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

...acatcacatgtctctagaacataaatttccatgttttctctctggcagccctctttccctcactattttctttccaaacattttttcaactggaattcagGTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATG

Basic information

species	Zea mays
transcript	GRMZM5G845755_T02
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G845755_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g02350.1 (Oryza sativa), 3'ss of exon 4

--acatcacatgtctctagaacataaatttccatgttttctctctggcagccctctttccctcactattttctttccaaacattttttcaactggaattcagGTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATG
     |    || || ||  ||    ||| |||| ||||| || | ||| |||| | |   |   | |||  ||  ||     | ||||| ||||||||||||||||||||||| |||||||||||||||||||||||||||||||| |||||| |||||||||||||||| || ||||||||||||||||||
atgtttgctgtgcctgtactactctcatt-ccatattttccctgttgcatccctttctttttttttttttggttgacatgttctgtttca-ctggaattcagGTACTTCAAGGGACCTGAGCTTCTTGTTGACTTGCAAGATTATGACTACTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG

upper sequence: GRMZM5G845755_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S230_93V6.1 (Physcomitrella patens), 3'ss of exon 4

acatcacatgtctctagaacataaatttccatgttttctctctggcagccctctttccct---cactattttctttccaaacatt----ttttcaactggaattcagGTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATG
        |     ||  |  | || | |  ||||  |||  || |  | |   || |       ||| ||| |   || | |||    | |      |    | |||||||| ||||| || ||| | ||||| ||  | ||||| || ||||| ||| |||||||||||||| | || ||||||||||||||||||
------ggttctattatgattttaagtact-tgttccctcagtgtcgtcacgtctttcagggatgctagtttttgctcatatattgcagtgtctcttcgtgtattagGTACTTTAAGGGCCCAGAGTTACTTGTCGATCTTCAAGACTACGATTATTCTTTGGACATGTGGAGTTTAGGATGCATGTTTGCTGGAATG

upper sequence: GRMZM5G845755_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S63_208V6.1 (Physcomitrella patens), 3'ss of exon 5

acatcacatgtctctagaacataaatttccatgttttct-ctctggcagccctctttccctcactattttctttccaaacattttttcaact--ggaattcagGTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATG
    |  || ||| |    |   | |    |   |   | |  || || |    |     |   |  || |  |  |||  || |||    |  || |   || ||||||||||| |||||| | || || ||  | ||||||||||| ||||| || || ||||||||  |||| |||||||||||||| |||
---acttatttctttcatgctccagtaggtactctgaatgcgttgtcaacttcatgctgtttttttcttgccatttaaaacttgttttggttttgggaaatagATACTTCAAGGGCCCTGAGTTGCTGGTGGATCTCCAAGATTATGACTACTCCCTTGATATGTGGAGCTTGGGATGCATGTTTGCTGGCATG

upper sequence: GRMZM5G845755_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S165_119V6.1 (Physcomitrella patens), 3'ss of exon 5

--aca-tcacatgtctctagaaca-taaatttccatg-ttttctctctggcagccctctttccctcactattttctttccaaacattttttcaactggaattcagGTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATG
  ||| |||||  ||| ||    | | || ||   || |||| ||| | | |    |  |     |  |   |    ||   ||| |||||     || |  |||||||||||||||||||||||| || |||||  | |||||||||||||||||||| |||||||||||  |||| ||||||||||| || |||
gaacagtcacagttctataatgtaatgaactttactgattttatcttttgtatgtttagtagatacgatgcatctcatcttcacagttttt-----gggaaacagGTACTTCAAGGGTCCTGAGCTGCTGGTTGATCTTCAAGATTATGATTACTCTCTCGACATGTGGAGCTTGGGGTGCATGTTTGCCGGCATG

upper sequence: GRMZM5G845755_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ20478 (Selaginella moellendorffii), 3'ss of exon 4

acatcacatgtctctagaacataaatttccatgttttctctctggcagccctctttccctcactattttctttccaaacattttttcaactggaattcagGTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATG
                         |    | |   |  || ||   |   |||      || || ||| | | |   |  || |        |  |||| |||||||| ||||| ||||| ||||| ||| |||| || || ||||||||||| ||||||||||| || ||||||||||| |||||||||
----------------------gtgtggaaaaggcgttgct-tgaatgtgatctcaattccaataatttgtgtgctgtcgcttctc-------acgtcagATACTTCAAAGGTCCGGAGCTGCTTGTGGACCTGCAGGACTACGATTACTCTCTCGACATGTGGAGCCTAGGCTGCATGTTCGCTGGAATG

upper sequence: GRMZM5G845755_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ28543 (Selaginella moellendorffii), 3'ss of exon 4

acatcacatgtctctagaacataaatttccatgttttctctctggcagccctctttccctcactattttctttccaaacattttttcaactggaattcagGTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATG
                         |    | |   |  || ||   |   |||      || |  ||| | | |      || |        |  |||| |||||||| ||||| ||||| ||||| ||| |||| || || ||||||||||| ||||||||||| || ||||||||||| |||||||||
----------------------gtgtggaaaaggcgttgct-tgaatgtgatctcaattccaatcatttgtgtgctgttgcttctc-------acgtcagATACTTCAAAGGTCCGGAGCTGCTTGTGGACCTGCAGGACTACGATTACTCTCTCGACATGTGGAGCCTAGGCTGCATGTTCGCTGGAATG

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|31359089|gb|CD443446.1|CD443446

EST:     GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCCTCCAG                         GTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
genomic: GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCCTCCAGgtagctgcag ... tggaattcagGTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC

EST: gi|31355313|gb|CD439670.1|CD439670

EST:     GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCCTCCAG                         GTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
genomic: GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCCTCCAGgtagctgcag ... tggaattcagGTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC

EST: gi|60345260|gb|DN212233.1|DN212233

EST:     GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCCTCCAG                         GTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
genomic: GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCCTCCAGgtagctgcag ... tggaattcagGTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC

EST: gi|60350778|gb|DN217751.1|DN217751

EST:     CATCCTGGCAAGGAATATAATGTCCGTGTTGCCTCCAG                         GTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
genomic: CATCCTGGCAAGGAATATAATGTCCGTGTTGCCTCCAGgtagctgcag ... tggaattcagGTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC

EST: gi|61117731|gb|DN558692.1|DN558692

EST:     TATCATCCTGCCTAGGAATATAATGTCCGTGTTGCCTCCAG                         GTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
genomic: TATCATCCTGGCAAGGAATATAATGTCCGTGTTGCCTCCAGgtagctgcag ... tggaattcagGTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC

EST: gi|61117730|gb|DN558691.1|DN558691

EST:     CTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCCTCCAG                         GTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
genomic: CTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCCTCCAGgtagctgcag ... tggaattcagGTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC

EST: gi|31355927|gb|CD440284.1|CD440284

EST:     GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCCTCCAG                         GTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
genomic: GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCCTCCAGgtagctgcag ... tggaattcagGTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC

EST: gi|61117732|gb|DN558693.1|DN558693

EST:     TATCATCCTGGCAAGGAATATAATGTCCGTGTTGCCTCCAG                         GTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
genomic: TATCATCCTGGCAAGGAATATAATGTCCGTGTTGCCTCCAGgtagctgcag ... tggaattcagGTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC

EST: gi|61117733|gb|DN558694.1|DN558694

EST:     TATCATCCTGGCAAGGAATATAATGTCCGTGTTGCCTCCAG                         GTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
genomic: TATCATCCTGGCAAGGAATATAATGTCCGTGTTGCCTCCAGgtagctgcag ... tggaattcagGTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC

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: 146

TTATGATAGATCATGAGCTTCGGAAACTCCGGCTGATAGACTGGGGCCTTGCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCCTCCAGgtagctgcag ... tggaattcagGTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATG

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 92

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 132

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 108

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

cagccctctttccctcactattttctttccaaacattttttcaactggaattcagGTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATG

           ccctcac  putative branch site (score: 108)
                              aaacattttttcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acatcacatgtctctagaacataaatttccatgttttctctctggcagccctctttccctcactattttctttccaaacattttttcaactggaattcagGTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - cacatgt
- - - - - - - - -aacataa
- - - - - - - - - - - - - - -catgttt