ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtttcatgtagttgagttttaatcactcattgatcaatcaatattggaaatcatgactgattttcttgggggtttgttgtagGTCTAATTGATATGGCGATCAGGAACAATGTTTTGATCGGTGGAGATGATTTCAAGAGTGGTCAAACCAAGATGAAATCTGTCTTGGTTGATTTCCTAGT

Basic information

species	Arabidopsis thaliana
transcript	AT4G39800.1
intron #	5
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 5

gtttcatgtagttga--gttttaatcactcattgatcaatcaatattggaaatcatgactgattttcttgggggtttgttgtagGTCTAATTGATATGGCGATCAGGAACAATGTTTTGATCGGTGGAGATGATTTCAAGAGTGGTCAAACCAAGATGAAATCTGTCTTGGTTGATTTCCTAGT
     ||||| ||    || |  |  | |    | |  ||   |  |     ||||| || ||||  ||      |   |  ||| || || ||| | || || | ||||||     |||| ||||| ||||||||||||||||| || || |||||||| |||||||||||||||||||||||
---gtatgtaattttctgtgtagagtagtatgcggtttatt--ttctcaggttcatggcttatttgttta----ctgtgtacagGGCTGATCGATCTTGCTATTAAGAACAACTGCCTGATTGGTGGTGATGATTTCAAGAGTGGACAGACAAAGATGAAGTCTGTCTTGGTTGATTTCCTAGT

upper sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G155242_T01 (Zea mays), 3'ss of exon 5

--------------------------gtttcatgtagttgagttttaatcactca--ttgatcaatcaatattggaaatc-atgactgattttcttgggggtttgtt-gtagGTCTAATTGATATGGCGATCAGGAACAATGTTTTGATCGGTGGAGATGATTTCAAGAGTGGTCAAACCAAGATGAAATCTGTCTTGGTTGATTTCCTAGT
                          | ||||||  ||||  |||   |  |  |  || ||       ||||     || | | || ||| |    |  |  |||| ||||| || |||||| | || || |  |||||    ||||| ||||| || || ||||||||||| || ||||||||||||||||||||||| |||||||| ||
gtgcgtggtttggtgtgtttgcaaaagcttcatggtgttgcatttctgttccaaagtttcatggtgttgtatttctgttccaaggcttattatacctgttgcatgttcgtagGGCTGATTGATCTTGCTATAAAAAACAACTGCTTGATTGGTGGTGACGACTTCAAGAGTGGACAGACCAAGATGAAATCTGTCTTGGTCGATTTCCTTGT

upper sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 5

----gtttcatgtagttgagttttaatcactcat--tgatcaatcaatattggaaatcatgactgattttcttgggggtttgttgtagGTCTAATTGATATGGCGATCAGGAACAATGTTTTGATCGGTGGAGATGATTTCAAGAGTGGTCAAACCAAGATGAAATCTGTCTTGGTTGATTTCCTAGT
    ||||  | | ||    |   ||    | ||  || |  |||  | ||  |||   | | |    || ||    ||||||   ||| || |||||| | || |||| ||||||     |||||||||| || || ||||||||||| || |||||||||||||| ||| |||||||||| || ||
gtgtgtttagtttggtgtgttcccaaagttttatggtgttgcatctctgttcaaaaaacttattatacttgtttcatgtttgt---agGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACTTCAAGAGTGGGCAGACCAAGATGAAATCGGTCCTGGTTGATTTTCTTGT

upper sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G392513_T02 (Zea mays), 3'ss of exon 3

-----------gtttcatgtagttgagttttaatcactcattga-tcaatcaatattggaaatc------atgactgatttt-cttgggggtttgttgtagGTCTAATTGATATGGCGATCAGGAACAATGTTTTGATCGGTGGAGATGATTTCAAGAGTGGTCAAACCAAGATGAAATCTGTCTTGGTTGATTTCCTAGT
           |  |  ||| ||| |||||       |     | |       | ||| |  ||      | |||| ||| | | ||  |  |  ||||||| || |||||| | || |||| ||||||     |||||||||| || || ||||||||||| || |||||||||||||| ||| | ||||| ||||||||
aacacttttgtgcctggtgt-gtttagtttggtgtgtttgcaaagttttatggtgttgcatttctgttcaaagacttattatacgtgttgcatgtttgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACTTCAAGAGTGGGCAGACCAAGATGAAATCAGTCCTAGTTGAATTCCTAGT

upper sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G392513_T01 (Zea mays), 3'ss of exon 1

----gtttcatgtagttgagttttaatcactcattgatcaatcaatattggaaatcatgactgatt-ttcttgggggtttgttgtagGTCTAATTGATATGGCGATCAGGAACAATGTTTTGATCGGTGGAGATGATTTCAAGAGTGGTCAAACCAAGATGAAATCTGTCTTGGTTGATTTCCTAGT
    ||||  | | || | ||||  |    |   || |    || |  ||   |  | |||| ||| | | ||  |  |  ||||||| || |||||| | || |||| ||||||     |||||||||| || || ||||||||||| || |||||||||||||| ||| | ||||| ||||||||
gtgtgtttagtttggt-gtgtttgcaaagttttatggtgttgcatttctgttca--aagacttattatacgtgttgcatgtttgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACTTCAAGAGTGGGCAGACCAAGATGAAATCAGTCCTAGTTGAATTCCTAGT

upper sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G145638_T02 (Zea mays), 3'ss of exon 1

----gtttcatgtagttgagttttaatcactcattgatcaatcaatattggaaatcatgactgatt-ttcttgggggtttgttgtagGTCTAATTGATATGGCGATCAGGAACAATGTTTTGATCGGTGGAGATGATTTCAAGAGTGGTCAAACCAAGATGAAATCTGTCTTGGTTGATTTCCTAGT-
    ||||  | | || | ||||  |    |   || |    || |  ||   |  | |||| ||| | ||||  |  |  ||||||| || |||||| | || |||| ||||||     |||||||||  || || ||||||||||| || |||||||||||||| ||| ||||||||||||| || 
gtgtgtttagtttggt-gtgtttgcaaagttttatggtgttgcatttctgttca--aagacttattatacttgttgcatgtttgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGTTGACGACTTCAAGAGTGG-CAGACCAAGATGAAATCAGTCCTGGTTGATTTCCTTGTT

upper sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G02210.4 (Glycine max), 3'ss of exon 5

----gtttcatgtagttgagttttaatcactcattgatcaatcaatattggaaatcatgactgatttt---cttgggggtttgttgt-agGTCTAATTGATATGGCGATCAGGAACAATGTTTTGATCGGTGGAGATGATTTCAAGAGTGGTCAAACCAAGATGAAATCTGTCTTGGTTGATTTCCTAGT
    | | | ||   ||  ||      |||   || |    |   ||||     | ||   |||  ||    ||| |   ||||  | ||| || |||||| | || |||  ||  ||   |||||| ||||||||||| |||||||||||||| ||||| ||||||||||| ||||||||||| || ||
gttggatgcttgcctttatgtcccccccacaacttaaattgtttgtatttatgctaatttgtgaactttggtttgtgttgttgtcatcagGGCTGATTGATCTTGCCATCGCGAGGAACACTTTGATTGGTGGAGATGACTTCAAGAGTGGTCAGACCAAAATGAAATCTGTGTTGGTTGATTTTCTTGT

upper sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G31450.2 (Glycine max), 3'ss of exon 5

----------gtttcatgtagttgagttt-taatcactcattgatcaatcaatattggaaatcatgactgattttcttgggggtttgttgtagGTCTAATTGATATGGCGATCAGGAACAATGTTTTGATCGGTGGAGATGATTTCAAGAGTGGTCAAACCAAGATGAAATCTGTCTTGGTTGATTTCCTAGT
          | ||  | |  ||  ||   | || |    ||  | |  ||| ||    ||   ||    |||||  |  | ||||     ||| || |||||| |||| |||| ||  ||   |||||| || |||||||| || ||||||||||| ||||| ||||||||||| ||||| |||||||| ||
gttcattattgattattattattatgtgggttattaaattttatttatgcaaaataaataaat-tggtgaattttgctttgtgttttcgtcagGGCTGATTGATCTGGCCATCAAGAGGAACAGTTTGATTGGAGGAGATGACTTTAAGAGTGGTCAGACCAAAATGAAATCTGTGTTGGTGGATTTCCTTGT

upper sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G14670.2 (Glycine max), 3'ss of exon 5

gtttcatgt-agttgagttttaatcactcattgatcaatcaatattggaaatcat---gactgattttcttgggggtttgttgtagGTCTAATTGATATGGCGATCAGGAACAATGTTTTGATCGGTGGAGATGATTTCAAGAGTGGTCAAACCAAGATGAAATCTGTCTTGGTTGATTTCCTAGT
||||  | | |       |  ||  | |   | |     ||| |||  |||  ||   |    ||||      | ||||     ||| || |||||| |||| ||||  |  |||  |||||| || |||||||| || ||||||||||| ||||| |||||||| || ||||| |||||||||||
gtttattattaaacattatgcaaaaaatagctaacgttacaaaatttaaaaatatatgggtgaatttgtacttgtgttttcatcagGACTCATTGATCTGGCCATCAAAAGGAATAGTTTGATTGGAGGAGATGACTTTAAGAGTGGTCAGACCAAAATGAAATCGGTGTTGGTGGATTTCCTAGT

upper sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv07s0031g00920.t01 (Vitis vinifera), 3'ss of exon 5

------------------gtttcatgtagttgagttttaatcactcattgatcaatcaatattggaaatcatgactgattttcttgggggtttgt-------tgtagGTCTAATTGATATGGCGATCAGGAACAATGTTTTGATCGGTGGAGATGATTTCAAGAGTGGTCAAACCAAGATGAAATCTGTCTTGGTTGATTTCCTAGT
                     |  | ||  |||   |||   | ||||     |       |   |  |||    || |||| |||    | | |       |  ||| || |||||| |||| || | ||  |||  |||||| ||||| |||||||| ||||||||||||||||||||||||||||| ||||| |||||||| ||
gttcttaatctgaaattttccttttctatgtgaaggttatgaattcatcatagagggggcgtctaatctcactcatgtttttgttgtcaatctttgtatgtcttcagGGCTGATTGATTTGGCTATTAAGAGGAATAGTTTGATTGGTGGGGATGATTTTAAGAGTGGTCAAACCAAGATGAAATCTGTATTGGTGGATTTCCTTGT

upper sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S267_10V6.1 (Physcomitrella patens), 3'ss of exon 5

-----------------------gtttcatgtagttgagttttaatcactcattgatcaa-tcaatattggaaatcatgactgattttcttgggggtttgttgtagGTCTAATTGATATGGCGATCAGGAACAATGTTTTGATCGGTGGAGATGATTTCAAGAGTGGTCAAACCAAGATGAAATCTGTCTTGGTTGATTTCCTAGT
                         || |||  ||    ||   |  | ||  | || || | || | ||    | |||     | |    ||   |||| || |||  |||||||    ||  |   ||| ||   | | || || || ||||| |||||||| || ||||||||||||||||||||  | || || ||||| ||
gcgacttattcgagcatctgaaaccttgatgaggtctgcttccgaaaattccctcataaacttaacagtgcgt-ttatg-----tatatcgggaactttggtgcagGCGTAATTGAGTACGCTGTAGAGAAGAAATCTCTTATTGGCGGTGATGACTTCAAGAGCGGACAAACCAAGATGAAATCTGTGCTTGTGGACTTCCTCGT

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|47829323|gb|CK119007.1|CK119007

EST:     TGAGGGAATCCCGTTCATCAATGGAAGCCCTCAAAACACCTTTGTTCCAG                         GTCTAATTGATATGGCGATCAGGA
genomic: TGAGGGAATCCCGTTCATCAATGGAAGCCCTCAAAACACCTTTGTTCCAGgtttcatgta ... tttgttgtagGTCTAATTGATATGGCGATCAGGA

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

cattgatcaatcaatattggaaatcatgactgattttcttgggggtttgttgtagGTCTAATTGATATGGCGATCAGGAACAATGTTTTGATCGGTGGAGATGATTTCAAGAGTGGTCAAACCAAGATGAAATCTGTCTTGGTTGATTTCCTAGT

                           gactgat  putative branch site (score: 3)
        aatcaatatt  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