ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

gtacgcagagcagtgttcttgcaacttacttgaacttttctcgttctcgtgtataccactctggttttaattctgtgtttgattttcctgtgaagCAAATATGCCATCGGGATCTGAAGCTGGAAAATACATTGTTAGATGGAAGTCCGGCACCTCGTTTGAAAATATGTGATTTTGGTTATTCCAAG

Basic information

species	Arabidopsis thaliana
transcript	AT3G50500.1
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g55600.1 (Oryza sativa), 3'ss of exon 4

---gtacgcagagcagtgttcttgcaacttacttgaacttttctcgttctcgtgtataccactctggttttaattctgtgtttgattttcctgtgaagCAAATATGCCATCGGGATCTGAAGCTGGAAAATACATTGTTAGATGGAAGTCCGGCACCTCGTTTGAAAATATGTGATTTTGGTTATTCCAAG
    | |  |   || || | ||     | |  |||   ||  ||  |     |   | |    |    | || | |     |   |    | | |||||| ||||||| || ||| ||||| |||| |||||| || | |||||||| || || || || |||||||||||||| ||||| ||||| |||
gtatttcttattacaatgattttct--ttcatctgattgttattctgtactaag-gcatcgtggtaagctgaactatcctactttctccattttcaagCAAGTATGCCACCGTGATTTGAAGTTGGAGAATACACTGCTGGATGGAAGCCCTGCTCCACGCTTGAAAATATGTGACTTTGGCTATTCTAAG

upper sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G06250.1 (Glycine max), 3'ss of exon 4

------------------------------------------------gtacgc-agagcagtgttcttgcaacttacttgaacttttctcgt-tctcgtgtataccactctggtttta-attctgtgtttgattttcctgtgaagCAAATATGCCATCGGGATCTGAAGCTGGAAAATACATTGTTAGATGGAAGTCCGGCACCTCGTTTGAAAATATGTGATTTTGGTTATTCCAAG
                                                 || || |||     ||    ||||  |  |  | |||   |  | | ||   | |         || |||  |    |  |   | | |   ||||| || | || || ||||| |||||| ||||||| || ||||| |||||||| ||||||| || |||||| |||||||||||||| || ||||||
gtaactgatctctttctccctcactatctaatataaattgtatttaacctatgccagaatgtagtataggcaatgtg-tcaatcttgagtattatgtctgatgtgatgtatgagtcttatgtatcataatatgtctcctcatgaagGAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACTTTGTTGGATGGAAGCCCGGCACTTCATTTGAAGATATGTGATTTTGGATACTCCAAG

upper sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G09460.1 (Glycine max), 3'ss of exon 4

----------------------------------------------------------------gtacgcagagcagtgttcttgcaacttacttgaacttttctcgttctcgtgtataccac-tctggttt-----taattctgtgtttgattttcctgtgaagCAAATATGCCATCGGGATCTGAAGCTGGAAAATACATTGTTAGATGGAAGTCCGGCACCTCGTTTGAAAATATGTGATTTTGGTTATTCCAAG
                                                                ||  | ||   |     | |||||  || | | | |  | |   |||  || | |  |  |||| | |     |  |  | |  |   | |      ||||||| |||| ||||||||  ||||||||||||| || ||| | ||||||||  ||||||||||||| || ||||| |||||||| || ||||||
gtaattgaacattttcccctttctgctctgtccaatctaaattgagtttacactgcactgaaatgt-tgtagtatatatgacatgcaatgtattagtattagtattactcttttgaacattatgtctgatgtatcagtcttcttataatatgtctcttcacgaagCAAGTATGTCATCGGGACTTGAAGCTGGAAAACACTTTGCTGGATGGAAGCTCGGCACCTCGTTTAAAGATATGCGATTTTGGGTACTCCAAG

upper sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G20610.4 (Glycine max), 3'ss of exon 4

--------------------------------------------------------gtacgcagagcagtgttcttgcaacttacttgaacttttctcgttc----tcgtgtataccactctggttttaattctgtgtttgattttcctgtgaagCAAATATGCCATCGGGATCTGAAGCTGGAAAATACATTGTTAGATGGAAGTCCGGCACCTCGTTTGAAAATATGTGATTTTGGTTATTCCAAG
                                                          || | |  | |   |  || ||  ||  | |  | ||    ||     |  ||| |         || ||   | | |  |   | |     | |||||| |||| ||||||||  ||||||| ||||| || ||| | |||||||| |||||||||||||| || ||||| |||||||| || ||||||
gtaattgaacattttccccttttctgttctatccaatctaaattgtgttttacacttcacactgcactgaaatgctgtaatatatgtaatgtattagtattaaacattatgtctgatgtatcagtcttg--tttataatatgtctcttcataaagCAAGTATGTCATCGGGACTTGAAGCTTGAAAACACTTTGCTGGATGGAAGCCCGGCACCTCGTTTAAAGATATGCGATTTTGGGTACTCCAAG

upper sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA01G39020.2 (Glycine max), 3'ss of exon 4

------------------gtacgcagagcagtgttcttgcaactta--cttgaacttt-tctcgttctcgtgtataccactctggtttta-attctgtgtttgattttcctgtgaagCAAATATGCCATCGGGATCTGAAGCTGGAAAATACATTGTTAGATGGAAGTCCGGCACCTCGTTTGAAAATATGTGATTTTGGTTATTCCAAG
                    ||         | |   |  ||| ||  || |||  |  | | |     ||||  | |  |   || |||       |  |   | | |   ||||| || | || || ||||| |||||| ||||||| || ||||| |||||||| ||||| | || |||||| |||||||||||||| || ||||||
gtaactgatctctttctcccacattatctgatataaatttaacctacgctagaatgtagtataggcaatgtgtcaatcttttgagtcttatgcatcataatatgtctcctcatgaagGAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACGTTGTTGGATGGAAGCCCGGCGCTTCATTTGAAGATATGTGATTTTGGATACTCCAAG

upper sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 4

------------------gtacgcagagcagtgttcttgcaacttacttgaacttttctcgttctcgtgtataccactctggttttaattctgtgtttgattttcctg-tgaagCAAATATGCCATCGGGATCTGAAGCTGGAAAATACATTGTTAGATGGAAGTCCGGCACCTCGTTTGAAAATATGTGATTTTGGTTATTCCAAG
                   | |  | |  |    ||||| || ||   |   | ||| |  | ||  |    |  |      || |    || |  |  ||| |  || ||||||||||||| || |||||  ||||| |||||||||| ||||| |||||||| || || || |||||||| |||||||||||||| || ||||||
gtatttgagcttttcttttttctgaaaaaaaaaatcttgaaaatt-tgtattcctttattctactaattccaattatataatttatctgacttttctatattcttttgatgaagCAAATATGTCACCGGGACTTGAAGTTGGAAAATACTTTGTTGGATGGAAGCCCAGCTCCACGTTTGAAGATATGTGATTTTGGGTACTCCAAG

upper sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S240_91V6.1 (Physcomitrella patens), 3'ss of exon 4

-----------gtacgcagagca----gtgttcttgcaactt---acttgaacttttctcgttctcgtgtataccactctggttttaattctgtgtttgattttcctgt-gaagCAAATATGCCATCGGGATCTGAAGCTGGAAAATACATTGTTAGATGGAAGTCCGGCACCTCGTTTGAAAATATGTGATTTTGGTTATTCCAAG
           | ||   ||       ||||| || ||| ||     ||| | ||||   ||| |  |   |    |        | || | |  | ||    | |  | | ||||||| |||||||| ||| ||||  ||||||| || ||||| ||||||||||| || ||| |  ||||||| ||||||||||| ||||| |||
gtaatgtttctgaaccttgaatcttgtgtgttgtttcaattttgagattggattttttgagttgtgattagttttccctcctgcctgatcccgaatgtgccggttcaattgcagCAAATTTGCCATCGTGATTTGAAATTGGAAAACACTTTGTTGGATGGAAGTCCTGCGCCTAGGCTGAAAATCTGTGATTTTGGGTATTCAAAG

upper sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S113_72V6.1 (Physcomitrella patens), 3'ss of exon 4

------------------gtacgcagagcagtgttcttgcaac--ttacttgaacttttctcgttctcgtgtataccactctggttttaattctgtgtttgattttcctgtgaagCAAATATGCCATCGGGATCTGAAGCTGGAAAATACATTGTTAGATGGAAGTCCGGCACCTCGTTTGAAAATATGTGATTTTGGTTATTCCAAG
                    |          ||| |    | |   ||| || |||||  |   | |    |    | ||||  |    ||||||    || |||||      ||||||| |||||||||||| ||||| ||||||||||  || | || |||||  | || ||| |  ||||||| ||||||||||| ||||| |||
gtattactctaatccttgaaattttagattatgtccagaaatcggctacctggactttatttagttttcaattcctcgctcttatcaatattctgctcgtggttttctc----agCAAATCTGCCATCGGGATTTGAAGTTGGAAAATACTCTGCTGGACGGAAGCGCCGCTCCTAGGCTGAAAATCTGTGATTTTGGATATTCGAAG

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|116422506|gb|EG465098.1|EG465098

EST:     GGTTCTTCTTTCAGCAGCTTATATCTGGATTTAGCTATTGTCATGCAATG                         CAAATATGCCATCGGGATCTGAAGCTGGAAAATACATTGTTAGATGGAAGT
genomic: GGTTCTTCTTTCAGCAGCTTATATCTGGAGTTAGCTATTGTCATGCAATGgtacgcagag ... tcctgtgaagCAAATATGCCATCGGGATCTGAAGCTGGAAAATACATTGTTAGATGGAAGT

EST: gi|164035085|gb|ES151173.1|ES151173

EST:     GGTTCTTCTTTCAGCAGCTTATATCTGGAGTTAGCTATTGTCATGCAATG                         CAAATATGCCATCGGGATC
genomic: GGTTCTTCTTTCAGCAGCTTATATCTGGAGTTAGCTATTGTCATGCAATGgtacgcagag ... tcctgtgaagCAAATATGCCATCGGGATC

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tcgttctcgtgtataccactctggttttaattctgtgtttgattttcctgtgaagCAAATATGCCATCGGGATCTGAAGCTGGAAAATACATTGTTAGATGGAAGTCCGGCACCTCGTTTGAAAATATGTGATTTTGGTTATTCCAAG

                                          ttttcctgt  CT-rich tract
                        ttttaattct  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