ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtacgttaaaagtctgtttccttgaaagcttcagatagatctatctgtcttgtattttcttcttcatacaatgaaaagatgcttgcagTCTGCGGACGTCACTCTGCCTGCAATTTAAGCCTCACCACATTGCGGCGGGAGCAATTTTTCTTGCTGCGAAGTTCCTTAAAGTGAAATTACCATCAGAT

Basic information

species	Arabidopsis thaliana
transcript	AT4G19600.1
intron #	6
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: AT4G19600.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G308570_T02 (Zea mays), 3'ss of exon 13

gtacgttaaaagtctgtttccttgaaagcttcagatagatctatctgtct-tgtattttcttcttcatacaatgaaaagatgcttgcagTCTGCGGACGTCACTCTGCCTGCAATTTAAGCCTCACCACATTGCGGCGGGAGCAATTTTTCTTGCTGCGAAGTTCCTTAAAGTGAAATTACCATCAGAT
||| | ||||| |    ||| |      || || ||||    |||        |   | |||  | ||||  | ||| |  |  ||||| || || || ||||| |||||||||||||| || ||||| |||||||| || ||||| || || ||||||||||| |||||||| ||  | |||||||||
gtatgctaaaattactcttcatca----ctgcaaatag--taatccacaaacatgcctacttact-ataccttaaaaggg-gtgtgcagGCTCCGCACTTCACTTTGCCTGCAATTTAAACCGCACCATATTGCGGCTGGCGCAATCTTCCTGGCTGCGAAGTTTCTTAAAGTCAAGCTTCCATCAGAT

upper sequence: AT4G19600.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: AC233979.1_FGT009 (Zea mays), 3'ss of exon 4

gtacgttaaaagtctgtttccttgaaagcttcagatagatctatctgtcttgtattttcttcttcatacaatgaaaagatgcttgcagTCTGCGGACGTCACTCTGCCTGCAATTTAAGCCTCACCACATTGCGGCGGGAGCAATTTTTCTTGCTGCGAAGTTCCTTAAAGTGAAATTACCATCAGAT
||| | ||||| |    |||||       | || ||||   ||     |    ||     | | |      | |||||  |  | ||| || || || ||||| |||||||||||||| || ||||| |||||||| || ||||| || || ||||||||||| || ||||| ||  | |||||||||
gtatgctaaaattactcttcctca----ttacaaatag---taatccacaaacatccctatttactacgccttaaaaggggtgtacagGCTCCGCACTTCACTTTGCCTGCAATTTAAACCGCACCATATTGCGGCTGGTGCAATCTTCCTCGCTGCGAAGTTTCTCAAAGTCAAGCTTCCATCAGAT

upper sequence: AT4G19600.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G02860.1 (Glycine max), 3'ss of exon 5

gtacgttaaaagtctgtttccttgaaagcttcagatagatctatctgtctt--gtattttcttcttcatacaatg---aaaagatgcttgcagTCTGCGGACGTCACTCTGCCTGCAATTTAAGCCTCACCACATTGCGGCGGGAGCAATTTTTCTTGCTGCGAAGTTCCTTAAAGTGAAATTACCATCAGAT
||| | |     |    ||  ||  ||  || |  |   || || | | ||    || |  ||  ||| ||| ||   |||||  |||| ||| ||| |||| || |||||||||||||||||||| || || |||||||| || || ||||| |||||||| |||||| | ||||||||  | |||||||||
gtatgatttggttgcaatttgtttgaa--tttaactgtgtcgatttatttttaaaatatatttgatcacacactggaaaaaagtggctttcagGCTGAGGACATCGCTCTGCCTGCAATTTAAGCCACATCATATTGCGGCAGGTGCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGAT

upper sequence: AT4G19600.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G02880.1 (Glycine max), 3'ss of exon 4

gtacgttaaaagtctgtttccttgaaagcttcagatagatctatctgtcttgtattttcttcttcatacaatgaaaagatg-cttgcagTCTGCGGACGTCACTCTGCCTGCAATTTAAGCCTCACCACATTGCGGCGGGAGCAATTTTTCTTGCTGCGAAGTTCCTTAAAGTGAAATTACCATCAGAT
||| | |     |    ||  ||  ||  |     | ||| ||| | |    ||| ||      || ||    ||||  || ||| ||| ||| |||| || |||||||||||||||||||| || || |||||||| || || ||||| |||||||| |||||| | ||||||||  | |||||||||
gtatgatttggttgcaatttgtttgaatttaactgtcgatttatttttaaaatatatttgatcacacactggaaaaaagtggctttcagGCTGAGGACATCGCTCTGCCTGCAATTTAAGCCACATCATATTGCGGCAGGTGCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGAT

upper sequence: AT4G19600.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA07G35010.1 (Glycine max), 3'ss of exon 4

gtacg-ttaaaagtctgtttccttgaa---agcttcagatagatctatctgtcttgtattttcttcttcatacaatgaaaagatgcttgcagTCTGCGGACGTCACTCTGCCTGCAATTTAAGCCTCACCACATTGCGGCGGGAGCAATTTTTCTTGCTGCGAAGTTCCTTAAAGTGAAATTACCATCAGAT
||| | ||      |  |||  |||||   | |||||  |  || ||| | | ||  || |  || |||| ||| || ||||  |||| ||| ||| |||| || |||||||||||||||||||| || || |||||||| || || ||||| |||||||| |||||| | ||||||||  | |||||||||
gtatgatttggttgccatttgtttgaatttaacttcat-tgaatttattttttttaaatatatttgttcacacactggaaagtggctttcagGCTGAGGACATCGCTCTGCCTGCAATTTAAGCCACATCATATTGCGGCAGGTGCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGAT

upper sequence: AT4G19600.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv00s0125g00270.t01 (Vitis vinifera), 3'ss of exon 4

-------------gtacgttaaaagtctgtttccttgaaagcttca----gatagatctatctgtcttgtattttcttcttcat----acaatgaaaagatgcttgcagTCTGCGGACGTCACTCTGCCTGCAATTTAAGCCTCACCACATTGCGGCGGGAGCAATTTTTCTTGCTGCGAAGTTCCTTAAAGTGAAATTACCATCAGAT
             |    || |        ||  |||| || | ||     |  | ||| |||  ||    || |||||||||     ||| || ||||  |||||||| ||| |||| |||||||||||||||||||||||  |||||||||| || || || ||||| |||||||| ||||| || ||||||||  | ||||| |||
gtatgattaagatgctttttcatgtctctcttttttgatagttccatttcaaatggtctctcttcctctctttctcttcttcactcacacactggaaagcggcttgcagGCTGAGGACATCACTCTGCCTGCAATTTAAGCCCGACCACATTGCAGCAGGTGCCATTTTCCTTGCTGCCAAGTTTCTCAAAGTGAAGCTTCCATCGGAT

upper sequence: AT4G19600.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S119_132V6.1 (Physcomitrella patens), 3'ss of exon 4

---------gtacgttaa--aagtctgtttccttgaaagcttcagatag-atctatctgtcttgtattttcttc-ttcatacaatgaaaagatgcttgcagTCTGCGGACGTCACTCTGCCTGCAATTTAAGCCTCACCACATTGCGGCGGGAGCAATTTTTCTTGCTGCGAAGTTCCTTAAAGTGAAATTACCATCAGAT
          |  |  |   ||| || |||    |||         ||   |  || | | ||| |  |   |   | |  ||| |  | | |   ||||| || || || || || || ||||||||||| ||||| || ||||| |||||||| || ||  | ||||| |||||||||||||||||  | ||   ||||
tccatagagatttgccaggtaagcctatttttcagaagaacatgtgtaatgtacatgtctgttgcaagtgaatggctgaggcaaggggagggt-tgtgcagCCTTCGCACCTCGCTATGTCTGCAATTTAAACCTCATCATATTGCTGCGGGAGCTATCTTCTTGGCTGCCAAGTTCCTTAAAGTGAACCTCCCCAAAGAT

upper sequence: AT4G19600.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S80_193V6.1 (Physcomitrella patens), 3'ss of exon 4

------gtacgttaaa-agtctgtttccttgaaagct---tcagatagatctatctgtcttgtattttctt--cttcatacaatgaaaagatgcttgcagTCTGCGGACGTCACTCTGCCTGCAATTTAAGCCTCACCACATTGCGGCGGGAGCAATTTTTCTTGCTGCGAAGTTCCTTAAAGTGAAATTACCATCAGAT
       |  |  |   |  || | |    |||       |   ||     | |||||      |     |  ||      |  | ||||     |||||||| || || ||||| ||||||||||| |||||||| || ||||| |||||||| || ||  | ||||| || || || ||||||||  ||||   ||||
ttagagatttgccaggtaagctatgttacagaagagcatgtttaatgagcatgtctgttgcaagtgagaatggctgaggctaggggaaagggttgtgcagTCTTCGCACATCACTGTGCCTGCAATTCAAGCCTCATCATATTGCTGCGGGAGCTATCTTCTTGGCTGCCAAATTTCTGAAAGTGAACCTACCCAAAGAT

upper sequence: AT4G19600.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S86_187V6.1 (Physcomitrella patens), 3'ss of exon 5

gtacgttaaaagtctgtttccttgaaagcttcagatagat-ctatctgtcttgtattttct--tcttcata-----------caatgaaaagatgcttg-----cagTCTGCGGACGTCACTCTGCCTGCAATTTAAGCCTCACCACATTGCGGCGGGAGCAATTTTTCTTGCTGCGAAGTTCCTTAAAGTGAAATTACCATCAGAT
       || |  |   ||  | || | |  |||||  ||  | | |||  || |   | |   |    ||            |||| || | || ||      ||| || || |||||||| |||||||||||||||||||||||||| || |||||||| || || || ||||| ||||| || ||||||||  | ||    || 
------caagatgccacttt-tagagatcagcagattaatgttctttgtgctgaaaactgtgaccactgtagtcggaaaggctaatgtaagggtgattattgtccagACTTCGCACGTCACTTTGCCTGCAATTTAAGCCTCACCACATCGCTGCGGGAGCTATCTTCCTCGCTGCTAAGTTTCTCAAAGTGAATCTGCCGAAGGAG

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|164062773|gb|ES210716.1|ES210716

EST:     GTCGCACAGAATGCTCTGGCCCAAGTTGCATGGAATTTTGTTAACGATGG                         TCTGCGGACGTCACTCTGCCTGCAATTTAAGCCTCACCACATTG
genomic: GTCGCACAGAATGCTCTGGCCCAAGTTGCATGGAATTTTGTTAACGATGGgtacgttaaa ... atgcttgcagTCTGCGGACGTCACTCTGCCTGCAATTTAAGCCTCACCACATTG

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gatagatctatctgtcttgtattttcttcttcatacaatgaaaagatgcttgcagTCTGCGGACGTCACTCTGCCTGCAATTTAAGCCTCACCACATTGCGGCGGGAGCAATTTTTCTTGCTGCGAAGTTCCTTAAAGTGAAATTACCATCAGAT

                ttgtatttt  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