCGGCGTCGTCCTGGGCGCCGATTCCAGGACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACA

EST: gi|211419584|gb|FK988617.1|FK988617

EST:     CTGCTACGAGGGCGGCGTCGTCCTGGGCGCCGATTCCAGGACCAGCACTG                         GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACA
genomic: CTGCTACGAGGGCGGCGTCGTCCTGGGCGCCGATTCCAGGACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACA

EST: gi|211422177|gb|FK988623.1|FK988623

EST:     CTGCTACGAGGGCGGCGTCGTCCTGGGCGCCGATTCCAGGACCAGCACTG                         GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACA
genomic: CTGCTACGAGGGCGGCGTCGTCCTGGGCGCCGATTCCAGGACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACA

EST: gi|211422175|gb|FK988621.1|FK988621

EST:     CTGCTACGAGGGCGGCGTCGTCCTGGGCGCCGATTCCAGGACCAGCACTG                         GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACA
genomic: CTGCTACGAGGGCGGCGTCGTCCTGGGCGCCGATTCCAGGACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACA

EST: gi|148946911|gb|EC892193.2|EC892193

EST:     CTGCTACGAGGGCGGCGTCGTCCTGGGCGCCGATTCCAGGACCAGCACTG                         GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACA
genomic: CTGCTACGAGGGCGGCGTCGTCCTGGGCGCCGATTCCAGGACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACA

EST: gi|211419582|gb|FK988615.1|FK988615

EST:     CTGCTACGAGGGCGGCGTCGTCCTNGGCTCCGATTCCAGGACCAGCACTG                         GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACA
genomic: CTGCTACGAGGGCGGCGTCGTCCTGGGCGCCGATTCCAGGACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACA

EST: gi|76925303|gb|DV170371.1|DV170371

EST:     CTGCTACGAGGGCGGCGTCCTCCTGGGCGCCGATTCCAGGACCAGCACTG                         GAATGTATGTAGCCCACCGTGCTTCCGACAAGATTTACTCAACTGACAGAC
genomic: CTGCTACGAGGGCGGCGTCGTCCTGGGCGCCGATTCCAGGACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATT-ACTCAACTGACAGAC

EST: gi|211419574|gb|FK988607.1|FK988607

EST:     CTGCTACGAGGGCGGCGTCGTCCTGGGCGCCGATTCCAGGACCAGCACTG                         GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACA
genomic: CTGCTACGAGGGCGGCGTCGTCCTGGGCGCCGATTCCAGGACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACA

EST: gi|211424796|gb|FK988645.1|FK988645

EST:     CTGCTACGAGGGCGGCGTCGTCCTGGGCGCCGATTCCAGGACCAGCACTG                         GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACA
genomic: CTGCTACGAGGGCGGCGTCGTCCTGGGCGCCGATTCCAGGACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACA

EST: gi|211424797|gb|FK988646.1|FK988646

EST:     CTGCTACGAGGGCGGCGTCGTCCTGGGCGCCGATTCCAGGACCAGCACTG                         GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACA
genomic: CTGCTACGAGGGCGGCGTCGTCCTGGGCGCCGATTCCAGGACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACA

EST: gi|161589696|gb|EY963443.1|EY963443

EST:     CTGCTACGAGGGCGGCGTCGTCCTGGGCGCCGATTCCAGGACCAGCACTG                         GAATGTATGTAGCCAACCGTGTCTTCA
genomic: CTGCTACGAGGGCGGCGTCGTCCTGGGCGCCGATTCCAGGACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTG-CTTCA

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: 397

GAGGCTCCGACCACCGGGGAGCACCGGATGGGGACTACCATCGTCGGGGTCTGCTACGAGGGCGGCGTCGTCCTGGGCGCCGATTCCAGGACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCT

Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 288

Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 344

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 381

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tttattttctatttggccaagtgctaatatttttgtgttgcctgctccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCT

                     tgctaat  putative branch site (score: 381)
                                        cctgctcc  putative PPT
                        taatatttttgtgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcctgtttccaccaaatagaattcgttattaagctgatgtagtctttattttctatttggccaagtgctaatatttttgtgttgcctgctccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCT

ctcctgt
- - - - -ccaccaa
- - - - - - - - - - - - - - - - -gctgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caagtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcctgc