ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

ACATCTATAGGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTACCCAAACAAGCCACCAACTGTTCGGTTCGTCTCTAGGATGTTTCATCCAAACAgtaatctctctccctaccttttttgctgatcccctcatcaccctctgtcttttgtgcacgttaacatcaatatcagatttgattgtcaaaaattgtgtaacaatttattattcatgcag

Basic information

species	Zea mays
transcript	GRMZM2G022206_T01
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G022206_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os07g07240.1 (Oryza sativa), 5'ss of exon 3

ACATCTATAGGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTACCCAAACAAGCCACCAACTGTTCGGTTCGTCTCTAGGATGTTTCATCCAAACAgtaatctctctccctacct--tttttgctgatcccctcatcaccctctgtcttttgtgcacgttaacatcaatatcagatttgattgtcaaaaa-ttgtgtaacaatttattattcatgcag
          ||||||||||||||||||||||||||||||||||||| || |||||||| || ||||||||||| || ||||||||||| || ||||| ||||| |||||| ||    |  || |   |  | |  | || ||| |   | || |   ||  | || |||    |    ||  ||  |  |||| || | |||||   || |||||||||||
----------GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGCCGACTGTTCGGTTTGTTTCTAGGATGTTCCACCCAAATAgtaagctctcttcccgtgtgattatatattgttcaataattaccttacat-ttgtaaacaaataaagatcttcgttt--ttgaataatggaaaacttatttaacatcatactattcatgcag

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|14245319|gb|BG873901.1|BG873901

EST:     AAACAAGCCACCAACTGTTCGGTTCGTCTCTAGGATGTTTCATCCAAACA                         TATATGCTGATGGAAGCATCTGCTTGGATATCCTACAGAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTTCGGTTCGTCTCTAGGATGTTTCATCCAAACAgtaatctctc ... attcatgcagTATATGCTGATGGAAGCATCTGCTTGGATATCCTACAGAACCAGTGGAGTC

EST: gi|60394682|gb|DN227552.1|DN227552

EST:     AAACAAGCCACCAACTGTTCGGTTCGTCTCTAGGATGTTTCATCCAAACA                         TATATGCTGATGGAAGCATCTGCTTGGATATCCTACAGAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTTCGGTTCGTCTCTAGGATGTTTCATCCAAACAgtaatctctc ... attcatgcagTATATGCTGATGGAAGCATCTGCTTGGATATCCTACAGAACCAGTGGAGTC

EST: gi|9953749|gb|BE640332.1|BE640332

EST:     AAACAAGCCACCAACTGTTCGGTTCGTCTCTAGGATGTTTCATCCAAACA                         TATATGCTGATGGAAGCATCTGCTTGGATATCCTACAGAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTTCGGTTCGTCTCTAGGATGTTTCATCCAAACAgtaatctctc ... attcatgcagTATATGCTGATGGAAGCATCTGCTTGGATATCCTACAGAACCAGTGGAGTC

EST: gi|60355643|gb|DN222616.1|DN222616

EST:     AAACAAGCCACCAACTGTTCGGTTCGTCTCTAGGATGTTTCATCCAAACA                         TATATGCTGATGGAAGCATCTGCTTGGATATCCTACAGAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTTCGGTTCGTCTCTAGGATGTTTCATCCAAACAgtaatctctc ... attcatgcagTATATGCTGATGGAAGCATCTGCTTGGATATCCTACAGAACCAGTGGAGTC

EST: gi|14244254|gb|BG842201.2|BG842201

EST:     TGTTCGGTTCGTCTCTAGCATGTTTCATCCAAACA                         TATATGCTGATGCAAGCATCTGCTTGGATATCCTACAGAACCAGTGGAGTC
genomic: TGTTCGGTTCGTCTCTAGGATGTTTCATCCAAACAgtaatctctc ... attcatgcagTATATGCTGATGGAAGCATCTGCTTGGATATCCTACAGAACCAGTGGAGTC

EST: gi|18170360|gb|BM340200.1|BM340200

EST:     AAACAAGCCACCAACTGTTCGGTTCGTCTCTAGGATGTTTCATCCAAACA                         TATATGCTGATGGAAGCATCTGCTTGGATATCCTACAGAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTTCGGTTCGTCTCTAGGATGTTTCATCCAAACAgtaatctctc ... attcatgcagTATATGCTGATGGAAGCATCTGCTTGGATATCCTACAGAACCAGTGGAGTC

EST: gi|31250386|gb|CD219410.1|CD219410

EST:     AAACAAGCCACCAACTGTTCGGTTTGTCTCTAGGATGTTTCATCCAAACA                         TATATGCTGATGGAAGCATCTGCTTGGATATCCTACAGAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTTCGGTTCGTCTCTAGGATGTTTCATCCAAACAgtaatctctc ... attcatgcagTATATGCTGATGGAAGCATCTGCTTGGATATCCTACAGAACCAGTGGAGTC

EST: gi|213192747|gb|FM193959.1|FM193959

EST:     AAACAAGCCACCAACTGTTCGGTTCGTCTCTAGGGTGTTTCATCCAAACA                         TATATGCTGATGGAAGCATCTGCTTGGATATCCTACAGAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTTCGGTTCGTCTCTAGGATGTTTCATCCAAACAgtaatctctc ... attcatgcagTATATGCTGATGGAAGCATCTGCTTGGATATCCTACAGAACCAGTGGAGTC

EST: gi|60348082|gb|DN215055.1|DN215055

EST:     AAACAAGCCACCAACTGTTCGGTTCGTCTCTAGGATGTTTCATCCAAACA                         TATATGCTGATGGAAGCATCTGCTTGGATATCCTACAGAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTTCGGTTCGTCTCTAGGATGTTTCATCCAAACAgtaatctctc ... attcatgcagTATATGCTGATGGAAGCATCTGCTTGGATATCCTACAGAACCAGTGGAGTC

EST: gi|211493066|gb|FL480139.1|FL480139

EST:     AAACAAGCCACCAACTGTTCGGTTCGTCTCTAGGATGTTTCATCCAAACA                         TATATGCTGATGGAAGCATCTGCTTGGATATCCTACAGAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTTCGGTTCGTCTCTAGGATGTTTCATCCAAACAgtaatctctc ... attcatgcagTATATGCTGATGGAAGCATCTGCTTGGATATCCTACAGAACCAGTGGAGTC

EST: gi|9954028|gb|BE640611.1|BE640611

EST:     AAACAAGCCACCAACTGTTCGGTTCGTCTCTAGGATGTTTCATCCAAACA                         TATATGCTGATGGAAGCATCTGCTTGGATATCCTACAGAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTTCGGTTCGTCTCTAGGATGTTTCATCCAAACAgtaatctctc ... attcatgcagTATATGCTGATGGAAGCATCTGCTTGGATATCCTACAGAACCAGTGGAGTC

EST: gi|6466737|gb|AW191397.1|AW191397

EST:     AAACAAGCCACCAACTGTTCGGTTCGTCTCTAGGATGTTTCATCCAAACA                         TATATGCTGATGGAAGCATCTGCTTGGATATCCTACAGAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTTCGGTTCGTCTCTAGGATGTTTCATCCAAACAgtaatctctc ... attcatgcagTATATGCTGATGGAAGCATCTGCTTGGATATCCTACAGAACCAGTGGAGTC

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 4 RNA-Seq libraries.

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 478

ACATCTATAGGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTACCCAAACAAGCCACCAACTGTTCGGTTCGTCTCTAGGATGTTTCATCCAAACAgtaatctctc ... attcatgcagTATATGCTGATGGAAGCATCTGCTTGGATATCCTACAGAACCAGTGGAGTCCTATATATGATGTTGCTGCAATCTTGACTTCTATTCAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 689

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 671

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 367

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACATCTATAGGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTACCCAAACAAGCCACCAACTGTTCGGTTCGTCTCTAGGATGTTTCATCCAAACAgtaatctctctccctaccttttttgctgatcccctcatcaccctctgtcttttgtgcacgttaacatcaatatcagatttgattgtcaaaaattgtgtaacaatttattattcatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG