ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtcaggctgttcatcgaatgattgctttaatgtcaggatatttctctgcttagaaggttgttgtaaacgtattggtatattgtacagGTCTTCCTTTTTGCAAACTCAAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAGCACAAGA

Basic information

species	Oryza sativa
transcript	LOC_Os05g40820.2
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os05g40820.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G074898_T01 (Zea mays), 3'ss of exon 3

gtcaggctgttcatcgaatgattgctttaatgtcaggatatttctctgcttagaaggttgttgtaaacgtattggtatattgt-acagGTCTTCCTTTTTGCAAACTCAAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAGCACAAGA
|| |   || |  |  | |  |||   ||   |    |  ||| | |    |  |  || | | ||    ||   | | || |   |||| ||||||||||| ||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||
gttac-ttgctgttacattttttgtaataggtttgtaagctttatatagc-atgatcttatggcaaggaaatacatctgtttttgtagGTTTTCCTTTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCAAAGCTTACCTGGACAGCAATGTACAGGAAGCAGCACAAGA

upper sequence: LOC_Os05g40820.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G142640_T03 (Zea mays), 3'ss of exon 2

gtcaggctgttcatcgaatgattgctttaatgtcaggatatttctctgcttagaaggttgttgta-aacgtattggtat--attgtacagGTCTTCCTTTTTGCAAACTCAAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAGCACAAGA
     | |  ||   |    |||  | |||       |||    | |    | | | ||||| |  || | | |   ||   || || |||||||||||||||| ||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||
-----gttactcgctgttacatttttataagagatttataagcttataga-aaatgtttgttatggaaagaacttacatttgttctatagGTCTTCCTTTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCAAAGCTTACCTGGACAGCAATGTACAGGAAGCAGCACAAGA

upper sequence: LOC_Os05g40820.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G110328_T04 (Zea mays), 3'ss of exon 3

gtcaggctgttcatcgaatgattgctttaatgtcaggatatttctctgcttagaaggttgt----tgtaaacgtattg-gtatattgtacagGTCTTCCTTTTTGCAAACTCAAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAGCACAAGA
        |||  |  |   ||    ||  ||| | || || |||  | ||| ||  |  |    || |||   | |   ||| || || |||| ||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||
--------gttact--agctatcatatttttgt-aagagatgtctaagattataaaatcttcttatggaaagaaactacatatgttttatagGTTTTCCTTTTTGCCAACTCAAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCAAAGCTTACCTGGACAGCAATGTACAGGAAGCAGCACAAGA

upper sequence: LOC_Os05g40820.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA03G34700.1 (Glycine max), 3'ss of exon 2

-------------------------------------------------------------gtcaggctgttcatcgaatgattgctttaa--tgtcaggatatttctctgct------tagaaggttgttgtaaacgtattggtatattg----tacagGTCTTCCTTTTTGCAAACTCAAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAGCACAAGA
                                                             ||     |    ||    ||||   ||| |  | |  || | ||||| || |      ||  |   || | | |  || || || | |||    || |||| ||||| ||||| ||||||||||| ||||| || ||||||||||||||||||||  ||||||| |||||||| || |||||||| ||||| ||||| |
gtgacataaaatatgtctcattgaattttgggtggatgtatctcatcatttcagtctggatgttcaatttgctatgatttgatcatttttaattatggggttttttctttgttactagttatgatactgatatgagggtttttgtttgttgaatctatagGTTTTCCTGTTTGCCAACTCAAAATGTAAGCGGTATTTCCACAACCGCCTGAAGCCCTCAAAGCTCACCTGGACTGCTATGTACAGAAAGCAACACAAAA

upper sequence: LOC_Os05g40820.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA13G21520.1 (Glycine max), 3'ss of exon 2

-----------------------------------------------------------gtcaggctgttcatcgaatgattgctttaa----tgtcaggatatttctctgct------tagaaggttgttgtaaacgtattggtatattg-----tacagGTCTTCCTTTTTGCAAACTCAAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAGCACAAGA
                                                           ||   | |    ||      ||    |||     | | |||   ||| | || |      ||  |   || | | |  |  || || | |||     ||||||| ||||| ||||| ||||||||||| ||| | || ||||||||| |  |||||||  ||||||| || ||||| || |||||| | |||||||| ||||
gtgacaatatgtttctcgttgagttttgggttgatgtatcgtttcatttgaaactggatgttctgtttactatgatgcaatcatattataagttatgaggggttttgtttgttatttgttatgatactgatatgaggggttttgtttgttgaaacttacagGTTTTCCTGTTTGCTAACTCAAAATGTAAGAGGTATTTCCACAACAGGTTGAAGCCGTCAAAGCTCACGTGGACTGCAATGTACCGAAAGCAGCATAAGA

upper sequence: LOC_Os05g40820.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA19G37370.2 (Glycine max), 3'ss of exon 2

-------------------------------------------gtcaggctgttc--------atcgaatgattgctttaatgtcaggatatttctctgctta--gaaggttgttgtaaacgtattggtat------------------attgtacagGTCTTCCTTTTTGCAAACTCAAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAGCACAAGA
                                           ||| || |||||        ||    ||||   |||   || | ||   || | || ||   |   ||| |  ||    || || |||                  | | ||||||| ||||| ||||||||||||||||| ||| | || |||||||| |||||||||||| ||||||| |||||||| || |||||||| ||||| ||||| |
gtaacataaaatatgttttgggttgatgtgtcgcattatttcagtctggttgttctgtttgcaatgatgtgatcattttttagttatgagggttttttgtttgttgctagttatgatattgatactgatatgaggatttttgtttgttgaatctacagGTTTTCCTGTTTGCAAACTCAAAATGTAAGAGGTATTTCCACAATCGCCTGAAGCCTTCAAAGCTCACCTGGACTGCAATGTACAGAAAGCAACACAAAA

upper sequence: LOC_Os05g40820.3 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv13s0074g00140.t01 (Vitis vinifera), 3'ss of exon 2

--------------------------------------------------------------------------------------gtcaggctgttcatcgaa---tgattgctttaatgtcaggatatttctctgcttag--------aaggttgttgtaaacgt---attggtatattgtacagGTCTTCCTTTTTGCAAACTCAAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAGCACAAGA
                                                                                       |     | || |  ||    || | |  ||  | |   | | ||| | | || |         ||  ||  | ||| |     |||| |  |||||  |||| || || ||||| || |||||||||||| | ||||| |||||||| || |||||| |||||||||||||||| || ||||| || ||||| || ||||
gtaaaaatgtggatttaattacatattttcaagtctcatatgaatatttaatttgcttgattgcctatcaaaaaatatttaatttccttgatttatttagagagcagtgttggggttgttattgtgctttttatattctgaatgtccattaatatttatataatctcgtaattgatcaattgt-tagGTATTTCTATTTGCCAATTCAAAATGCAAGAGATACTTTCACAACCGACTTAAGCCTTCAAAGCTTACCTGGACGGCTATGTATAGAAAGCAACATAAGA

upper sequence: LOC_Os05g40820.3 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv16s0100g00650.t01 (Vitis vinifera), 3'ss of exon 1

-------------------------------------------------gtcaggctgttcatcgaat--gattgctttaatgtcaggatatttctctgcttagaaggttgttgt--aaacgtattggtatattgta---cagGTCTTCCTTTTTGCAAACTCAAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAGCACAAGA
                                                  ||||    |       ||   |  ||||   |||   |   |   | | |||  |    |||     ||  | ||  || |  | ||   ||||| || || ||||| || || ||||||||| | |||||||||||||| || |||||  | |||||||| ||||||||||||||||| |||||||||||||
gtaaaatgtgatgatattttcaatttggttctgtcaggggcatgtatcattcagagcatatcctacattcaaacgcttccctgtattggcttaattttacttcaattactgtaactgaatagcatctgtttcatttatatcagGTTTTTCTCTTTGCCAATTCTAAATGCAAGAGGTACTTCCACAACCGGCTTAAGCCATCGAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGA

upper sequence: LOC_Os05g40820.3 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv08s0007g04210.t01 (Vitis vinifera), 3'ss of exon 2

--------------------------------------------------------------------gtcaggctg-ttcatcgaatgattgctttaatgtcaggatat----ttctctgcttagaaggttgttgtaaacgtattggtatattgtacagGTCTTCCTTTTTGCAAACTCAAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAGCACAAGA
                                                                    || |  ||  ||  |  | ||  |   ||    |||||   |    |  | | |||      |||   | ||  || |   |   | |  |||| || || ||||| || |||||||||||| | |||||||||||||| ||||||||  |||||||||||||||||||||||||||||||||| || || |
gtaattttatagctcattaaaatttatgttctgtatcagattattagccaactaaatttctactgaatgttaatcttctttcttcattgtcttggttgggctcaggggttgacctcttgtacttgtttaattgacattaaattactctcaatatatttagGTGTTTCTATTTGCCAATTCAAAATGCAAGAGGTACTTCCACAACCGGCTGAAGCCATCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAACATAAAA

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|88397656|gb|CI684589.1|CI684589

EST:     GAAGATATATCCAGGGAAAGGGCATTCGCTTTATTCGTGCTGATTCACAG                         GTCTTCCTTTTTGCAAACTCAAAATGCAAGCGCTACTTCCACAACCGCCTG
genomic: GAAGATATATCCAGGG-AAGGGCATTCGCTTTATTCGTGCTGATTCACAGgtcaggctgt ... tattgtacagGTCTTCCTTTTTGCAAACTCAAAATGCAAGCGCTACTTCCACAACCGCCTG

EST: gi|86417460|gb|CI031669.1|CI031669

EST:     TCGCTTTATTCGTGCTGATTCACAG                         GTCTTCCTTTTTGCAAACTCAAAATGCAAGCGCTACTTCCACAACCGCCTG
genomic: TCGCTTTATTCGTGCTGATTCACAGgtcaggctgt ... tattgtacagGTCTTCCTTTTTGCAAACTCAAAATGCAAGCGCTACTTCCACAACCGCCTG

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tcaggatatttctctgcttagaaggttgttgtaaacgtattggtatattgtacagGTCTTCCTTTTTGCAAACTCAAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAGCACAAGA

                                           tatattgta  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