ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtatgttcttcttttttaatcaaaagactttgttatccatttgccaagatcctttttgaaagataacttgacagTACCAATCACAGGTATTCGATTTGTTTGACACAAAGCATAATGGAATACTGGGGTTTGAGGAGTTTGCGCGTGCTCTCTCTGTCTTTCATCCAAATGCTC

Basic information

species	Arabidopsis thaliana
transcript	AT4G26570.2
intron #	5
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: AT4G26570.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os12g40510.1 (Oryza sativa), 3'ss of exon 4

------------gtatgttcttcttttttaatcaaaagactttgttatccatttgccaagatcctttttgaaaga--taacttgacagTACCAATCACAGGTATTCGATTTGTTTGACACAAAGCATAATGGAATACTGGGGTTTGAGGAGTTTGCGCGTGCTCTCTCTGTCTTTCATCCAAATGCTC------------
              |  |   | | |  ||      ||      || | | |||  |    | ||   | |      |||  |        |  | ||||||||| ||||||||||||||||| || ||||||||  | || ||||| || ||||| ||||| ||||| || |||||||||| |||||            
aattctttgtagaaaaatagctgtatgatagatgtcagtgcagattttgcctttatctccgtgctgcctcatgttcttaatattctccctgctcttacagGTATTTGATTTGTTTGACACAAAACACAATGGAATTTTAGGATTTGATGAATTTGCTCGTGCACTCTCAGTATTTCATCCAAGTGCTCCACTTGATGAGA

upper sequence: AT4G26570.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G007555_T01 (Zea mays), 3'ss of exon 4

--------------------gtatgttcttcttttttaatcaaaagactttgttatccatttgccaa-gatcctttttgaaagataacttgacagTACCAATCACAGGTATTCGATTTGTTTGACACAAAGCATAATGGAATACTGGGGTTTGAGGAGTTTGCGCGTGCTCTCTCTGTCTTTCATCCAAATGCTC------------
                    | |  || |   |   | |||       || ||||   || |   |   ||| | |    || ||  ||||       |  |  |||||||| |||||||||||||||||||| ||||||||  | || ||||| || ||||| ||||||||||| || |||||||| |||||||            
tgtagaaaaattagctgcacgaaaattgtgggtccctgatcttgct-tttggttactgatataaaagtaatcatgtccctaatattccttg------tcccttgcagGTATTTGATTTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGA

upper sequence: AT4G26570.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G173424_T02 (Zea mays), 3'ss of exon 4

------------------gtatgttcttcttttttaatcaaaagactttgttatccatttgccaagatcctttttgaaagataacttgacagTACCAATCACAGGTATTCGATTTGTTTGACACAAAGCATAATGGAATACTGGGGTTTGAGGAGTTTGCGCGTGCTCTCTCTGTCTTTCATCCAAATGCTC------------
                    |  || |   |  || |||       || ||||   || |   |  ||    | |     |||  ||     |  | ||   ||||||| ||||| |||||||||||||| | ||||||  |||| ||||| || ||||| ||||||||||| || |||||||| |||||||            
tagaaaaattagctgcacaaaaattgtggatccttgatcttgct-tttggttactgatataaaagtatatcatgtccctaatattttct---tgtccattgtagGTATTTGATTTATTTGACACAAAGCACAGTGGAATTTTGGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGA

upper sequence: AT4G26570.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G08230.1 (Glycine max), 3'ss of exon 5

gtatgttcttcttttttaatcaaaagactttgtt-----atccatttgcca---agatcctttttgaaagataacttga------cagTACCAATCACAGGTATTCGATTTGTTTGACACAAAGCATAATGGAATACTGGGGTTTGAGGAGTTTGCGCGTGCTCTCTCTGTCTTTCATCCAAATGCTC-------------
 | | | | | || ||| | ||  | | ||||||     ||  |||  | |   |  |  |  ||| ||  |||  |||      |  || |  |   ||||||| ||||| |||||||||||||| ||||| ||||| || ||||| |||||||| ||||||||||| || |||||||||||||| |             
-tgtttacgtattatttcaacattatattttgttcaaaaattgattcacaattcaacttgtgattggaatctaatatgaacttctctctaactctattaggTATTTGATTTATTTGACACAAAGCACAATGGGATACTAGGTTTTGAAGAGTTTGCTCGTGCTCTCTCCGTTTTTCATCCAAATGCCCCTATTGATGATAA

upper sequence: AT4G26570.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G39940.1 (Glycine max), 3'ss of exon 4

-----------------gtatgttcttcttttttaatcaaaagactttgttatccatttgccaagatcctttttgaaagataacttgacagTACCAATCACAGGTATTCGATTTGTTTGACACAAAGCATAATGGAATACTGGGGTTTGAGGAGTTTGCGCGTGCTCTCTCTGTCTTTCATCCAAATGCTC------------
                   | |||  |    |    |  | | |    |||| || |       |    | |       || | ||    ||||       |||| || || |||||||| |||||||| ||||| ||||| |  ||||| |||||||| ||||||||||||||||||||||| ||||| |            
atatttatgatctgattacaagttagttgcataccgtatacatatggggttaaccttagaatttgtatttgtcctgttcatgatttt---gtactgtctgtagGTGTTTGACTTGTTTGATACAAAGCACAATGGGATACTTGATTTTGAAGAGTTTGCACGTGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATA

upper sequence: AT4G26570.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G44580.1 (Glycine max), 3'ss of exon 4

-----gtatgttcttcttttttaatcaaaagactttgtt----atccatttgccaagatcctttttgaaagataacttgacagTACCAATCAC------AGGTATTCGATTTGTTTGACACAAAGCATAATGGAATACTGGGGTTTGAGGAGTTTGCGCGTGCTCTCTCTGTCTTTCATCCAAATGCTC------------
      | | | | | ||||| ||| |  | | ||||||    |     ||  ||  |  | || ||   | || ||     | ||   || |      ||||||| ||||| ||||||||||| || ||||| |||||||| ||||| |||||||| ||||||||||| || || ||||| ||||| |            
tatatctgtttacgtatttttcaat-attatattttgttcaaaaattgattcacattactccttgtggttggtatctcatatgaacttctctctaacttagGTATTTGATTTATTTGACACAAAACACAATGGGATACTGGGTTTTGAAGAGTTTGCTCGTGCTCTCTCCGTTTTCCATCCTAATGCCCCCATTGATGATA

upper sequence: AT4G26570.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G01870.2 (Glycine max), 3'ss of exon 4

gtatgttcttcttttttaatcaaaagactttgttatccatttgccaagatcctttttgaaag----------------ataactt----gacagTACCAATCACAGGTATTCGATTTGTTTGACACAAAGCATAATGGAATACTGGGGTTTGAGGAGTTTGCGCGTGCTCTCTCTGTCTTTCATCCAAATGCTC------------
        ||  |||  ||||||     |    ||| |||||   | ||||| ||||  ||                 || | ||         |||   |   |||| || || ||||||||||||||||||| ||||||||| |  ||  | |||||||| | ||||||||||||||||||||| |  ||              
------agttactttgaaatcaatcacatgccatatacatttaatatgatcccttttagaaatgtatttgtgctattcatgatttttatattgttacattttgtagGTGTTTGACTTGTTTGACACAAAGCATAGTGGAATACTTGATTTCAAAGAGTTTGCACTTGCTCTCTCTGTCTTTCATCCCAGCGCATCAATTGATGATA

upper sequence: AT4G26570.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G00830.1 (Glycine max), 3'ss of exon 4

gtatgttcttcttttttaa---tcaaaagactttgttatccatttgccaagatcct------ttttgaaagataacttgaca-----gTACCAATCACAGGTATTCGATTTGTTTGACACAAAGCATAATGGAATACTGGGGTTTGAGGAGTTTGCGCGTGCTCTCTCTGTCTTTCATCCAAATGCTC------------
 |||| |||  ||  ||||   | |   |  |    ||| ||| ||    || |||      ||||    |     || |       ||||   |   |||| || || |||||||| |||||||| || || ||||| |  ||||| |||||||| || |||||||||||||||||||| ||||| |            
ttatgatctgattacttaagagttagttgtatgccatatacatatgatgtgaaccttagaatttttatttgtcctgttcatgattttgtactgtttgtagGTGTTTGACTTGTTTGATACAAAGCACAACGGGATACTTGATTTTGAAGAGTTTGCACGAGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATA

upper sequence: AT4G26570.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv00s1569g00020.t01 (Vitis vinifera), 3'ss of exon 3

gtatgttcttctttt--ttaatcaaaagactttgttatccatttgccaa--gatcctttttgaaagat------aacttga----cagTACCAATC--ACAGGTATTCGATTTGTTTGACACAAAGCATAATGGAATACTGGGGTTTGAGGAGTTTGCGCGTGCTCTCTCTGTCTTTCATCCAAATGCTC------------
  |||||| |   ||  ||       || |||  ||     ||| | ||  ||  |    | ||  ||      || ||      |  | | ||||    ||||||| || ||||||||||||||||| ||||||||||| |  ||||| |||||||||||||| ||||||||||||||||| ||||| |            
--atgttccttcattagttggcttgtagtcttctttcagttttttcaaaatgagtccaaataaattattcctacaatttatgcctctattcaaatcttgtagGTATTTGACTTGTTTGACACAAAGCACAATGGAATACTAGATTTTGAAGAGTTTGCGCGTGCCCTCTCTGTCTTTCATCCCAATGCACCCATTGAAGACA

upper sequence: AT4G26570.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv19s0015g01070.t01 (Vitis vinifera), 3'ss of exon 3

-----------gtatgttcttcttttttaatcaaaagactttgttatccatttgccaagatcctttttgaaagataacttgacagTACCAATCA----CAGGTATTCGATTTGTTTGACACAAAGCATAATGGAATACTGGGGTTTGAGGAGTTTGCGCGTGCTCTCTCTGTCTTTCATCCAAATGCTC------------
              ||   |  |  ||| ||   |    ||||  |    ||    ||||  ||  ||      |   |    | | | |||||     ||||||| || |||||||||||||||||||| |||||||| || |||||||||||||| |||||||| ||||| ||||| || || || |            
aactcttgcatcattgaattggtagtttcattggatatttttggaaga-gttccaaaagacgctcatttgccattgtatatgtaatgctaatcaattgtagGTATTTGACTTGTTTGACACAAAGCATAACGGAATACTTGGCTTTGAGGAGTTTGCTCGTGCTCTATCTGTTTTTCACCCCAACGCACCTATCGACGACA

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|86019689|gb|DR315435.1|DR315435

EST:     AGTTAGCCTTGTTCAAGACAAATAAAAAAGAGAGCTTGTTTGCAGACCGG                         TACCAATCACAGGTATTCGATTTGTTTGACACA
genomic: AGTTAGCCTTGTTCAAGACAAATAAAAAAGAGAGCTTGTTTGCAGACCGGgtatgttctt ... aacttgacagTACCAATCACAGGTATTCGATTTGTTTGACACA

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tcaaaagactttgttatccatttgccaagatcctttttgaaagataacttgacagTACCAATCACAGGTATTCGATTTGTTTGACACAAAGCATAATGGAATACTGGGGTTTGAGGAGTTTGCGCGTGCTCTCTCTGTCTTTCATCCAAATGCTC

                                         agataac  putative branch site (score: 3)
                                 tttttgaaagataa  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