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

...ttgaatatttattgcaaaaagttctcatcttttgtggggtcctttgcgttatatttttttattgccaataagcctcactgtttgttctcttattatgcagGCCCCATGGTAGTGATTGTGGTATAGTGAATGTGAACATACCTACTAATGGTGCTGAAATTGGTGGAGCATTTGGTGGAGAAAAAGCAGCTGGTGGTGGA

Basic information

species	Zea mays
transcript	GRMZM2G382159_T01
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G382159_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os09g26880.3 (Oryza sativa), 3'ss of exon 12

ttgaatatttattgcaaaaagttctcatcttttgtggggtcctttgcgttatatttttttat-tgccaata--agcctcactgtttgttctcttattatgcagGCCCCATGGTAGTGATTGTGGTATAGTGAATGTGAACATACCTACTAATGGTGCTGAAATTGGTGGAGCATTTGGTGGAGAAAAAGCAGCTGGTGGTGGA
    |  ||| ||  | |  | |||||  |||  |    | |  |||   |||     | |  || | ||   ||      | ||  |  ||||  | | |||||| ||||||||||| ||||| || || ||||| || || || || ||||||||||||||||||||||| |||||||||||||||||  |||||||||||
--acacctttcttttacac-gctctcagatttcttttactgccatgccccataagacatgaaatgactatggtagtgatgttcttgctcttcttgctgtacagGCCTCATGGTAGTGACTGTGGCATTGTTAATGTAAATATTCCCACAAATGGTGCTGAAATTGGTGGAGCTTTTGGTGGAGAAAAAGCTACTGGTGGTGGA

upper sequence: GRMZM2G382159_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA15G19670.4 (Glycine max), 3'ss of exon 12

---------------------------------------------------ttgaatatttattgcaaaaagttctca----tcttttgtggggtcctttgcgttatatttttttattgccaataagcctcactgttt-----gttctcttattatgcagGCCCCATGGTAGTGATTGTGGTATAGTGAATGTGAACATACCTACTAATGGTGCTGAAATTGGTGGAGCATTTGGTGGAGAAAAAGCAGCTGGTGGTGGA--------
                                                   | |  ||   | | ||  |  |    |    || | |  |  ||   | | | | |||  ||  ||    | ||    | |||  ||     ||     |||  |||||||| |  |||||||||||||||||||||||||  ||||||||||| ||||| ||||| |||||||| || |||||||||||||| ||  | ||||||||         
gtacttacaaacttatttttgtcctatcctttcgatctctgctgatgagtttggcctacacacttcagtacttgactaacactcctataagatgtttgtggtgatttatagttgcataaatagtatattttacttgttcatgggtgtgaatatggtgcaggccacgagGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGGAGCTGAGATTGGTGGTGCCTTTGGTGGAGAAAAGGCGACCGGTGGTGGCCGTGAGGC

upper sequence: GRMZM2G382159_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA15G19670.1 (Glycine max), 3'ss of exon 12

-------------------------------------------------------ttgaatatttattgcaaaaagttctca----tcttttgtggggtcctttgcgttatatttttttattgccaataagcctcactgttt-----gttctcttattatgcagGCCCCATGGTAGTGATTGTGGTATAGTGAATGTGAACATACCTACTAATGGTGCTGAAATTGGTGGAGCATTTGGTGGAGAAAAAGCAGCTGGTGGTGGA
                                                       | |  ||   | | ||  |  |    |    || | |  |  ||   | | | | |||  ||  ||    | ||    | |||  ||     ||     |||  |||||||| |  |||||||||||||||||||||||||  ||||||||||| ||||| ||||| |||||||| || |||||||||||||| ||  | |||||||| 
gtaagtacttacaaacttatttttgtcctatcctttcgatctctgctgatgagtttggcctacacacttcagtacttgactaacactcctataagatgtttgtggtgatttatagttgcataaatagtatattttacttgttcatgggtgtgaatatggtgcagGCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGGAGCTGAGATTGGTGGTGCCTTTGGTGGAGAAAAGGCGACCGGTGGTGGC

upper sequence: GRMZM2G382159_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA09G08150.2 (Glycine max), 3'ss of exon 11

-------------------------------------------------------ttgaatatttattgcaaaa----agttctcatcttttgtggggtcctttgcgttatatttttttattgccaataagcctcact-gtt------tgttctcttattatgcagGCCCCATGGTAGTGATTGTGGTATAGTGAATGTGAACATACCTACTAATGGTGCTGAAATTGGTGGAGCATTTGGTGGAGAAAAAGCAGCTGGTGGTGGA
                                                       | |  ||   | | ||  |    | |    ||| | |  |  ||   | | | | |||  ||  |     | ||    | ||| |||      |||     |  |  ||||||| |  |||||||||||||||||||||||||  ||||||||||| ||||| |||||||||||||| || |||||||||||||| ||  | |||||||| 
gtaagtactcacaaacttatttttgtcctatcctttggatctctgctaatgagtttggcctacacacttcagtacttgactaacaatcctataagatgtttgtggtgatttatagttgcacaaatagtatattttacttgttcatgggtgtaaatatggtgcgcagGCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGGAGCTGAAATTGGTGGTGCCTTTGGTGGAGAAAAGGCGACAGGTGGTGGC

upper sequence: GRMZM2G382159_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G54100.2 (Arabidopsis thaliana), 3'ss of exon 12

ttgaatatttattgcaaaaagttctcatcttttgtggggtcctttgcgttatatttttttattgccaataagcctcactgtttgttctcttattatgcagGCCCCATGGTAGTGATTGTGGTATAGTGAATGTGAACATACCTACTAATGGTGCTGAAATTGGTGGAGCATTTGGTGGAGAAAAAGCAGCTGGTGGTGGA
     ||  |  |  |||||     || |||   |       |  |    ||||  | | | ||  ||| |   | | |||   |  | ||| ||   || || |  || ||||| ||||| || ||||||||||||||||| || ||||| ||||| ||||||||||| ||||| || || |||||  |||||||||| 
----gtaagtgctataaaaa--caacaacttaactcaatctttccgaccaatataatct-actga-aattaattttaatgtg-atggttttactac-tagACCACTGGGAAGTGACTGTGGCATTGTGAATGTGAACATACCGACGAATGGAGCTGAGATTGGTGGAGCTTTTGGAGGCGAGAAAGCGACTGGTGGTGGT

upper sequence: GRMZM2G382159_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv11s0016g00900.t01 (Vitis vinifera), 3'ss of exon 12

ttgaatattta-ttgcaaaaagttctcatcttttgtggggtcctttgcgttatatttttttattgccaataagcctcactgtttgttctct--tattatgcagGCCCCATGGTAGTGATTGTGGTATAGTGAATGTGAACATACCTACTAATGGTGCTGAAATTGGTGGAGCATTTGGTGGAGAAAAAGCAGCTGGTGGTGGA
  ||| |   | |||   || ||  | |    |   ||  |  |     |  |   ||  | |  ||  | |       ||||  |       |||||| |||||| ||||| ||||| |||||||| |||||||| || |||||||| ||||| ||||| ||||||||||| ||||| |||||||| ||| |||||||||| 
--gaagaggcagttgttgaatgtcatgacacataagggattggtggatctagtgcattaatgtc-cctgtgaaatattttgttcatatatgagtattatacagGCCACATGGAAGTGACTGTGGTATTGTGAATGTAAATATACCTACAAATGGAGCTGAGATTGGTGGAGCTTTTGGGGGAGAAAAGGCAACTGGTGGTGGT

upper sequence: GRMZM2G382159_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S237_29V6.1 (Physcomitrella patens), 3'ss of exon 13

----ttgaatatttattgcaaaaagttctcatcttttgtggggtcctttgcgttatatttttttattgccaataagcctcactgtttgttctcttattatgcagGCCCCATGGTAGTGATTGTGGTATAGTGAATGTGAACATACCTACTAATGGTGCTGAAATTGGTGGAGCATTTGGTGGAGAAAAAGCAGCTGGTGGTGGA
     |||  || ||     ||      ||||      |    | |||    |   ||||||  |||   | | |    ||   | | ||||||  || ||||| ||    || |||||||||||||| || |||||||||||||| || ||||| || || ||||| |||||||| |||||||| || ||| | || || |||
attagtgacaatgtacgaggaagctacttcatgcacc-tcatttacttcatttcgaatttttacatt-ttagtgacaagcaagatgt-ttctctcgtt-tgcagACCTACAGGCAGTGATTGTGGTATTGTCAATGTGAACATACCAACCAATGGAGCGGAGATTGGGGGAGCATTCGGTGGAGAGAAGGCAACAGGGGGCGGA

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|211256040|gb|FL474139.1|FL474139

EST:     ATATTATTTTTAAGTGGCTCGG                         GCCCCATGGTAGTGATTGTGGTATAGTGAATGTGAACATACCTACTAATGG
genomic: ATATTATTTTTAAGTGGCTCGGgtaagtagct ... tattatgcagGCCCCATGGTAGTGATTGTGGTATAGTGAATGTGAACATACCTACTAATGG

EST: gi|211322923|gb|FL468805.1|FL468805

EST:     AGCAGTTCTATATTTACAAAGAGGCCAGATATTATTTTTAAGTGGCTCGG                         GCCCCATGGTAGTGATTGTGGTATAGTGAATGTGAACATACCTACTAATGG
genomic: AGCAGTTCTATGTTTACAAAGAGGCCAGATATTATTTTTAAGTGGCTCGGgtaagtagct ... tattatgcagGCCCCATGGTAGTGATTGTGGTATAGTGAATGTGAACATACCTACTAATGG

EST: gi|60358165|gb|DN225138.1|DN225138

EST:     AGCAGTTTTATATTTACAAAGTGGCCAGATATTATTTTTAAGTGGCTCGG                         GCCCCATGGTAGTGATTGTGGTATAGTGAATGTGAACATACCTACTAATGG
genomic: AGCAGTTCTATGTTTACAAAGAGGCCAGATATTATTTTTAAGTGGCTCGGgtaagtagct ... tattatgcagGCCCCATGGTAGTGATTGTGGTATAGTGAATGTGAACATACCTACTAATGG

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), 34 (downstream exon)
Score: 212

ACCTTGAAGGAAGCAATTGAAATCAATAACTCTGTTCCTCAAGGATTGAGCAGTTCTATGTTTACAAAGAGGCCAGATATTATTTTTAAGTGGCTCGGgtaagtagct ... tattatgcagGCCCCATGGTAGTGATTGTGGTATAGTGAATGTGAACATACCTACTAATGGTGCTGAAATTGGTGGAGCATTTGGTGGAGAAAAAGCAGCTGGTGGTGGA

Block sizes: 48 (upstream exon), 40 (downstream exon)
Score: 285

Block sizes: 48 (upstream exon), 34 (downstream exon)
Score: 292

Block sizes: 48 (upstream exon), 34 (downstream exon)
Score: 204

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gcgttatatttttttattgccaataagcctcactgtttgttctcttattatgcagGCCCCATGGTAGTGATTGTGGTATAGTGAATGTGAACATACCTACTAATGGTGCTGAAATTGGTGGAGCATTTGGTGGAGAAAAAGCAGCTGGTGGTGGA

                          gcctcac  putative branch site (score: 204)
                                ctgtttgttctctt  CT-rich tract
     atatttttttattgcc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgaatatttattgcaaaaagttctcatcttttgtggggtcctttgcgttatatttttttattgccaataagcctcactgtttgttctcttattatgcagGCCCCATGGTAGTGATTGTGGTATAGTGAATGTGAACATACCTACTAATGGTGCTGAAATTGGTGGAGCATTTGGTGGAGAAAAAGCAGCTGGTGGTGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - -gcaaaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttgt