ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GCACACGATCTGGGTTAAGAATGGGAACACCGGATATGATGACATCCGCGCAGCCATTAAGGAGGCGAAGGCAGTTACTGACAAGCCCACCTTGATCAAGgttggtttcttttgtatctgcaacctttatgtttttttcgctgtggattttataatgttggtctaatttatactccttttag

Basic information

species	Zea mays
transcript	GRMZM2G033208_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G033208_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os06g04270.1 (Oryza sativa), 5'ss of exon 4

GCACACGATCTGGGTTAAGAATGGGAACACCGGATATGATGACATCCGCGCAGCCATTAAGGAGGCGAAGGCAGTTACTGACAAGCCCACCTTGATCAAGgttggtttcttttgtatctgcaacctttatgtttt-tttcgctgtggattttataatgttggtctaatttatactccttttag
||| || ||||||||||||||||| |||   || |||||||| || || || ||||||||||| || ||||| || ||||||||||| ||  | ||||||||| | ||| | |  ||      |  ||||| | | ||| | | | ||  |||| || ||   | ||  | ||||| ||||||
GCATACAATCTGGGTTAAGAATGGAAACGATGGCTATGATGAGATTCGTGCCGCCATTAAGGAAGCAAAGGCGGTAACTGACAAGCCAACACTAATCAAGgttagattcctgtacatt-----ctgttatgctgtgttttgttatagagcttatcatatttagccaaaatgtactctttttag

upper sequence: GRMZM2G033208_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA20G38720.1 (Glycine max), 5'ss of exon 4

GCACACGATCTGGGTTAAGAATGGGAACACCGGATATGATGACATCCGCGCAGCCATTAAGGAGGCGAAGGCAGTTACTGACAAGCCCACCTTGATCAAGgttggtttctt---ttgtatctgcaacctttatgtttttttcgctgtggattttataatgttggt--ctaatttatactccttttag-------------------------------------------------------------------------------------------------------
|||    || ||||| |||||||| || || ||||||||||| || || |||||||||||||| || ||||| || |  ||||| |||||  ||||||||||| ||| | |    || || |  || |    || ||| | |         ||||      | ||  ||    ||||||  |   ||                                                                                                       
GCATGTAATTTGGGTGAAGAATGGAAATACTGGATATGATGAAATTCGTGCAGCCATTAAGGAAGCAAAGGCTGTCAAAGACAAACCCACTATGATCAAGgttagttacatgaactgaatattgaagcaaattgatttatccaaaacatcatttacgtcactagttacttgagtatactagtggaagtagcataatgtgatttctgtgagcgaaagtaaaccatttttatttgctatttttggggggtattttatcagctttatgttcatctgtgattactatttcacag

upper sequence: GRMZM2G033208_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA10G43990.1 (Glycine max), 5'ss of exon 4

GCACACGATCTGGGTTAAGAATGGGAACACCGGATATGATGACATCCGCGCAGCCATTAAGGAGGCGAAGGCAGTTACTGACAAGCCCACCTTGATCAAGgttggtttctt---ttgtatctgcaacctttatgtttttttcgctgtggattttataatgttggtctaatt---tatactccttttag------------
|||    || ||||| |||||||| || || ||||||||||| || || ||||||||||| || || ||||| || |  ||||| ||||| |||||||||||| ||| | |    || |  |  || |     | ||  |           |||||     | ||    ||   ||||||  |   ||            
GCATGTAATTTGGGTGAAGAATGGAAATACTGGATATGATGAAATTCGTGCAGCCATTAAAGAAGCAAAGGCTGTCAAAGACAAACCCACTTTGATCAAGgttagttacatgaactgaagattgaagcaaatggattgatcaaaaacatcatttatgtcactagttaccttgagtatactagtgaaagtagcataatgtg

upper sequence: GRMZM2G033208_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT3G60750.1 (Arabidopsis thaliana), 5'ss of exon 4

GCACACGATCTGGGTTAAGAATGGGAACACCGGATATGATGACATCCGCGCAGCCATTAAGGAGGCGAAGGCAGTTACTGACAAGCCCACCTTGATCAAGgttggtttcttttgtatctgcaacctttatgtttttttcgctgtggattttataatgttggtctaatttat-actccttttag
|||    |||||||| |||||||| ||||| || ||||| || ||||| || ||||||||||| || ||  | |||||||||||||| || |||||||||||   |      | | |   | | |   |  |   ||   ||   ||  || | || ||| | ||   |||  |    |  ||
GCATGTTATCTGGGTGAAGAATGGAAACACTGGGTATGACGAGATCCGTGCTGCCATTAAGGAAGCTAAAACTGTTACTGACAAGCCTACTTTGATCAAGgtaactacacaatttcttaaccatcaa-acatcggttggtctaaagacctt-tgatattgatttaccatattgcgtaatccag

upper sequence: GRMZM2G033208_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT2G45290.1 (Arabidopsis thaliana), 5'ss of exon 4

GCACACGATCTGGGTTAAGAATGGGAACACCGGATATGATGACATCCGCGCAGCCATTAAGGAGGCGAAGGCAGTTACTGACAAGCCCACCTTGATCAAGgt---tg---gtttcttttgtatctgcaacctttatgtttttttcgctgtgg-attttataatgttggtctaatttatactccttttag
|||    |||||||| |||||||| ||||  || |||||||| ||||| || ||||||| ||| || ||||| || || ||||||||||| ||||| |||||   ||     || ||||     || |  | ||| |     || | | |       | |  ||||  |    ||    |    |||||
GCATGTTATCTGGGTAAAGAATGGAAACAATGGTTATGATGAGATCCGTGCTGCCATTAGGGAAGCTAAGGCTGTAACAGACAAGCCCACTTTGATTAAGgtatctgcacactttttttagccatgaactcattaagcaacgtttgatctcatggcctttggtgttaattgttttgtggcatggtttag

upper sequence: GRMZM2G033208_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv16s0022g01440.t01 (Vitis vinifera), 5'ss of exon 4

GCACACGATCTGGGTTAAGAATGGGAACACCGGATATGATGACATCCGCGCAGCCATTAAGGAGGCGAAGGCAGTTACTGACAAGCCCACCTTGATCAAGgttggtttcttttgtatctgcaacctttatgtttttttcgctgtggattttataatgttggtctaatttatactccttttag---------------------------------------
|||   ||| ||||| |||||||| ||||| || |||||||| || || || ||||| ||||| || ||||| ||||  ||||||||||| ||||| |||||   |||||     ||     | ||||| | ||||   |    |    ||  ||  |     |  |||   |   || |                                         
GCATGTGATTTGGGTGAAGAATGGTAACACTGGGTATGATGAAATTCGTGCTGCCATCAAGGAAGCAAAGGCTGTTAAAGACAAGCCCACATTGATTAAGgtca-tttctccaacat----gatctttaaggtttt--ggtcaagagagttccaacttaaacttcttttcccccttttctgaagttggactttacctctataaacttctctgtttatgcag

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|211471115|gb|FL255208.1|FL255208

EST:     CAGCCATTAAGGAGGCGAAGGCAGTTACTGACAAGCCCACCTTGATCAAG                         GTGACTACCACGATCGGTTTTGGATCTCCCAACAAGGCCAACTCATACAGT
genomic: CAGCCATTAAGGAGGCGAAGGCAGTTACTGACAAGCCCACCTTGATCAAGgttggtttct ... ctccttttagGTGACTACCACGATCGGTTTTGGATCTCCCAACAAGGCCAACTCATACAGT

EST: gi|6952400|gb|AW424468.1|AW424468

EST:     CAGCCATTAAGGAGGCGAAGGCAGTTACTGACAAGCCCACCTTGATCAAG                         GTGACTACCACGATCGGTTTTGGATCTCCCAACAAGGCCAACTCATACAGT
genomic: CAGCCATTAAGGAGGCGAAGGCAGTTACTGACAAGCCCACCTTGATCAAGgttggtttct ... ctccttttagGTGACTACCACGATCGGTTTTGGATCTCCCAACAAGGCCAACTCATACAGT

EST: gi|149086592|gb|EE176136.2|EE176136

EST:     CAGCCATTAAGGAGGCGAAGGCAGTTACTGACAAGCCCACCTTGATCAAG                         GTGACTACCACGATCGGTTTTGGATCT
genomic: CAGCCATTAAGGAGGCGAAGGCAGTTACTGACAAGCCCACCTTGATCAAGgttggtttct ... ctccttttagGTGACTACCACGATCGGTTTTGGATCT

EST: gi|71311290|gb|DR791959.1|DR791959

EST:     CAGCCATTAAGGAGGCGAAGGCAGTTACTGACAAGCCCACCTTGATCAAG                         GTGACTACCACGATCGGTTTTGGATCTCCCAACAAGGCCAACTCATACAGT
genomic: CAGCCATTAAGGAGGCGAAGGCAGTTACTGACAAGCCCACCTTGATCAAGgttggtttct ... ctccttttagGTGACTACCACGATCGGTTTTGGATCTCCCAACAAGGCCAACTCATACAGT

EST: gi|148999663|gb|EE036652.2|EE036652

EST:     CAGCCATTAAGGAGGCGAAGGCAGTTACTGACAAGCCCACCTTGATCAAG                         GTGACTACCACGATCGGTTTTGGATCTCCCAACAAGGCCAACTCATACAGT
genomic: CAGCCATTAAGGAGGCGAAGGCAGTTACTGACAAGCCCACCTTGATCAAGgttggtttct ... ctccttttagGTGACTACCACGATCGGTTTTGGATCTCCCAACAAGGCCAACTCATACAGT

EST: gi|32803318|gb|CD955554.1|CD955554

EST:     TAAGGAGGCGAAGGCAGTTACTGACAAGCCCACCTTGATCAAG                         GTGACTACCACGATCGGTTTTGGATC
genomic: TAAGGAGGCGAAGGCAGTTACTGACAAGCCCACCTTGATCAAGgttggtttct ... ctccttttagGTGACTACCACGATCGGTTTTGGATC

EST: gi|78083891|gb|DV512284.1|DV512284

EST:     CAGCCATTAAGGAGGCGAAGGCAGTTACTGACAAGCCCACCTTGATCAAG                         GTGACTACCACGATCGGTTTTGGATCTCCCAACAAGGCCAACTCATACAGT
genomic: CAGCCATTAAGGAGGCGAAGGCAGTTACTGACAAGCCCACCTTGATCAAGgttggtttct ... ctccttttagGTGACTACCACGATCGGTTTTGGATCTCCCAACAAGGCCAACTCATACAGT

EST: gi|78079232|gb|DV507644.1|DV507644

EST:     CAGCCATTAAGGAGGCGAAGGCAGTTACTGACAAGCCCACCTTGATCAAG                         GTGACTACCACGATCGGTTTTGGATCTCCCAACAAGGCCAACTCATACAGT
genomic: CAGCCATTAAGGAGGCGAAGGCAGTTACTGACAAGCCCACCTTGATCAAGgttggtttct ... ctccttttagGTGACTACCACGATCGGTTTTGGATCTCCCAACAAGGCCAACTCATACAGT

EST: gi|148938610|gb|EC882938.2|EC882938

EST:     CAGCCATTAAGGAGGCGAAGGCAGGTACTGACAAGCCCACCTTGATCAAG                         GTGACTACCACGATCCGTTTTGGAT
genomic: CAGCCATTAAGGAGGCGAAGGCAGTTACTGACAAGCCCACCTTGATCAAGgttggtttct ... ctccttttagGTGACTACCACGATCGGTTTTGGAT

EST: gi|149074164|gb|EE162522.2|EE162522

EST:     CAGCCATTAAGGAGGCGAAGGCAGTTACTGACAAGCCCCCCTTGATCAAG                         GTGACTACCACGATCGGTTTTGGATCTCCCAA
genomic: CAGCCATTAAGGAGGCGAAGGCAGTTACTGACAAGCCCACCTTGATCAAGgttggtttct ... ctccttttagGTGACTACCACGATCGGTTTTGGATCTCCCAA

EST: gi|32920684|gb|CF025496.1|CF025496

EST:     CAGCCATTAAGGAGGCGAAGGCAGTTACTGACAAGCCCACCTTGATCAAG                         GTGACTACCACGATCGGTTTTGGATCTCCCAACAAGGCCAACTCATACAGT
genomic: CAGCCATTAAGGAGGCGAAGGCAGTTACTGACAAGCCCACCTTGATCAAGgttggtttct ... ctccttttagGTGACTACCACGATCGGTTTTGGATCTCCCAACAAGGCCAACTCATACAGT

EST: gi|9952380|gb|BE638963.1|BE638963

EST:     CAGCCATTAAGGAGGCGAAGGCAGTTACTGACAAGCCCACCTTGATCAAG                         GTGACTACCACGATCGGTTTTGGATCTCCCAACAAGGCCAACTCATACAGT
genomic: CAGCCATTAAGGAGGCGAAGGCAGTTACTGACAAGCCCACCTTGATCAAGgttggtttct ... ctccttttagGTGACTACCACGATCGGTTTTGGATCTCCCAACAAGGCCAACTCATACAGT

EST: gi|76281987|gb|DV021555.1|DV021555

EST:     CAGCCATTAAGGAGGCGAAGGCAGTTACTGACAAGCCCACCTTGATCAAG                         GTGACTACCACGATCGGTTTTGGATCTCCCAACAAGGCCAACTCATACAGT
genomic: CAGCCATTAAGGAGGCGAAGGCAGTTACTGACAAGCCCACCTTGATCAAGgttggtttct ... ctccttttagGTGACTACCACGATCGGTTTTGGATCTCCCAACAAGGCCAACTCATACAGT

EST: gi|78079231|gb|DV507643.1|DV507643

EST:     CAGCCATTAAGGAGGCGAAGGCAGTTACTGACAAGCCCACCTTGATCAAG                         GTGACTACCACGATCGGTTTTGGATCTCCCAACA-GGCCAACTCATACAGT
genomic: CAGCCATTAAGGAGGCGAAGGCAGTTACTGACAAGCCCACCTTGATCAAGgttggtttct ... ctccttttagGTGACTACCACGATCGGTTTTGGATCTCCCAACAAGGCCAACTCATACAGT

EST: gi|71311289|gb|DR791958.1|DR791958

EST:     CAGCCATTAAGGAGGCGAAGGCAGTTACTGACAAGCCCACCTTGATCCAG                         GTGACTACCACGATCGGTTTTGGATCTCCCAACAAGGTCAACTCATACAGT
genomic: CAGCCATTAAGGAGGCGAAGGCAGTTACTGACAAGCCCACCTTGATCAAGgttggtttct ... ctccttttagGTGACTACCACGATCGGTTTTGGATCTCCCAACAAGGCCAACTCATACAGT

EST: gi|76285425|gb|DV024993.1|DV024993

EST:     AGGCAGTTACTGACAAGCCCACCTTGATCAAG                         GTGACTACCACGATCGG-TTTGGATCTCCCAACAAGGCCAACTCATACAGT
genomic: AGGCAGTTACTGACAAGCCCACCTTGATCAAGgttggtttct ... ctccttttagGTGACTACCACGATCGGTTTTGGATCTCCCAACAAGGCCAACTCATACAGT

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), 49 (downstream exon)
Score: 337

GCACACGATCTGGGTTAAGAATGGGAACACCGGATATGATGACATCCGCGCAGCCATTAAGGAGGCGAAGGCAGTTACTGACAAGCCCACCTTGATCAAGgttggtttct ... ctccttttagGTGACTACCACGATCGGTTTTGGATCTCCCAACAAGGCCAACTCATACAGTGTTCATGGAAGTGCACTGGGTGCCAAAGAGGTTGAAGCAACCAGGCAGA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1395

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 615

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1458

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCACACGATCTGGGTTAAGAATGGGAACACCGGATATGATGACATCCGCGCAGCCATTAAGGAGGCGAAGGCAGTTACTGACAAGCCCACCTTGATCAAGgttggtttcttttgtatctgcaacctttatgtttttttcgctgtggattttataatgttggtctaatttatactccttttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG