ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CGCCAAGAGCGTGCGTGATGGAGGCAAAGCTGTTATGATCGGGCTTGCTGCAACGAACGTAATGGGAGAGGTTGATATAACCCGTCTTGTCCGACGACAGgtatgcaattgattccttgttcatccttctgtattgtggttccttgtccatccgctcatgtttatttggaaccag

Basic information

species	Zea mays
transcript	GRMZM2G024303_T01
intron #	7
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G024303_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os08g01760.1 (Oryza sativa), 5'ss of exon 7

CGCCAAGAGCGTGCGTGATGGAGGCAAAGCTGTTATGATCGGGCTTGCTGCAACGAACGTAATGGGAGAGGTTGATATAACCCGTCTTGTCCGACGACAGgtat-gcaattgattccttgttcatccttctgtattgtggttccttgtcc--------atccgctcatgtttatttggaaccag----------------
|||||| || || || ||||||||||||||||||||||| || |||||||| || || || ||||| ||||| ||||||||||||||||| || |||||||||  | || |   |||       | ||  ||  |||   |||   |           |    || ||   |  |||| || |                 
CGCCAAAAGTGTACGAGATGGAGGCAAAGCTGTTATGATTGGCCTTGCTGCCACAAATGTGATGGGGGAGGTGGATATAACCCGTCTTGTTCGCCGACAGgtacagaaactagctccaatgaagtactattgacttggttttctaagaaagagaagagagatactaataccttcttggtacaaacagcaaagccatttga

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|71306508|gb|DR789408.1|DR789408

EST:     CAACGAACGTAATGGGAGAGGTTGATATAACCCGTCTTGTCCGACGACAG                         GTGAAAATCATTGGCTCATATGGCGCAAGGGCTAGGCAAGACCTTCCTCAG
genomic: CAACGAACGTAATGGGAGAGGTTGATATAACCCGTCTTGTCCGACGACAGgtatgcaatt ... ttggaaccagGTGAAAATCATTGGCTCATATGGCGCAAGGGCTAGGCAAGACCTTCCTCAG

EST: gi|149101664|gb|EE187798.2|EE187798

EST:     CAACGAACGTAATGGGAGAGGTTGATATAACCCGTCTTGTCCGACGACAG                         GTGAAAATCATTGGCTCATATGGCGCAAGGGCTAGGCAAGACCTTCTTCAG
genomic: CAACGAACGTAATGGGAGAGGTTGATATAACCCGTCTTGTCCGACGACAGgtatgcaatt ... ttggaaccagGTGAAAATCATTGGCTCATATGGCGCAAGGGCTAGGCAAGACCTTCCTCAG

EST: gi|8367688|gb|BE050633.1|BE050633

EST:     CAACGAACGTAATGGGAGAGGTTGATATAACCCGTCTTGTCCGACGACAG                         GTGAAAATCATTGGCTCATATGGCGCAAGGGCCAGGCAAGACCTTCCTCAG
genomic: CAACGAACGTAATGGGAGAGGTTGATATAACCCGTCTTGTCCGACGACAGgtatgcaatt ... ttggaaccagGTGAAAATCATTGGCTCATATGGCGCAAGGGCTAGGCAAGACCTTCCTCAG

EST: gi|149001207|gb|EE038478.2|EE038478

EST:     CAACGAACGTAATGGGAGAGGTTGATATAACCCGTCTTGTCCGACGACAG                         GTGAAAATCATTGGCTCATATGGCGCAAGGGCTAGGCAAGACCTTCCTCAG
genomic: CAACGAACGTAATGGGAGAGGTTGATATAACCCGTCTTGTCCGACGACAGgtatgcaatt ... ttggaaccagGTGAAAATCATTGGCTCATATGGCGCAAGGGCTAGGCAAGACCTTCCTCAG

EST: gi|38688326|gb|CK145357.1|CK145357

EST:     CAACGAACGTAATGGGAGAGGTTGATATAACCCGTCTTGTCCGACGACAG                         GTGAAAATCATTGGCTCATATGGCGCAAGGGCTAGGCAAGACCTTCCTCAG
genomic: CAACGAACGTAATGGGAGAGGTTGATATAACCCGTCTTGTCCGACGACAGgtatgcaatt ... ttggaaccagGTGAAAATCATTGGCTCATATGGCGCAAGGGCTAGGCAAGACCTTCCTCAG

EST: gi|71312652|gb|DR792844.1|DR792844

EST:     CAACGAACGTAATGGGAGAGGTTGATATAACCCGTCTTGTCCGACGACAG                         GTGAAAATCATTGGCTCATATGGCGCAAGGGCTAGGCAAGACCTTCCTCAG
genomic: CAACGAACGTAATGGGAGAGGTTGATATAACCCGTCTTGTCCGACGACAGgtatgcaatt ... ttggaaccagGTGAAAATCATTGGCTCATATGGCGCAAGGGCTAGGCAAGACCTTCCTCAG

EST: gi|149076497|gb|EE165123.2|EE165123

EST:     CAACGAACGTAATGGGAGAGGTTGATATAACCCGTCTTGTCCGACGACAG                         GTGAAAATCATTGGCTCATATGGCGCAAGGGCCAGGCAAGACCTTCCTCAG
genomic: CAACGAACGTAATGGGAGAGGTTGATATAACCCGTCTTGTCCGACGACAGgtatgcaatt ... ttggaaccagGTGAAAATCATTGGCTCATATGGCGCAAGGGCTAGGCAAGACCTTCCTCAG

EST: gi|113844883|gb|DW955939.1|DW955939

EST:     CGAACGTAATGGGAGAGGTTGATATAACCCGTCTTGTCCGACGACAG                         GTGAAAATCATTGGCTCATATGGCGCAAGGGCTAGGCAAGACCTTCCTCAG
genomic: CGAACGTAATGGGAGAGGTTGATATAACCCGTCTTGTCCGACGACAGgtatgcaatt ... ttggaaccagGTGAAAATCATTGGCTCATATGGCGCAAGGGCTAGGCAAGACCTTCCTCAG

EST: gi|113630127|gb|DW787862.1|DW787862

EST:     CGAACGTAATGGGAGAGGTTGATATAAAACCCGTCTTGTCCGACGACAG                         GTGAAAATCATTGGCTCATATGGCGCAAGGGCTAGGCAAGACCTTCCTCAG
genomic: CGAACGTAATGGGAGAGGTTGATAT--AACCCGTCTTGTCCGACGACAGgtatgcaatt ... ttggaaccagGTGAAAATCATTGGCTCATATGGCGCAAGGGCTAGGCAAGACCTTCCTCAG

EST: gi|60340906|gb|DN207879.1|DN207879

EST:     CAACGAACGTAATGGGAGAGGTTGATATAACCCGTCTTGTCCGACGACAG                         GTGAAAATCATTGGCTCATATGGCGCAAGGGCTAGGCAAGACCTTCCTCAG
genomic: CAACGAACGTAATGGGAGAGGTTGATATAACCCGTCTTGTCCGACGACAGgtatgcaatt ... ttggaaccagGTGAAAATCATTGGCTCATATGGCGCAAGGGCTAGGCAAGACCTTCCTCAG

EST: gi|148962894|gb|EE013828.2|EE013828

EST:     CAACGAACGTAATGGGAGAGGTTGATATAACCCGTCTTGTCCGACGACAG                         GTGAAAATCATTGGCTCATATGGCGCAAGGGCTAGGCAAGACCTTCCTCAG
genomic: CAACGAACGTAATGGGAGAGGTTGATATAACCCGTCTTGTCCGACGACAGgtatgcaatt ... ttggaaccagGTGAAAATCATTGGCTCATATGGCGCAAGGGCTAGGCAAGACCTTCCTCAG

EST: gi|113686780|gb|DW841927.1|DW841927

EST:     GTCCGACGACAG                         GTGAAAATCATTGGCTCATATGGCGCAAGGGCTAGGCAAGACCTTCCTCAG
genomic: GTCCGACGACAGgtatgcaatt ... ttggaaccagGTGAAAATCATTGGCTCATATGGCGCAAGGGCTAGGCAAGACCTTCCTCAG

EST: gi|71759582|gb|DR957519.1|DR957519

EST:     CAACGAACGTAATGGGAGAGGTTGATATAACCCGTCTTGTCCGACGACAG                         GTGAAAATCATTGGCTCATATGGCGCAAGGGCTAGGCAAGACCTTCCTCAG
genomic: CAACGAACGTAATGGGAGAGGTTGATATAACCCGTCTTGTCCGACGACAGgtatgcaatt ... ttggaaccagGTGAAAATCATTGGCTCATATGGCGCAAGGGCTAGGCAAGACCTTCCTCAG

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: 49 (upstream exon), 47 (downstream exon)
Score: 135

CGCCAAGAGCGTGCGTGATGGAGGCAAAGCTGTTATGATCGGGCTTGCTGCAACGAACGTAATGGGAGAGGTTGATATAACCCGTCTTGTCCGACGACAGgtatgcaatt ... ttggaaccagGTGAAAATCATTGGCTCATATGGCGCAAGGGCTAGGCAAGACCTTCCTCAGATAGTGAAGCTCGCGGAGAGTGGTGCCTTCAATCTCCAAAACACCATAT

Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 341

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 328

Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 132

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCCAAGAGCGTGCGTGATGGAGGCAAAGCTGTTATGATCGGGCTTGCTGCAACGAACGTAATGGGAGAGGTTGATATAACCCGTCTTGTCCGACGACAGgtatgcaattgattccttgttcatccttctgtattgtggttccttgtccatccgctcatgtttatttggaaccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG