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

gtagctgcagatatactaaaaactctcattgttggttcaatggctaacagcagttaattcagGTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTCTTTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGGATG

Basic information

species	Zea mays
transcript	GRMZM2G143602_T03
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G143602_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g02350.1 (Oryza sativa), 3'ss of exon 4

------------------------------------gtagctgcagatatactaaaaactctcattgttggttca-atggctaacagcagtt-aattcagGTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTCTTTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGGATG
                                     |  |||  |     ||      | |  || |||||| | |||        || |  ||||||||||||||||||| |||||||||||||||||||||||||||||||| ||||||||||||||||||||||| || |||||||||||||| |||
atgtttgctgtgcctgtactactctcattccatattttccctgttgcatccctttctttttttttttttggttgacatgttctgtttcactggaattcagGTACTTCAAGGGACCTGAGCTTCTTGTTGACTTGCAAGATTATGACTACTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG

upper sequence: GRMZM2G143602_T03 (Zea mays), 3'ss of exon 4
lower sequence: PP1S230_93V6.1 (Physcomitrella patens), 3'ss of exon 4

----------------------------------gtagctgcagatatactaaaaactctcattgttggttcaatggc-taacagcagttaat---tcagGTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTCTTTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGGATG
                                  ||  |  ||  | |   |   |  ||  || ||| |   ||     |    |  ||  |   | |||||||| ||||| || ||| | ||||| ||  | ||||| || ||||| |||||||||||||||||| | || |||||||||||||| |||
ggttctattatgattttaagtacttgttccctcagtgtcgtcacgtctttcagggatgctagtttttgctcatatattgcagtgtctcttcgtgtattagGTACTTTAAGGGCCCAGAGTTACTTGTCGATCTTCAAGACTACGATTATTCTTTGGACATGTGGAGTTTAGGATGCATGTTTGCTGGAATG

upper sequence: GRMZM2G143602_T03 (Zea mays), 3'ss of exon 4
lower sequence: PP1S165_119V6.1 (Physcomitrella patens), 3'ss of exon 5

-------------------------------------------gtagctgcagatatactaaaaactctcattgttggttcaatggctaacagcagttaattcagGTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTCTTTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGGATG
                                                || |  | || || | ||  |   | |    |  |  | |    |      |  ||||||||||||||| |||||||| || |||||  | |||||||||||||||||| | |||||||||||  |||| ||||||||||| || |||
gaacagtcacagttctataatgtaatgaactttactgattttatcttttgtatgtttagtagatacgatgcatctcatcttcacagtttttgg-----gaaacagGTACTTCAAGGGTCCTGAGCTGCTGGTTGATCTTCAAGATTATGATTACTCTCTCGACATGTGGAGCTTGGGGTGCATGTTTGCCGGCATG

upper sequence: GRMZM2G143602_T03 (Zea mays), 3'ss of exon 4
lower sequence: EFJ20478 (Selaginella moellendorffii), 3'ss of exon 4

-------------gtagctgcagatatactaaaaactctcattgttggttcaatggctaacagcagttaattcagGTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTCTTTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGGATG
             || |||    || |  |   || ||  ||  || ||      |||  |     | |  |||| |||||||| || || ||||| ||||| ||| |||| || || ||||||||| | ||||||||||| || ||||||||||| ||||| |||
gtgtggaaaaggcgttgct-tgaatgtgatctcaattccaataatttgtgt----gctgtcgcttctcacgtcagATACTTCAAAGGTCCGGAGCTGCTTGTGGACCTGCAGGACTACGATTACTCTCTCGACATGTGGAGCCTAGGCTGCATGTTCGCTGGAATG

upper sequence: GRMZM2G143602_T03 (Zea mays), 3'ss of exon 4
lower sequence: EFJ28543 (Selaginella moellendorffii), 3'ss of exon 4

-------------gtagctgcagatatactaaaaactctcattgttggttcaatggctaacagcagttaattcagGTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTCTTTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGGATG
             || |||    || |  |   || ||  ||  || ||      |||        | |  |||| |||||||| || || ||||| ||||| ||| |||| || || ||||||||| | ||||||||||| || ||||||||||| ||||| |||
gtgtggaaaaggcgttgct-tgaatgtgatctcaattccaatcatttgtgt----gctgttgcttctcacgtcagATACTTCAAAGGTCCGGAGCTGCTTGTGGACCTGCAGGACTACGATTACTCTCTCGACATGTGGAGCCTAGGCTGCATGTTCGCTGGAATG

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|211466861|gb|FL187159.1|FL187159

EST:     GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAG                         GTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
genomic: GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAGgtagctgcag ... gttaattcagGTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC

EST: gi|19822196|gb|BQ048220.1|BQ048220

EST:     GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAG                         GTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
genomic: GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAGgtagctgcag ... gttaattcagGTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC

EST: gi|21389960|gb|BQ528009.1|BQ528009

EST:     GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAG                         GTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
genomic: GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAGgtagctgcag ... gttaattcagGTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC

EST: gi|29576768|gb|CB616880.1|CB616880

EST:     GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAG                         GTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
genomic: GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAGgtagctgcag ... gttaattcagGTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC

EST: gi|20507674|gb|BQ279724.1|BQ279724

EST:     TAATGTCCGTGTTGCATCCAG                         GTGCTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
genomic: TAATGTCCGTGTTGCATCCAGgtagctgcag ... gttaattcagGTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC

EST: gi|87156472|gb|DY401261.1|DY401261

EST:     GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAG                         GTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGNCA-GATTATGATTACT
genomic: GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAGgtagctgcag ... gttaattcagGTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTG-CAAGATTATGATTACT

EST: gi|71770653|gb|DR968590.1|DR968590

EST:     GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAG                         GTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
genomic: GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAGgtagctgcag ... gttaattcagGTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC

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: 391

TTATGATAGATCATGAGCTTCGGAAACTCCGGCTGATAGACTGGGGTCTTGCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAGgtagctgcag ... gttaattcagGTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTCTTTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGGATG

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 319

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 363

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 332

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

cagatatactaaaaactctcattgttggttcaatggctaacagcagttaattcagGTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTCTTTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGGATG

     atactaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagctgcagatatactaaaaactctcattgttggttcaatggctaacagcagttaattcagGTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTCTTTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG