ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CGCTTCCTCCTCAAGGAGACTCTCAACGTCTTGCTTGTGGAGAGTGATGATTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAGgtttgttttatcccaattcatccttcagtcgtttttctgacaggctatgatttcgcatattcatagcatcgatcataacttggagctgtttaacatctat...

Basic information

species	Zea mays
transcript	GRMZM2G005732_T02
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G005732_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os07g49460.3 (Oryza sativa), 5'ss of exon 4

CGCTTCCTCCTCAAGGAGACTCTCAACGTCTTGCTTGTGGAGAGTGATGATTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAGgtttgttttatcccaattcatccttcagtcgtttttctgacaggctatgatttcgcatattcatagcatcg-atcataacttggagctgtttaacatctat
|||||| |||  ||| ||||| |||| |||||||| || || || ||||| || ||||||||||| ||||||||||||||||||  |||||||||  ||||| ||| |  ||     || | || |  ||    ||||| |    |||   |  |  |     |  ||    ||  |  | |     |  |||  ||||  
CGCTTCATCCAGAAGAAGACTATCAAAGTCTTGCTAGTTGATAGCGATGACTCCACCAGGCAGGTGGTCAGTGCCCTGCTTCGTCACTGCATGTATGAAGgtctgtctcttctttcctccttctaccttctcacttctgtctatttatttatatgtttgcctttttcacaacatattttcctattattacttactatctg-

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|211360151|gb|FL133707.1|FL133707

EST:     TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCNTTGCTGCATGTACCAAG                         TTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAANATAAGA
genomic: TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAGgtttgtttta ... cctttttcagTTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA

EST: gi|211264499|gb|FL189953.1|FL189953

EST:     TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAG                         TTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA
genomic: TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAGgtttgtttta ... cctttttcagTTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA

EST: gi|211264494|gb|FL189948.1|FL189948

EST:     TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAG                         TTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA
genomic: TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAGgtttgtttta ... cctttttcagTTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA

EST: gi|211264496|gb|FL189950.1|FL189950

EST:     TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAG                         TTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA
genomic: TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAGgtttgtttta ... cctttttcagTTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA

EST: gi|211262066|gb|FL189945.1|FL189945

EST:     TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAG                         TTATCTCTGACGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA
genomic: TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAGgtttgtttta ... cctttttcagTTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA

EST: gi|211262067|gb|FL189946.1|FL189946

EST:     TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAG                         TTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA
genomic: TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAGgtttgtttta ... cctttttcagTTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA

EST: gi|211264495|gb|FL189949.1|FL189949

EST:     TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAG                         TTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA
genomic: TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAGgtttgtttta ... cctttttcagTTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA

EST: gi|211264502|gb|FL189956.1|FL189956

EST:     TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAG                         TTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA
genomic: TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAGgtttgtttta ... cctttttcagTTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA

EST: gi|211264497|gb|FL189951.1|FL189951

EST:     TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAG                         TTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA
genomic: TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAGgtttgtttta ... cctttttcagTTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA

EST: gi|211264493|gb|FL189947.1|FL189947

EST:     TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAG                         TTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA
genomic: TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAGgtttgtttta ... cctttttcagTTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA

EST: gi|211264506|gb|FL189960.1|FL189960

EST:     TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAG                         TTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA
genomic: TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAGgtttgtttta ... cctttttcagTTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA

EST: gi|211264505|gb|FL189959.1|FL189959

EST:     TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAG                         TTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA
genomic: TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAGgtttgtttta ... cctttttcagTTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA

EST: gi|211264501|gb|FL189955.1|FL189955

EST:     TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAG                         TTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA
genomic: TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAGgtttgtttta ... cctttttcagTTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA

EST: gi|211264504|gb|FL189958.1|FL189958

EST:     TTCAACCAGGCAGGTCGTCAGNGCCCTGCTTCGTTGCTGCATGTACCAAG                         NTATCTCTGCCGAAAATGGNCAGCAAGCATGGGCTTATCTTGAAGATAAGA
genomic: TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAGgtttgtttta ... cctttttcagTTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA

EST: gi|211264507|gb|FL189961.1|FL189961

EST:     TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAG                         TTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA
genomic: TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAGgtttgtttta ... cctttttcagTTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA

EST: gi|211266931|gb|FL189964.1|FL189964

EST:     TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAG                         TTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA
genomic: TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAGgtttgtttta ... cctttttcagTTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA

EST: gi|211264498|gb|FL189952.1|FL189952

EST:     TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAG                         TTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA
genomic: TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAGgtttgtttta ... cctttttcagTTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA

EST: gi|211264500|gb|FL189954.1|FL189954

EST:     TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAG                         TTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA
genomic: TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAGgtttgtttta ... cctttttcagTTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA

EST: gi|211266930|gb|FL189963.1|FL189963

EST:     TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAG                         TTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA
genomic: TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAGgtttgtttta ... cctttttcagTTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA

EST: gi|211264503|gb|FL189957.1|FL189957

EST:     TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAG                         TTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA
genomic: TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAGgtttgtttta ... cctttttcagTTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA

EST: gi|211262065|gb|FL189944.1|FL189944

EST:     TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAG                         TTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA
genomic: TTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAGgtttgtttta ... cctttttcagTTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGA

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: 48 (upstream exon), 45 (downstream exon)
Score: 40

CGCTTCCTCCTCAAGGAGACTCTCAACGTCTTGCTTGTGGAGAGTGATGATTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAGgtttgtttta ... cctttttcagTTATCTCTGCCGAAAATGGCCAGCAAGCATGGGCTTATCTTGAAGATAAGAGAAACAACATAGATCTTGTTTTGACTGAGGTTTTTATGCCCGGTGTATC

Block sizes: 37 (upstream exon), 25 (downstream exon)
Score: 2

Block sizes: 37 (upstream exon), 49 (downstream exon)
Score: 9

Block sizes: 47 (upstream exon), 29 (downstream exon)
Score: 15

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCTTCCTCCTCAAGGAGACTCTCAACGTCTTGCTTGTGGAGAGTGATGATTCAACCAGGCAGGTCGTCAGTGCCCTGCTTCGTTGCTGCATGTACCAAGgtttgttttatcccaattcatccttcagtcgtttttctgacaggctatgatttcgcatattcatagcatcgatcataacttggagctgtttaacatctat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC