ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gttaagctagcgagcaataaaatttcattgattagtataagtttatgattatctttctgaaaatactttttttttctcttcctttcagCTAATGTCTTTCATCGGGATCTTAAACCCAAAAACATATTGGCAAATGCTGATTGCAAACTCAAGATCTGTGATTTTGGACTTGCAAGAGTCGCATTCAA

Basic information

species	Arabidopsis thaliana
transcript	AT5G19010.1
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: AT5G19010.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os11g17080.1 (Oryza sativa), 3'ss of exon 2

gttaagctagcg-agcaataaaatttcattgattagtataagtt----tatgattatctttctgaaaatac-------tttttttttctcttcctttcagCTAATGTCTTTCATCGGGATCTTAAACCCAAAAACATATTGGCAAATGCTGATTGCAAACTCAAGATCTGTGATTTTGGACTTGCAAGAGTCGCATTCAA
  ||  ||       |      || |||||  | | ||||  ||    ||  |  || || |||| |  ||       |||  || | | ||   | |||| ||||| ||||| || ||||||||||| ||||| || ||||||||||||||||| || ||||| || ||||||||||| ||||||||||| || |||| 
agtagcctgatatgactgctccatctcattattcaatatattttgttatactagaattttactgatatgacagctgtctttcattatttgtttactgcagCAAATGTGTTTCACCGAGATCTTAAACCAAAAAATATTTTGGCAAATGCTGATTGTAAGCTCAAAATATGTGATTTTGGCCTTGCAAGAGTTGCTTTCAG

upper sequence: AT5G19010.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os05g05160.1 (Oryza sativa), 3'ss of exon 2

-----------gttaagctagcgagcaataaaatttcattgattagtataagtttatgattatctttctgaa--aatactttttttttctcttcctttcagCTAATGTCTTTCATCGGGATCTTAAACCCAAAAACATATTGGCAAATGCTGATTGCAAACTCAAGATCTGTGATTTTGGACTTGCAAGAGTCGCATTCAA
           |||        | |  ||     || ||   |   |   | ||| ||| | |  |||   |   || | | ||||      |  || |||| ||||| |||||||| ||||| ||||| ||||| || ||||| ||||||||||| || ||||| || |||||||| || |||||||| || || || | 
ctgtactcagtgttctatgtttgtgtgattcctatttatcagtccatccta-tttgtgactctaattcctgactgatgcatcttttgatagctttttgcagCAAATGTATTTCATCGAGATCTCAAACCAAAAAATATCTTGGCGAATGCTGATTGTAAGCTCAAAATATGTGATTTCGGCCTTGCAAGGGTAGCTTTTAG

upper sequence: AT5G19010.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G017351_T01 (Zea mays), 3'ss of exon 1

------------gttaagctagcgagcaataaaatttcattgattagtataagtttatgattatctttctgaa-aatactttttttttctcttcctttcagCTAATGTCTTTCATCGGGATCTTAAACCCAAAAACATATTGGCAAATGCTGATTGCAAACTCAAGATCTGTGATTTTGGACTTGCAAGAGTCGCATTCAA
             |    ||      || | |  ||   ||  |     |     ||  ||      | |||   || | | |||       |  || |||| ||||| || ||||| ||||| ||||| ||||| ||  |||||||||||||||| || ||||| || ||||||||||| || |||||||| || |||| 
taggggcttctcttcttactgttttccagtgag-ttctgttagtggcagtggcactaacatgcctgatatgactgatgcatctttcaatagcttattgcagCAAATGTATTCCATCGAGATCTCAAACCAAAAAATATTCTGGCAAATGCTGATTGTAAGCTCAAAATATGTGATTTTGGCCTAGCAAGAGTAGCTTTCAG

upper sequence: AT5G19010.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G089484_T01 (Zea mays), 3'ss of exon 2

-----gttaa--gctagcgagcaataaaatttcattgattagtataagt----ttatgattatctttctgaa-aatactttttttttctcttcctttcagCTAATGTCTTTCATCGGGATCTTAAACCCAAAAACATATTGGCAAATGCTGATTGCAAACTCAAGATCTGTGATTTTGGACTTGCAAGAGTCGCATTCAA
       ||   |||    | |  |    || |  ||  |  | | |||     ||  ||      | |||   || | | |||       |  || |||| ||||| |||||||| ||||| ||||| ||||| ||  |||||||||||||||| || ||||| || ||||| |||||  | |||||||| || |||||
tcattactaggggctcctaatctgtctgtttccgctgtgtccttttagtggcactaacatgcctgatatgactgatgcatctttcaatagcttattgcagCAAATGTATTTCATCGAGATCTCAAACCAAAAAATATTCTGGCAAATGCTGATTGTAAGCTCAAAATATGTGACTTTGGCTTAGCAAGAGTAGCTTTCAA

upper sequence: AT5G19010.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G10940.4 (Glycine max), 3'ss of exon 2

gttaagctagcgagcaat---aaaatttcattgattagtataagtt-tatgattatctttctgaaaatactttttttttctcttcctttcagCTAATGTCTTTCATCGGGATCTTAAACCCAAAAACATATTGGCAAATGCTGATTGCAAACTCAAGATCTGTGATTTTGGACTTGCAAGAGTCGCATTCAA
|||| | ||| ||    |    | ||| | |    ||| |||  || |||||| | || |     | |     ||| ||      |||  ||| ||||| ||||| || ||||| || || |||||||| || ||||||||||| |||||||| ||||| ||||| ||||| ||||| ||||| || |||||
gtta-gttagggaatctttcttagattgcttgctgtagcatatattatatgatca-ctgtggctgattttgaatttcttaatggacttgtagCAAATGTTTTTCACCGTGATCTAAAGCCAAAAAACATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGTGACTTTGGTCTTGCCAGAGTGGCTTTCAA

upper sequence: AT5G19010.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G28120.1 (Glycine max), 3'ss of exon 2

---------------------------gttaagctagcgagca-ataaaatt-tcattgattagtataagtt-tatgattatct---ttctgaaaatactttt----tttttctcttcctttcagCTAATGTCTTTCATCGGGATCTTAAACCCAAAAACATATTGGCAAATGCTGATTGCAAACTCAAGATCTGTGATTTTGGACTTGCAAGAGTCGCATTCAA
                            ||    ||||    | ||| | || | ||||  ||  |  |||   |  ||||| |     ||     |  ||||    || ||      |||  ||| ||||| ||||| || ||||| || || |||||||| || ||||||||||| |||||||| ||||| || || ||||| ||||| ||||| || |||||
gttagttagggaatctttcttagattgcttgctgtagcatatatatatatttgttattgcataaaactagtagcaaaattatatgatcactatggctgattttgaacttcttaatggacttgtagCAAATGTTTTTCACCGTGATCTAAAGCCAAAAAACATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGCGACTTTGGTCTTGCCAGAGTGGCTTTCAA

upper sequence: AT5G19010.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G02220.1 (Glycine max), 3'ss of exon 2

---------------------------------------------gttaagctagcgagcaataaaatttcattgattagtataagtttatgattat---ctttctgaaaatactttt----tttttctcttcctttcagCTAATGTCTTTCATCGGGATCTTAAACCCAAAAACATATTGGCAAATGCTGATTGCAAACTCAAGATCTGTGATTTTGGACTTGCAAGAGTCGCATTCAA
                                             |  |   |    |    |||  ||| |||        ||| | |   || |     |   ||    |  ||||    |||||       ||  ||| ||||| ||||| || ||||| || || ||||| || || ||||||||||| |||||||| ||||| ||||| || || ||||| ||||| || |||||
gttatgatcactatatttagctagtttttatttttagattcctaaggcagctttttcatagttaatgttttattataagagctaattattaaatcacatgatcattgtggctgattttaaactttttaatgggtttgtagCAAATGTTTTTCACCGAGATCTAAAGCCAAAAAATATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGTGACTTCGGTCTTGCCAGAGTGGCTTTCAA

upper sequence: AT5G19010.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G38510.1 (Glycine max), 3'ss of exon 1

--------------------------------------------gttaagctagcgagcaat-aaaatttcattgattagtataagtttatgattat---ctttctgaaaatactttt----tttttctcttcctttcagCTAATGTCTTTCATCGGGATCTTAAACCCAAAAACATATTGGCAAATGCTGATTGCAAACTCAAGATCTGTGATTTTGGACTTGCAAGAGTCGCATTCAA
                                             |  ||||       | | ||  ||| |||    |   ||| | |   || |     |   ||    |  ||||    |||||       ||  ||| ||||| ||||| || ||||| || || ||||| || || ||||||||||| |||||||| ||||| ||||| || || ||||| ||||| || |||||
gttatgatctttatatttagctagtttttatttttagattcctaatgcagctttttcatagttaatgttttattataaaagctaattattgaatcacatgatcattgtggctgattttaaactttttaatgggtttgtagCAAATGTATTTCACCGAGATCTAAAGCCAAAAAATATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGTGACTTCGGTCTTGCCAGAGTGGCTTTCAA

upper sequence: AT5G19010.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 2

----------------------------------------------------------------------------gttaagctagc--gagcaataaaatttcattgattagtataagtttatgattatct----------ttctgaaaatactttttttttctcttcctttc--agCTAATGTCTTTCATCGGGATCTTAAACCCAAAAACATATTGGCAAATGCTGATTGCAAACTCAAGATCTGTGATTTTGGACTTGCAAGAGTCGCATTCAA
                                                                            ||  || | ||  ||| |||||  ||| ||   ||    |  ||    |  |||            | ||||   | |  | ||| | |  | ||||   ||| |||||||||||||||||||| ||||| || ||||| || ||||||||||| |||||||||||||||||||| ||||| ||||||||||| || || ||
gttatatgatgctacaatattgtattttaactttttggccttggtttagcatactttattacaatctaattagcttgtgcagatggcatgagtaataatgttt-ataacttgaagtgggtgcccggatattcagtattccggtcctgattttgccatatttctttaattcttttgtagCAAATGTCTTTCATCGGGATCTGAAACCAAAGAACATCTTAGCAAATGCTGACTGCAAACTCAAGATCTGTGACTTTGGTCTTGCAAGAGTAGCCTTTAA

upper sequence: AT5G19010.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 2

----------gtta-agctagcgagcaataaaatttcattgattagtataagtttatgat-tatctttctgaaaatactttttttttctcttcctttcagCTAATGTCTTTCATCGGGATCTTAAACCCAAAAACATATTGGCAAATGCTGATTGCAAACTCAAGATCTGTGATTTTGGACTTGCAAGAGTCGCATTCAA
            || |  |   ||  ||||     | ||    || |  | || | |    | |   | |  |  | ||| | |||         || ||||||||| |||||||| ||||| || || || ||  |||||||||| ||||||||||| || || || |||||||||||||||||  | || || |||| 
tgaaaatgtaactatatttcaagaagaatagtggattatgatctaatgaatgtgtgtctcgtttggatgttgacgtgcttctatttgggtgatgctttagCTAATGTATTTCATCGCGATCTCAAGCCAAAGAATGTATTGGCAAACGCTGATTGCAAGCTGAAAATTTGTGATTTTGGACTTGCTCGGGTGGCTTTCAG

upper sequence: AT5G19010.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S80_71V6.2 (Physcomitrella patens), 3'ss of exon 2

-----------gttaagctagcgagcaataaaatttcattgattagtataagtttatgattatctttctgaa----aatactttttttttctcttcctttcagCTAATGTCTTTCATCGGGATCTTAAACCCAAAAACATATTGGCAAATGCTGATTGCAAACTCAAGATCTGTGATTTTGGACTTGCAAGAGTCGCATTCAA
             |   | |  ||   ||   || |  |   |   | |   ||| ||  | | ||| || |     |    ||  | ||        |||||||||||| |||||||| || || || || || ||| | |||||||| ||||| || ||||| || || ||||| |||||||||||  |||| || || | 
tcacaactctcactgtacaaaagactgatgggatgtggtcctt---tttggatttctgtctgtttttgtggatgttgacgtcttcatgtttgggattgttcagCTAATGTGTTTCATCGCGACCTGAAGCCAAAGAACGTGTTGGCAAACGCTGACTGTAAACTGAAAATTTGTGACTTTGGACTTGCTCGAGTGGCCTTTAG

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|125197513|gb|EL212467.1|EL212467

EST:     AGTTTTTCCTTCTATCAGCTTCTTCGTGGCCTCAAGTATATACACACAG                         CTAATGTCTTTCATCGGGATCTT
genomic: AGTTTTTCC-TCTATCAGCTTCTTCGTGGCCTCAAGTATATACACACAGgttaagctag ... ttcctttcagCTAATGTCTTTCATCGGGATCTT

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

agtataagtttatgattatctttctgaaaatactttttttttctcttcctttcagCTAATGTCTTTCATCGGGATCTTAAACCCAAAAACATATTGGCAAATGCTGATTGCAAACTCAAGATCTGTGATTTTGGACTTGCAAGAGTCGCATTCAA

                              tactttttttttctct  CT-rich tract
        tttatgattatctttc  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