ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CAAGTCAGCGAGGCTCAGGCAAGCAAAAGAGGAGGCTGAGCGGGAAATAGCCGAATACCGTGCCCAGATGGAGGCTGAGTTTCAGAGGAAGGTTGCAGAGgtatgcacgccatgtcccatttttccccactggactacaggacctcacttctgtgtcttggtgactacag

Basic information

species	Zea mays
transcript	GRMZM2G094928_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G094928_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os04g51270.1 (Oryza sativa), 5'ss of exon 3

CAAGTCAGCGAGGCTCAGGCAAGCAAAAGAGGAGGCTGAGCGGGAAATAGCCGAATACCGTGCCCAGATGGAGGCTGAGTTTCAGAGGAAGGTTGCAGAGgtatgcacgccatgtcccatttttccccactggactacaggacctcacttctgtgtcttggtgactacag------------------------------
 || || || ||||| |||||||||||||||||||||||| |||||||||| |||||||||||||||||||||||||| ||||||||||||||||||||||||||  |  |  |  | || |||    |   | ||   |    |    |   | ||    |  | | |                               
AAAATCGGCAAGGCTTAGGCAAGCAAAAGAGGAGGCTGAGAGGGAAATAGCTGAATACCGTGCCCAGATGGAGGCTGAATTTCAGAGGAAGGTTGCAGAGgtatgttcatcgggaac-atatttgtgtagaaggcttgtgtgtataggatacat-tcccaattcccatattcatctaatggtcctatttgttatttccag

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|116828248|gb|EC856042.1|EC856042

EST:     CTGAATACCGTGCCCAGATGGAGGCTGAGTTTCAGAGGAAGGTTGCAGAG                         AGCAGCGGCGACTCCGGTGCAAACGTCAAGCGTCTCGAGGAAGAAACTGCG
genomic: CCGAATACCGTGCCCAGATGGAGGCTGAGTTTCAGAGGAAGGTTGCAGAGgtatgcacgc ... gtgactacagAGCAGCGGCGACTCCGGTGCAAACGTCAAGCGTCTCGAGGAAGAAACGGCG

EST: gi|37376966|gb|CF625049.1|CF625049

EST:     CCGAATACCGTGCCCAGATGGAGGCTGAATTTCAGAGGAAGGTTGCAGAG                         AGCAGCGGCGACTCTGGTGCAAACGTCAAGCGTCTGGAGGAAGAAACGGCG
genomic: CCGAATACCGTGCCCAGATGGAGGCTGAGTTTCAGAGGAAGGTTGCAGAGgtatgcacgc ... gtgactacagAGCAGCGGCGACTCCGGTGCAAACGTCAAGCGTCTCGAGGAAGAAACGGCG

EST: gi|40334838|gb|CK368908.1|CK368908

EST:     CCGAATACCGTGCCCAGATGGAGGCTGAATTTCAGAGGAAGGTTGCAGAG                         AGCAGCGGCGACTCTGGTGCAAACGTCAAGCGTCTGGAGGAAGAAACGGCG
genomic: CCGAATACCGTGCCCAGATGGAGGCTGAGTTTCAGAGGAAGGTTGCAGAGgtatgcacgc ... gtgactacagAGCAGCGGCGACTCCGGTGCAAACGTCAAGCGTCTCGAGGAAGAAACGGCG

EST: gi|32923710|gb|CF028522.1|CF028522

EST:     CCGAATACCGTGCCCAGATGGAGGCTGAATTTCAGAGGAAGGTTGCAGAG                         AGCAGCGGCGACTCTGGTGCAAACGTCAAGCGTCTGGAGGAAGAAACGGCG
genomic: CCGAATACCGTGCCCAGATGGAGGCTGAGTTTCAGAGGAAGGTTGCAGAGgtatgcacgc ... gtgactacagAGCAGCGGCGACTCCGGTGCAAACGTCAAGCGTCTCGAGGAAGAAACGGCG

EST: gi|32923648|gb|CF028460.1|CF028460

EST:     CCGAATACCGTGCCCAGATGGAGGCTGAATTTCAGAGGAAGGTTGCAGAG                         AGCAGCGGCGACTCTGGTGCAAACGTCAAGCGTCTGGAGGAAGAAACGGCG
genomic: CCGAATACCGTGCCCAGATGGAGGCTGAGTTTCAGAGGAAGGTTGCAGAGgtatgcacgc ... gtgactacagAGCAGCGGCGACTCCGGTGCAAACGTCAAGCGTCTCGAGGAAGAAACGGCG

EST: gi|88758348|gb|DY542717.1|DY542717

EST:     CCGAATACCGTGCCCAGATGGAGGCTGAATTTCAGAGGAAGGTTGCAGAG                         AGCAGCGGCGACTCTGGTGCAAACGTCAAGCGTCTGGAGGAAGAAACGGCG
genomic: CCGAATACCGTGCCCAGATGGAGGCTGAGTTTCAGAGGAAGGTTGCAGAGgtatgcacgc ... gtgactacagAGCAGCGGCGACTCCGGTGCAAACGTCAAGCGTCTCGAGGAAGAAACGGCG

EST: gi|32914943|gb|CF019755.1|CF019755

EST:     CCGAATACCGTGCCCAGATGGAGGCTGAATTTCAGAGGAAGGTTGCAGAG                         AGCAGCGGCGACTCTGGTGCAAACGTCAAGCGTCTGGAGGAAGAAACGGCG
genomic: CCGAATACCGTGCCCAGATGGAGGCTGAGTTTCAGAGGAAGGTTGCAGAGgtatgcacgc ... gtgactacagAGCAGCGGCGACTCCGGTGCAAACGTCAAGCGTCTCGAGGAAGAAACGGCG

EST: gi|32868000|gb|CF007682.1|CF007682

EST:     CCGAATACCGTGCCCAGATGGAGGCTGAATTTCAGAGGAAGGTTGCAGAG                         AGCAGCGGCGACTCTGGTGCAAACGTCAAGCGTCTGGAGGAAGAAACGGCG
genomic: CCGAATACCGTGCCCAGATGGAGGCTGAGTTTCAGAGGAAGGTTGCAGAGgtatgcacgc ... gtgactacagAGCAGCGGCGACTCCGGTGCAAACGTCAAGCGTCTCGAGGAAGAAACGGCG

EST: gi|37378333|gb|CF625852.1|CF625852

EST:     CCGAATACCGTGCCCAGATGGAGGCTGAATTTCAGAGGAAGGTTGCAGAG                         AGCAGCGGCGACTCTGGTGCAAACGTCAAGCGTCTGGAGGAAGAAACGGCG
genomic: CCGAATACCGTGCCCAGATGGAGGCTGAGTTTCAGAGGAAGGTTGCAGAGgtatgcacgc ... gtgactacagAGCAGCGGCGACTCCGGTGCAAACGTCAAGCGTCTCGAGGAAGAAACGGCG

EST: gi|6964683|gb|AW433376.1|AW433376

EST:     CCGAATACCGTGCCCAGATGGAGGCTGAATTTCAGAGGAAGGTTGCAGAG                         AGCAGCGGCGACTCTGGTGCAAACGTCAAGCGTCTGGAGGAAGAAACGGCG
genomic: CCGAATACCGTGCCCAGATGGAGGCTGAGTTTCAGAGGAAGGTTGCAGAGgtatgcacgc ... gtgactacagAGCAGCGGCGACTCCGGTGCAAACGTCAAGCGTCTCGAGGAAGAAACGGCG

EST: gi|211488772|gb|FK974291.1|FK974291

EST:     CCGAATACCGTGCCCAGATGGAGGCTGAATTTCAGAGGAAGGTTGCAGAG                         AGCAGCGGCGACTCTGGTGCAAACGTCAAGCGTCTGGAGGAAGAAACGGCG
genomic: CCGAATACCGTGCCCAGATGGAGGCTGAGTTTCAGAGGAAGGTTGCAGAGgtatgcacgc ... gtgactacagAGCAGCGGCGACTCCGGTGCAAACGTCAAGCGTCTCGAGGAAGAAACGGCG

EST: gi|32924033|gb|CF028845.1|CF028845

EST:     CCGAATACCGTGCCCAGATGGAGGCTGAATTTCAGAGGAAGGTTGCAGAG                         AGCAGCGGCGACTCTGGTGCAAAC
genomic: CCGAATACCGTGCCCAGATGGAGGCTGAGTTTCAGAGGAAGGTTGCAGAGgtatgcacgc ... gtgactacagAGCAGCGGCGACTCCGGTGCAAAC

EST: gi|33942272|gb|CF348872.1|CF348872

EST:     CTGAATACCGTGCCCAGATGGAGGCTGAGTTTCAGAGGAAGGTTGCAGAG                         AGCAGCGGCGACTCCGGTGCAAACGTCAAGCGTCTCGAGGAAGAAACTGCG
genomic: CCGAATACCGTGCCCAGATGGAGGCTGAGTTTCAGAGGAAGGTTGCAGAGgtatgcacgc ... gtgactacagAGCAGCGGCGACTCCGGTGCAAACGTCAAGCGTCTCGAGGAAGAAACGGCG

EST: gi|47961542|gb|CN844251.1|CN844251

EST:     CTGAATACCGTGCCCAGATGGAGGCTGAGTTTCAGAGGAAGGTTGCAGAG                         AGCAGCGGCGACTCCGGTGCAAACGTCAAGCGTCTCGAGGAAGAAACTGCG
genomic: CCGAATACCGTGCCCAGATGGAGGCTGAGTTTCAGAGGAAGGTTGCAGAGgtatgcacgc ... gtgactacagAGCAGCGGCGACTCCGGTGCAAACGTCAAGCGTCTCGAGGAAGAAACGGCG

EST: gi|37399671|gb|CF637168.1|CF637168

EST:     CCGAATACCGTGCCCAGATGGAGGCTGAATTTCAGAGGAAGGTTGCAGAG                         AGCAGCGGCGACTCTGGTGCAAACGTCAAGCGTCTGGAGGAAGAAACGGCG
genomic: CCGAATACCGTGCCCAGATGGAGGCTGAGTTTCAGAGGAAGGTTGCAGAGgtatgcacgc ... gtgactacagAGCAGCGGCGACTCCGGTGCAAACGTCAAGCGTCTCGAGGAAGAAACGGCG

EST: gi|211500319|gb|FK974353.1|FK974353

EST:     CCGAATACCGTGCCCAGATGGAGGCTGAATTTCAGAGGAAGGTTGCAGAG                         AGCAGCGGCGACTCTGGTGCAAACGTCAAGCGTCTGGAGGAAGAAACGGCG
genomic: CCGAATACCGTGCCCAGATGGAGGCTGAGTTTCAGAGGAAGGTTGCAGAGgtatgcacgc ... gtgactacagAGCAGCGGCGACTCCGGTGCAAACGTCAAGCGTCTCGAGGAAGAAACGGCG

EST: gi|211500326|gb|FK974360.1|FK974360

EST:     CCGAATACCGTGCCCAGATGGAGGCTGAATTTCAGAGGAAGGTTGCAGAG                         AGCAGCGGCGACTCTGGTGCAAACGTCAAGCGTCTGGAGGAAGAAACGGCG
genomic: CCGAATACCGTGCCCAGATGGAGGCTGAGTTTCAGAGGAAGGTTGCAGAGgtatgcacgc ... gtgactacagAGCAGCGGCGACTCCGGTGCAAACGTCAAGCGTCTCGAGGAAGAAACGGCG

EST: gi|211488776|gb|FK974295.1|FK974295

EST:     CCGAATACCGTGCCCAGATGGAGGCTGAGTTTCAGAGGAAGGTTGCAGAG                         AGCAGCG-CGACTCCGGTGCAAACGTCAAGCGTCTCGAGGAAKAAACGGCG
genomic: CCGAATACCGTGCCCAGATGGAGGCTGAGTTTCAGAGGAAGGTTGCAGAGgtatgcacgc ... gtgactacagAGCAGCGGCGACTCCGGTGCAAACGTCAAGCGTCTCGAGGAAGAAACGGCG

EST: gi|32924355|gb|CF029167.1|CF029167

EST:     CCGAATACCGTGCCCAGATGGAGGCTGAATTTCAGAGGAAGGTTGCAGAG                         AGCAGCGGCGACTCTGGTGCAAACGTCAAGCGTCTGGAGGAAGAAACGGCG
genomic: CCGAATACCGTGCCCAGATGGAGGCTGAGTTTCAGAGGAAGGTTGCAGAGgtatgcacgc ... gtgactacagAGCAGCGGCGACTCCGGTGCAAACGTCAAGCGTCTCGAGGAAGAAACGGCG

EST: gi|32915380|gb|CF020192.1|CF020192

EST:     CCGAATACCGTGCCCAGATGGAGGCTGAATTTCAGAGGAAGGTTGCAGAG                         AGCAGCGGCGACTCTGGTGCAAACGTCAAGCGTCTGGAGGAAGAAACGGCG
genomic: CCGAATACCGTGCCCAGATGGAGGCTGAGTTTCAGAGGAAGGTTGCAGAGgtatgcacgc ... gtgactacagAGCAGCGGCGACTCCGGTGCAAACGTCAAGCGTCTCGAGGAAGAAACGGCG

EST: gi|32924060|gb|CF028872.1|CF028872

EST:     CCGAATACCGTGCCCAGATGGAGGCTGAATTTCAGAGGAAGGTTGCAGAG                         AGCAGCGGCGACTCTGGTGCAAACGTCAAGCGTCTGGAGGAAGAAACGGCG
genomic: CCGAATACCGTGCCCAGATGGAGGCTGAGTTTCAGAGGAAGGTTGCAGAGgtatgcacgc ... gtgactacagAGCAGCGGCGACTCCGGTGCAAACGTCAAGCGTCTCGAGGAAGAAACGGCG

EST: gi|32865624|gb|CF005306.1|CF005306

EST:     CCGAATACCGTGCCCAGATGGAGGCTGAATTTCAGAGGAAGGTTGCAGAG                         AGCAGCGGCGACTCTGGTGCAAACGTCAAGCGTCTGGAGGAAGAAACGGCG
genomic: CCGAATACCGTGCCCAGATGGAGGCTGAGTTTCAGAGGAAGGTTGCAGAGgtatgcacgc ... gtgactacagAGCAGCGGCGACTCCGGTGCAAACGTCAAGCGTCTCGAGGAAGAAACGGCG

EST: gi|4646350|gb|AI621680.1|AI621680

EST:     CCGAATACCGTGCCCAGATGGAGGCTGAGTTTCAGAGGAAGGTTGCAGAG                         AGCAGCGGCGACTCCGGTGCAAACGTCAAGCGTCTCGAGGAAGAAACGGCG
genomic: CCGAATACCGTGCCCAGATGGAGGCTGAGTTTCAGAGGAAGGTTGCAGAGgtatgcacgc ... gtgactacagAGCAGCGGCGACTCCGGTGCAAACGTCAAGCGTCTCGAGGAAGAAACGGCG

EST: gi|32923900|gb|CF028712.1|CF028712

EST:     CCGAATACCGTGCCCAGATGGAGGCTGAATTTCAGAGGAAGGTTGCAGAG                         AGCAGCGGCGACTCTGGTGCAAACGTCAAGCGTCTGGAGGAAGAAACGGCG
genomic: CCGAATACCGTGCCCAGATGGAGGCTGAGTTTCAGAGGAAGGTTGCAGAGgtatgcacgc ... gtgactacagAGCAGCGGCGACTCCGGTGCAAACGTCAAGCGTCTCGAGGAAGAAACGGCG

EST: gi|37377039|gb|CF625090.1|CF625090

EST:     CCGAATACCGTGCCCAGATGGAGGCTGAATTTCAGAGGAAGGTTGCAGAG                         AGCAGCGGCGACTCTGGTGCAAACGTCAAGCGTCTGGAGGAAGAAACGGCG
genomic: CCGAATACCGTGCCCAGATGGAGGCTGAGTTTCAGAGGAAGGTTGCAGAGgtatgcacgc ... gtgactacagAGCAGCGGCGACTCCGGTGCAAACGTCAAGCGTCTCGAGGAAGAAACGGCG

EST: gi|116822787|gb|EC866223.1|EC866223

EST:     CCGAATACCGTGCCCAGATGGAGGCTGAGTTTCAGAGGAAGGTTGCAGAG                         AGCAGCGGCGACTCCGGTGCAAACGTCAAGCGTCTCGAGGAAGAAACGGCG
genomic: CCGAATACCGTGCCCAGATGGAGGCTGAGTTTCAGAGGAAGGTTGCAGAGgtatgcacgc ... gtgactacagAGCAGCGGCGACTCCGGTGCAAACGTCAAGCGTCTCGAGGAAGAAACGGCG

EST: gi|32923845|gb|CF028657.1|CF028657

EST:     CCGAATACCGTGCCCAGATGGAGGCTGAATTTCAGAGGAAGGTTGCAGAG                         AGCAGCGGCGACTCTGGTGCAAACGTCAAGCGTCTGGAGGAAGAAACGGCG
genomic: CCGAATACCGTGCCCAGATGGAGGCTGAGTTTCAGAGGAAGGTTGCAGAGgtatgcacgc ... gtgactacagAGCAGCGGCGACTCCGGTGCAAACGTCAAGCGTCTCGAGGAAGAAACGGCG

RNA-Seq data

ATGC Supported by RNA-Seq exonic block that spans over the splice site

atgs Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.

Found data for 8 RNA-Seq libraries.

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 46

CAAGTCAGCGAGGCTCAGGCAAGCAAAAGAGGAGGCTGAGCGGGAAATAGCCGAATACCGTGCCCAGATGGAGGCTGAGTTTCAGAGGAAGGTTGCAGAGgtatgcacgc ... gtgactacagAGCAGCGGCGACTCCGGTGCAAACGTCAAGCGTCTCGAGGAAGAAACGGCGGCGAAGATCGAGCAACTCACCCAGCAGGCCGCAAGCATCTCCCCGGATG

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 513

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 141

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 984

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 185

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 645

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 154

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 694

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

        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGTCAGCGAGGCTCAGGCAAGCAAAAGAGGAGGCTGAGCGGGAAATAGCCGAATACCGTGCCCAGATGGAGGCTGAGTTTCAGAGGAAGGTTGCAGAGgtatgcacgccatgtcccatttttccccactggactacaggacctcacttctgtgtcttggtgactacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA