ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TGCTTGCTTGTTCTTCACATTTATTGGTGGGTTTTGATGTATCGGATGCTTGTGAAACAAATACAAGATAGAGGCAAGCTTAGTGAAGATGTCAGATCAGgtaagtttggtttactgtaataaaaatcggttttcgcaccatccaaatcaaagaagagatcttcaagtttgtgtctttctcgcag

Basic information

species	Arabidopsis thaliana
transcript	AT1G13580.2
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: AT1G13580.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os02g37080.2 (Oryza sativa), 5'ss of exon 5

---TGCTTGCTTGTTCTTCACATTTATTGGTGGGTTTTGATGTATCGGATGCTTGTGAAACAAATACAAGATAGAGGCAAGCTTAGTGAAGATGTCAGATCAGgtaagtttggtttactgtaataaaaatcggttttcgcaccatccaaat---caaagaagagatcttcaagtttgtgtctttctcgcag------------------------------------------------------------------------------------------------------------
   |   | |||||||||||||| |||||||||||| |||| |||||||||||||||| |||||| ||||| |     ||  || | || |||||  |||| |||||| |  |    ||    || ||    ||||| ||||      |     ||||   |     |   | |||  |||      |||                                                                                                             
TTTTCACTACTTGTTCTTCACATATATTGGTGGGTTCTGATATATCGGATGCTTGTGAGACAAAT-CAAGACAAGA--AATGTTGGAGATGATGTTCGATCTGgtaagctctgccccct----tagaatcttgtttttgcacaggatgagcatgcaaaattgcatggtcttattttcagtcccatctgcattgggacaagacaaagtctgcttataacatgcattactccaaccaccattgtgagttgaaaattattttgagtttgctaccatctaaaactgttctgctttatgtgcag

upper sequence: AT1G13580.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G315726_T02 (Zea mays), 5'ss of exon 3

TGCTTGCTTGTTCTTCACATTTATTGGTGGGTTTTGATGTATCGGATGCTTGTGAAACAAATACAAGATAGAGGCAAGCTTAGTGAAGATGTCAGATCAGgtaagtttggtttactgtaataaaaatcggttttcgcacca--------tccaaatcaaagaagagat-cttcaagtttgtgtctttctcgcag------
|   | |||||||| ||||| |||||||||||||| |||||||||||||||||||| ||||||||   ||||||  |  || | || ||| |  |||| |||| |||    ||    | | |    || ||| |   |  |        |  ||||   | || | || |||     ||   |  |  |   ||      
TCTCTACTTGTTCTACACATATATTGGTGGGTTTTAATGTATCGGATGCTTGTGAAGCAAATACAGTCTAGAGGGCACGTTGGCGATGATATACGATCTGgtaggttctccttttccttagattcttctgttattatatgaggttgaacttaaaattggataaaacattctttggagttaaattctggttatagttgaat

upper sequence: AT1G13580.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G444643_T01 (Zea mays), 5'ss of exon 6

---TGCTTGCTTGTTCTTCACATTTATTGGTGGGTTTTGATGTATCGGATGCTTGTGAAACAAATACAAGATAGAGGCAAGCTTAGTGAAGATGTCAGATCAGgtaagtttggtttactgtaataaaaatcggt---tttcgcaccatc--caaatcaaagaagagatcttcaagtttgtgtc--tttctcgcag---------------------------------------------------------------------------------------
   |   | |||||||| ||||| |||||||||||||| || |||||||||||||||| |||||| ||||| |     ||  || | || |||||  |||| |||||||   ||   ||||   ||   | |||    | | ||| | |      |     ||  | |   ||| |  || |   || || |  |                                                                                       
TTTTCACTACTTGTTCTCCACATATATTGGTGGGTTTTAATATATCGGATGCTTGTGAGACAAAT-CAAGACAAGA--AATGTTGGAGATGATGTTCGATCTGgtaagtcctgtc--ctgtctgaagttttggtatgctgcacacgagcatttttttttgaaaatgctgcgcaaatcagttttgtttgcttgtgggtaaaacttagttataattatgttctttcaacttgtgttgaggtgaaaaactttcttcgattttactttgccttgctttccatacag

upper sequence: AT1G13580.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G170868_T01 (Zea mays), 5'ss of exon 5

---TGCTTGCTTGTTCTTCACATTTATTGGTGGGTTTTGATGTATCGGATGCTTGTGAAACAAATACAAGATAGAGGCAAGCTTAGTGAAGATGTCAGATCAGgtaagtttggtttactgtaataaaaatcggttttcgcac-----catccaaatcaaagaagagatc-ttcaagtttgtgtc--tttctcgcag---------------------------------------------------
   |   | |||||||| ||||| ||||||||||| || || |||||||||||| ||| |||||| ||||| |     ||  || | || |||||  |||| ||||||    |||   | | |      | |  |   ||||     |||     |    ||| |  |  | ||  |   | |   || || |  |                                                   
TTTTCACTACTTGTTCTCCACATATATTGGTGGGTCTTAATATATCGGATGCTTCTGAGACAAAT-CAAGACAAGA--AATGTTGGAGATGATGTTCGATCTGgtaagccctgttctgtctgaagcctttggtatgctgcacacgagcatttttttttttgaaaaatttgtgcagatcaattttgtttgcttgtggataaaacatagttataactttgaattttactttgccttgcttttcatacag

upper sequence: AT1G13580.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA16G12080.1 (Glycine max), 5'ss of exon 5

TGCTTGCTTGTTCTTCACATTTATTGGTGGGTTTTGATGTATCGGATGCTTGTGAAACAAATACAAGATAGAGGCAAGCTTAGTGAAGATGTCAGATCAGgtaagtttg-----gtttactgtaataaaaatcggttttcgcaccatccaaatcaaagaagagatcttc----aagtttgtgtctttct-cgcag-------
|||||||||||| | || |||||||||||||| ||||| |||||||||||||| |||||||| ||||  ||||| ||  |||||||||||||  |||| ||||||||       || | ||||   |    |  || |    ||  | ||  | ||   ||  | |||     || |||||  |  | | |  ||       
TGCTTGCTTGTTATGCATATTTATTGGTGGGTGTTGATATATCGGATGCTTGTTAAACAAATCCAAGCAAGAGGAAAAGTTAGTGAAGATGTTCGATCTGgtaagttgaaagatgtgttctgtgcaaggctttcgtatgtaaacttttca--ttaactgagcaaccttgtgaaaaatttgttcccctgtgcctagtatctgc

upper sequence: AT1G13580.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA08G36370.1 (Glycine max), 5'ss of exon 5

TGCTTGCTTGTTCTTCACATTTATTGGTGGGTTTTGATGTATCGGATGCTTGTGAAACAAATACAAGATAGAGGCAAGCTTAGTGAAGATGTCAGATCAGgtaagtttg---gtttactgtaataaaaatcggttttcgcaccatccaaatcaaagaagagatcttc----aagtttgtgtctttctcgcag--------
|||||||||||| | || ||||||||||||||  |||| | |||||||||||| |||||||| ||||  ||||| ||  |||||||||||||  |||| ||||||||      |  | | |    ||       ||  | |   |    ||  |   ||    |||     || |||||  |     |  ||        
TGCTTGCTTGTTATGCATATTTATTGGTGGGTGCTGATATTTCGGATGCTTGTTAAACAAATCCAAGCAAGAGGAAAAGTTAGTGAAGATGTTCGATCTGgtaagttgaaaaatgcattctgtgcaaggctttcttatgtaaactttccattgactgagcagccttgtgaaaaatttgttccccatgcctagtatctgca

upper sequence: AT1G13580.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA02G14060.1 (Glycine max), 5'ss of exon 9

TGCTTGCTTGTTCTTCACATTTATTGGTGGGTTTTGATGTATCGGATGCTTGTGAAACAAATACAAGATAGAGGCAAGCTTAGTGAAGATGTCAGATCAGgtaagtttggtttactgtaataaaaatcggttttcgcaccatccaaatcaaagaagagatcttcaagtttgtgtctttctcgcag-----------------------------------------------------------------------------------------------------------
| |||||| |||||||| || |||||||||||| |||||  | |||||||||| |||||||| ||||| | ||| ||  ||||||||||| |  |||| |||||| |   |    || | |||| ||  |  ||   |  ||  |  |   |      || |   |   | |    ||   || |                                                                                                           
TTCTTGCTAGTTCTTCATATATATTGGTGGGTTCTGATGCTTAGGATGCTTGTTAAACAAATCCAAGAAAAAGGAAAAGTTAGTGAAGATATACGATCTGgtaagctgaat--gatgcactaaatatatgcctttctaagatgaactttttatgcattatgtcagaaaatattaacttgatgctgatgatccctatccatgtagcctcgggttttgaagtggccttactcaatagaaattttaacttgttatctgattgtaatctgtttcacatcacattttctttatgcag

upper sequence: AT1G13580.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA02G14040.1 (Glycine max), 5'ss of exon 5

TGCTTGCTTGTTCTTCACATTTATTGGTGGGTTTTGATGTATCGGATGCTTGTGAAACAAATACAAGATAGAGGCAAGCTTAGTGAAGATGTCAGATCAGgtaagtttggtttactgtaataaaaatcggttttcgcaccatccaaatcaaagaagagatcttcaagtttgtgtctttctcgcag-----------------------------------------------------------------------------------------------------------
| |||||  |||||||| || |||||||||||| |||||  | |||||||||| |||||||| ||||| | ||| ||  ||||||||||| || |||| |||||| |   |    || | |||| ||  |  ||   |  ||  |  |   |      || |   |   | |    ||   || |                                                                                                           
TTCTTGCAAGTTCTTCATATATATTGGTGGGTTCTGATGCTTAGGATGCTTGTTAAACAAATCCAAGAAAAAGGAAAAGTTAGTGAAGATATCCGATCTGgtaagctgaat--gatgcactaaatatatgcctttctaagatgaactttttatgcattatgtcagaaaatattaacttgatgctgatgatccctatccatgtagcctcgggttttgaagtggccttactcaatagaaattttaacttgttatctgattgtaatctgtttcacatcacattttcgttatgcag

upper sequence: AT1G13580.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv01s0010g01110.t01 (Vitis vinifera), 5'ss of exon 5

TGCTTGCTTGTTCTTCACATTTATTGGTGGGTTTTGATGTATCGGATGCTTGTGAAACAAATACAAGATAGAGGCAAGCTTAGTGAAGATGTCAGATCAGgtaagtttggtttactgtaataaaaatcggtttt---cgcaccatcca--aatcaaagaagagatcttcaagtttgtgtctttctcgcag------------
|||||||||||||||||||||||||||||||| |||||||||||||||||||| |||||| | ||||  |||||| | |||||||| ||||| ||||| |||||||||     |   |  |||     |  | |    |    ||       | |   | | || | | |  |   ||  |||   | |             
TGCTTGCTTGTTCTTCACATTTATTGGTGGGTGTTGATGTATCGGATGCTTGTTAAACAAGTCCAAGCAAGAGGCCAACTTAGTGATGATGTTAGATCTGgtaagtttaaaacaaaatgttaattcatgactctatatggtttattagttggttatgaatgggagcatga--tcaatggttttggagaaatagttggaaatt

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|164115090|gb|ES044491.1|ES044491

EST:     GAAACAAATACAAGATAGAGGCAAGCTTAGTGAAGATGTCAGATCAG                         ATTCTGAAGGCGAAGATGAGCACGAAGACTGATTTGATCACAAAGG
genomic: GAAACAAATACAAGATAGAGGCAAGCTTAGTGAAGATGTCAGATCAGgtaagtttgg ... tttctcgcagATTCTGAAGGCGAAGATGAGCACGAAGACTGATTTGATCACAAAGG

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