ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

...aggtacagattccatttttcttactttgatctaatgagtgtgaagattagcatttcgaagcagatgatgatgttttgtttatgaattgttgttattgcagGAGTTCAAAGGATACGTTTTCAAGATCAAGGGTGGTTGCGATAAGCAAGGTTTCCCAATGAAGCAGGGAGTTTTGACTCCAGGCCGTGTTCGCCTTTTGC

Basic information

species	Arabidopsis thaliana
transcript	AT4G31700.2
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: AT4G31700.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os07g42950.1 (Oryza sativa), 3'ss of exon 3

aggtacagattccatttttcttactttgatctaatgagtgtgaagattagcatttcgaagcagatgatgatgttttgtttatgaattgttgttattgcagGAGTTCAAAGGATACGTTTTCAAGATCAAGGGTGGTTGCGATAAGCAAGGTTTCCCAATGAAGCAGGGAGTTTTGACTCCAGGCCGTGTTCGCCTTTTGC
                |    |  |  |  ||     || |    ||||   || |  ||    | | ||||||     |||   |     || |  ||||| ||||| || || || |||||||||| ||| ||||| || ||||| |||||||| ||||||||||||||  | ||| | || ||||| |||||| | |
---------------gtaatatcgtgaggcctctgatgtttcctaattactgttacctagtc--ttaagatgtta-acatatctctctcctttttctcagGAATTCAAGGGCTATGTCTTCAAGATCATGGGGGGTTGTGACAAGCAGGGTTTCCCTATGAAGCAGGGAGTGCTCACTGCTGGACGTGTCCGCCTTCTTC

upper sequence: AT4G31700.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os03g27260.1 (Oryza sativa), 3'ss of exon 3

aggtacagattccatttttcttactttgatctaatgagtgtgaagattagcatttcgaagcagatgatgatgttttgtttatgaattgttgttattgcagGAGTTCAAAGGATACGTTTTCAAGATCAAGGGTGGTTGCGATAAGCAAGGTTTCCCAATGAAGCAGGGAGTTTTGACTCCAGGCCGTGTTCGCCTTTTGC
         |    | |||   | |||| || | ||| | |  |  |  |  || | |   | ||||   |    ||  || |  |   ||||  | ||||| ||||| || || || |||||||||| ||| || || || |||||||||||||| ||||||||||| ||  | ||| | || ||||| |||||| | |
--------gtaatttctttggcaatttgctcca-tgattcttcaact--gtcttgctattta-atga--gttggatgactaagtttgtctgtttgtacagGAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGTTTCCCCATGAAGCAGGGTGTGCTTACTTCTGGACGTGTCCGCCTTCTCC

upper sequence: AT4G31700.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G040600_T01 (Zea mays), 3'ss of exon 5

-------aggtacagattcc---atttttcttactttgatctaatgagtgtgaagattagcatttcgaagcagatgatgatgttttgtttatgaattgttgttattgcagGAGTTCAAAGGATACGTTTTCAAGATCAAGGGTGGTTGCGATAAGCAAGGTTTCCCAATGAAGCAGGGAGTTTTGACTCCAGGCCGTGTTCGCCTTTTGC
       |  |||| | |     ||   |  |   |||||| | ||| | |      |  |||    ||  | | | || || | ||||  |   |||||    |||||||||||||| || || || |||||||||| |||||| || || |||||||| |||||||||||||| |||||||||||| | || |||||||||||| |||
gagttgaatttacaaactttgggatgacttatttcttgatcca-tgactcttgctgatgtcatacttaaatata-ggtg-tgatatgttcct---ttgtt----ttgcagGAGTTCAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGGTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGCCTTCTGC

upper sequence: AT4G31700.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G054136_T09 (Zea mays), 3'ss of exon 3

aggtacagattcc-atttttcttactttgatctaatgagtgtgaagattagcatttcgaagcagatgatgatgttttgtttatgaattgttgttattgcagGAGTTCAAAGGATACGTTTTCAAGATCAAGGGTGGTTGCGATAAGCAAGGTTTCCCAATGAAGCAGGGAGTTTTGACTCCAGGCCGTGTTCGCCTTTTGC
  ||| |  ||   ||   |  |   |||||| |       ||  ||||  |||    ||  | | | || || | ||||| |   |||||    |||||||||||||| || || || |||||||||| |||||| || || |||||||| |||||||||||||| |||||||||||| | || |||||||| ||| |||
--gtaaactttgggatgacttatttcttgatccatgactcttgctgattt-catacttaaatata-ggtg-tgatatgtttct---ttgtt----ttgcagGAGTTCAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGC

upper sequence: AT4G31700.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G054136_T08 (Zea mays), 3'ss of exon 3

----------------------aggtacagattccatttttcttactt--tgatctaatgagtgtgaagattagcatttcgaagcagatgatgatgttttgtttatgaattgttgttattgcagGAGTTCAAAGGATACGTTTTCAAGATCAAGGGTGGTTGCGATAAGCAAGGTTTCCCAATGAAGCAGGGAGTTTTGACTCCAGGCCGTGTTCGCCTTTTGC
                      ||||| |  ||     |  |||| ||  ||||| |       ||  ||||  |||    ||  | ||     || | ||||| |   |||||    |||||||||||||| || || || |||||||||| |||||| || || |||||||| |||||||||||||| |||||||||||| | || |||||||| ||| |||
gtcagtggtgatgctctgggtgaggta-aactttggggtgacttatttcttgatccatgactcttgctgattt-catacttaaaaatataggtgtgatatgtttct---ttgtt----ttgcagGAGTTCAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGC

upper sequence: AT4G31700.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G054136_T05 (Zea mays), 3'ss of exon 3

-------aggtacagattccatttttcttactt--tgatctaatgagtgtgaagattagcatttcgaagcagatgatgatgttttgtttatgaattgttgttattgcagGAGTTCAAAGGATACGTTTTCAAGATCAAGGGTGGTTGCGATAAGCAAGGTTTCCCAATGAAGCAGGGAGTTTTGACTCCAGGCCGTGTTCGCCTTTTGC
       ||||| |  ||     |  |||| ||  ||||| |       ||  ||||  |||    ||  | ||     || | ||||| |   |||||    |||||||||||||| || || || |||||||||| |||||| || || |||||||| |||||||||||||| |||||||||||| | || |||||||| ||| |||
ctgggtgaggta-aactttggggtgacttatttcttgatccatgactcttgctgattt-catacttaaaaatataggtgtgatatgtttct---ttgtt----ttgcagGAGTTCAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGC

upper sequence: AT4G31700.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G054136_T01 (Zea mays), 3'ss of exon 3

aggtacagattccatttttcttactt--tgatctaatgagtgtgaagattagcatttcgaagcagatgatgatgttttgtttatgaattgttgttattgcagGAGTTCAAAGGATACGTTTTCAAGATCAAGGGTGGTTGCGATAAGCAAGGTTTCCCAATGAAGCAGGGAGTTTTGACTCCAGGCCGTGTTCGCCTTTTGC
  ||| |  ||     |  |||| ||  ||||| |       ||  ||||  |||    ||  | ||     || | ||||| |   |||||    |||||||||||||| || || || |||||||||| |||||| || || |||||||| |||||||||||||| |||||||||||| | || |||||||| ||| |||
--gta-aactttggggtgacttatttcttgatccatgactcttgctgattt-catacttaaaaatataggtgtgatatgtttct---ttgtt----ttgcagGAGTTCAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGC

upper sequence: AT4G31700.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM5G851698_T02 (Zea mays), 3'ss of exon 3

aggtacagattccatttttct-tactttgatctaatgagtgtgaagattagcatttcgaagcagatgatgatgttttgtttatgaattgttgttattgcagGAGTTCAAAGGATACGTTTTCAAGATCAAGGGTGGTTGCGATAAGCAAGGTTTCCCAATGAAGCAGGGAGTTTTGACTCCAGGCCGTGTTCGCCTTTTGC
  ||| |  |||   |||  | |   |||||| | ||      |    |   |||||  |    || ||   | | ||   |||  ||  | || ||||||||||| || || || || |||||||||| |||||| || || || ||||| |||||||||||||| |||||| ||||| | || ||||| |||||| |||
--gtaaattttctgctttcttatttcttgatcca-tgccccctattgctg--atttcatacttaattata--ggtgtg---atgtgtttctttt-ttgcagGAGTTTAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAACAAGGCTTCCCAATGAAGCAAGGAGTTCTGACTTCTGGTCGTGTCCGCCTTCTGC

upper sequence: AT4G31700.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G24630.1 (Glycine max), 3'ss of exon 3

--aggt---acagattccatttttcttactttgatctaatgagtgtgaagattagcatttcgaagcagatgatgatgt-tttgtttatgaattgttgttattgcagGAGTTCAAAGGATACGTTTTCAAGATCAAGGGTGGTTGCGATAAGCAAGGTTTCCCAATGAAGCAGGGAGTTTTGACTCCAGGCCGTGTTCGCCTTTTGC
  | ||     || |   | | || |||  |  || | |   ||    |  ||||  |   |    |  | ||||| | ||    |||  |   ||| || || ||||||| |||||||| |||||||| ||||  ||||| || || || ||||| |||||||||||||||||||| ||||| || || |||||||| || ||||
gtatgtttgttagctggaaatcttattatatcaatgtcagttgttcctattttag-gtggagctttaattaatgatctattaacctatataactttgctactgaagGAGTTTAAAGGATATGTTTTCAAAATCACTGGTGGGTGTGACAAACAAGGATTCCCAATGAAGCAGGGAGTGTTGACCCCTGGTCGTGTTCGACTCTTGC

upper sequence: AT4G31700.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA07G31840.3 (Glycine max), 3'ss of exon 2

aggtacagattccatttttcttactttgatctaatgagtgtgaagattagcatttcgaag-----cagatgatgatgt-tttgtttatgaattgttgttattgcagGAGTTCAAAGGATACGTTTTCAAGATCAAGGGTGGTTGCGATAAGCAAGGTTTCCCAATGAAGCAGGGAGTTTTGACTCCAGGCCGTGTTCGCCTTTTGC
      |   ||  |   |   | | | ||   ||  ||||           ||| |  |      |    ||||| | ||    | |  |   |||  | || ||||||| |||||||| |||||||| ||||  ||||| || || || ||||| ||||| ||||||||||||||  |||| || || |||||||| |||||||
----gtatgctcgttagctggaaatcttattatatctgtgtctgttcctattttttgtggagcattaagaaatgatctattaacctctataactttgccactgaagGAGTTTAAAGGATATGTTTTCAAAATCACCGGTGGGTGTGACAAACAAGGATTCCCTATGAAGCAGGGAGTGCTGACCCCTGGTCGTGTTCGACTTTTGC

upper sequence: AT4G31700.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G31130.1 (Glycine max), 3'ss of exon 4

aggtacagattccatttttcttactttgatctaatgagtgtgaagattagcatttcgaagcagatgatgatgttttgtttatgaattgttgtta-ttgcagGAGTTCAAAGGATACGTTTTCAAGATCAAGGGTGGTTGCGATAAGCAAGGTTTCCCAATGAAGCAGGGAGTTTTGACTCCAGGCCGTGTTCGCCTTTTGC
  |||  | ||    |    |   |      |   | || |   ||  | ||||    |     ||    | || |  || |    | ||| || |||||||| |||||||| || || ||||| || |  || |||||||| |||||||| || ||||||||||| ||||| ||||| || || ||||||||||| ||||
--gtatggttttggctggaatccttccacagtgcagtgtttcctgagaaacattgatcaatgattggct-tattctccttttcttgttttgctacttgcagGAATTCAAAGGTTATGTCTTCAAAATTACTGGAGGTTGCGACAAGCAAGGATTTCCAATGAAGCAAGGAGTGTTGACCCCTGGTCGTGTTCGCCTCTTGC

upper sequence: AT4G31700.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA15G08210.1 (Glycine max), 3'ss of exon 3

aggtacagattccatttt--tcttactttgatctaatgagtgtgaagattagcatttcgaagcagatgatgatgttttgtttatg----------aattgttgtta-ttgcagGAGTTCAAAGGATACGTTTTCAAGATCAAGGGTGGTTGCGATAAGCAAGGTTTCCCAATGAAGCAGGGAGTTTTGACTCCAGGCCGTGTTCGCCTTTTGC
  |||  | ||    |     | | |  |  |  |  |  |    |  ||| |  |  ||| ||       ||| || | ||||            ||  ||| || || ||||| |||||||| || || ||||| || |  || |||||||| |||||||| || ||||||||||| ||||| ||||| || || ||||||||||| ||||
--gtatggtttttgctggaacccttccatagtgcagagtttcctgaagttacc--tgagaaacattgatcaatgattggcttatccgtcctttcttatatttgctacttacagGAATTCAAAGGCTATGTCTTCAAAATTACTGGAGGTTGCGACAAGCAAGGATTTCCAATGAAGCAAGGAGTGTTGACCCCTGGTCGTGTTCGCCTCTTGC

upper sequence: AT4G31700.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA16G09330.1 (Glycine max), 3'ss of exon 1

-----aggtacagattccatttttcttac-tttgatctaatgagtgtgaagattagcatttcgaagcagatgatgatgttttgtttatgaattgttgttattgcagGAGTTCAAAGGATACGTTTTCAAGATCAAGGGTGGTTGCGATAAGCAAGGTTTCCCAATGAAGCAGGGAGTTTTGACTCCAGGCCGTGTTCGCCTTTTGC
        |  ||||   |   |||  |   ||| |  |||   | |  ||   ||||||   ||  |  ||||  |||    ||||  |||| |  |  |   |||| || |||||||| || ||||| ||||  |||||||| || || ||||| || |||||||||||||||||  | || || ||| ||||||  |||||||
gtatgctctgtagatcaaaaccttcaaatacttgtttcaatatcttttgagg--agcattgataattat-tgatcttgtcaacttta-aaattatgctactaatagGAATTTAAAGGATATGTCTTCAAAATCACTGGTGGTTGTGACAAACAAGGATTTCCAATGAAGCAGGGAGTGCTAACACCTGGCTGTGTTCATCTTTTGC

upper sequence: AT4G31700.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv18s0001g06290.t01 (Vitis vinifera), 3'ss of exon 3

aggtacagattccatttttcttactttgatctaatgagtgtgaagattagcatttcgaagcagatgatgatgttttgtttatgaattgttgttattgcagGAGTTCAAAGGATACGTTTTCAAGATCAAGGGTGGTTGCGATAAGCAAGGTTTCCCAATGAAGCAGGGAGTTTTGACTCCAGGCCGTGTTCGCCTTTTGC
  |||   |||  |   || |||       | ||  | |   |  || ||    | ||   | || |  || | || ||  |   |||||  | |  ||||| || || || || || ||||| |||| ||| || || || |||||||| |||||||||||||||||||| || ||||| || |||||| | || ||||
--gtaagcattt-accattgttatgcaatgccaa--aattctactatcaga--ctagatttatataac-atttatttttgtttgtttgtttgtgtgacagGAATTTAATGGCTATGTATTCAAAATCATGGGAGGCTGTGACAAGCAAGGGTTCCCAATGAAGCAGGGAGTGTTAACTCCTGGTCGTGTTAGTCTCTTGC

upper sequence: AT4G31700.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv07s0191g00060.t01 (Vitis vinifera), 3'ss of exon 3

aggtacagattccatttttcttactttgatctaatgagtgtgaagattagcatttcgaagcagatgatgatgttttgtttatgaattgttgttattgcagGAGTTCAAAGGATACGTTTTCAAGATCAAGGGTGGTTGCGATAAGCAAGGTTTCCCAATGAAGCAGGGAGTTTTGACTCCAGGCCGTGTTCGCCTTTTGC
          |    |||| ||||| |  |||  | ||   ||  | | ||  || |      |||||    |  ||| | | ||  ||  ||    ||||||||||| || || || ||||| || | ||| || || || ||||||||||| |||||||||||||||||  |||| |||||||| || |  ||| |||
---------gtatgattttgttactat--tcttcttag---gataacttgccctttgttaggaatgatttattgatgtatcttaagcgtgtttg--acagGAGTTCAAGGGTTATGTATTCAAAATAATGGGAGGCTGTGACAAGCAAGGTTTTCCAATGAAGCAGGGAGTACTGACCCCAGGCCGAGTCCAACTTCTGC

upper sequence: AT4G31700.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv03s0017g01350.t01 (Vitis vinifera), 3'ss of exon 3

aggtacagattccatttttcttactttgatctaatgagtgtgaagattagcatttcgaagcagatgatgatgttttgtttatgaattgttgttattgcagGAGTTCAAAGGATACGTTTTCAAGATCAAGGGTGGTTGCGATAAGCAAGGTTTCCCAATGAAGCAGGGAGTTTTGACTCCAGGCCGTGTTCGCCTTTTGC
          |     |||  | || |  ||  |    | |      ||   |||   | |   | || ||        | | |  || |    |  ||||||||||| || || ||||||||||||| ||||||||| || |||||||| || || ||||||||||||||  ||||||| ||||||||| | |||||||
---------gtatgccttttctgctcttctcccacttatttatctcatattgttt--gatctactaatcatacaaaacatgtcatctgct----tcacagGAGTTCAAGGGCTATGTTTTCAAGATCATGGGTGGTTGTGACAAGCAAGGGTTTCCCATGAAGCAGGGAGTACTGACTCCTGGCCGTGTTAGTCTTTTGC

upper sequence: AT4G31700.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S311_33V6.2 (Physcomitrella patens), 3'ss of exon 3

aggtacagattccatttttcttactttgatctaatgagtgtgaagattagcatttcgaagcagatgatgatgttttgtttatgaattgttgttattgcagGAGTTCAAAGGATACGTTTTCAAGATCAAGGGTGGTTGCGATAAGCAAGGTTTCCCAATGAAGCAGGGAGTTTTGACTCCAGGCCGTGTTCGCCTTTTGC---------
                                                                          |   |  |||   | |  |  || | |||||||| ||||||||||||||||| | ||| || || || ||||| |||||||| ||||||||||| || ||||| |  || ||||| |  ||  ||          
-------------------------------------------------------------------------gtcagtggtgaccagct--tggtg-atgagttcaagggatacgttttcaagattatgggaggatgtgacaagcagggtttccccatgaagCAGGGTGTCTTGACCCAGGGACGTGTGCAACTGCTGATGCACCGAG

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|86040573|gb|DR336328.1|DR336328

EST:     AGACGTCGAAGATGAAGTTCAACGTTG-CG                         GAGTTCAAAGGATACGTTTTCAAGATCAAGGGTGGTTGCGATAAGCAAGG
genomic: AGACGTCGAAGATGAAGGT--GCG-TGACGgcgaaatcga ... gttattgcagGAGTTCAAAGGATACGTTTTCAAGATCAAGGGTGGTTGCGATAAGCAAGG

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

attagcatttcgaagcagatgatgatgttttgtttatgaattgttgttattgcagGAGTTCAAAGGATACGTTTTCAAGATCAAGGGTGGTTGCGATAAGCAAGGTTTCCCAATGAAGCAGGGAGTTTTGACTCCAGGCCGTGTTCGCCTTTTGC

                           ttttgtttatgaatt  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