ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TTGCTACAATAGCATCTGCTGATGAAGCTGAGCATGGTTTGGCAGCCCCAGATTATCCGTGGCCACATGCTGGCATCATGAGCTCTTATGATCATGCATCgtaagtcaaccatagcttcttcttttcatgaagctttgtttcatatgatatggcgtgatgtttacaaattcatgtaagccttatttatgaaatatggatt...

Basic information

species	Zea mays
transcript	GRMZM2G032367_T04
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G032367_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os05g23620.1 (Oryza sativa), 5'ss of exon 4

TTGCTACAATAGCATCTGCTGATGAAGCTGAGCATGGTTTGGCAGCCCCAGATTATCCGTGGCCACATGCTGGCATCATGAGCTCTTATGATCATGCATCgtaagtcaaccat----agcttcttcttttcatgaagctttgtttcatatgatatggcgtgatgtttacaaatt-catgtaagccttatttatgaaatatggatt
||||||||||||| ||||| ||||||||||||||||||||||||||  | || ||||| |||||||||||||||||  | ||||||||||| |||||||||| ||||| || |    | |||| |      ||  || || | |   |   ||||  |    | ||| || |    || |     ||||| ||  |         
TTGCTACAATAGCTTCTGCAGATGAAGCTGAGCATGGTTTGGCAGCAGCTGAATATCCCTGGCCACATGCTGGCATTCTTAGCTCTTATGACCATGCATCgtgagtcatcctttttcaacttccttacaaaatagagtttagctcattgcaatatttcagagtctttgcatacggtatttggttattattaattgatcca-----

upper sequence: GRMZM2G032367_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA19G22530.2 (Glycine max), 5'ss of exon 3

TTGCTACAATAGCATCTGCTGATGAAGCTGAGCATGGTTTGGCAGCCCCAGATTATCCGTGGCCACATGCTGGCATCATGAGCTCTTATGATCATGCATCgtaagtcaaccatagcttcttcttttcatgaagctttgtttcatatgatatggcgtgatg-tttacaaattcatgtaagccttatttatgaaatatggatt-
|||| |||| ||||| |||||||||||||||||||||  |||||   |||   ||||| ||||| ||    |||||| | || || ||||||||||| |||| |||    | |    | |||| | |||    |||| | |  | |       |   ||| |||   || | | | || | |  ||| | |||   |     
TTGCAACAACAGCATTTGCTGATGAAGCTGAGCATGGCCTGGCATGTCCAAGCTATCCATGGCCTCACAAGGGCATCCTTAGTTCATATGATCATGCTTCgtgagtttgacctgaaat-ttctctacattttcctttctattttcttgctcaacaatatgatttgtgaagtta-gcaaccatgttttgtcaaactagtccct

upper sequence: GRMZM2G032367_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA05G07020.1 (Glycine max), 5'ss of exon 3

TTGCTACAATAGCATCTGCTGATGAAGCTGAGCATGGTTTGGCAGCCCCAGATTATCCGTGGCCACATGCTGGCATCATGAGCTCTTATGATCATGCATCgtaagtc-aaccatagcttcttcttttcatgaagctttgtttcatatgatatggcgtgatgtttacaaattcatgtaagccttatttatgaaatatggatt-
|||| |||| ||||| |||||||||||||||||||||  |||||   ||    ||||| ||||| |||   |||||| | || || ||||||||||| |||| |||   |||  |  ||  |||     |     | | |||    || |      |    ||| | || | | | || |  | || |   ||  | |    
TTGCAACAACAGCATTTGCTGATGAAGCTGAGCATGGCCTGGCATGTCCTAGCTATCCATGGCCTCATAAGGGCATCCTTAGTTCATATGATCATGCTTCgtgagtttgacctgaaatttctctacattttcctttctatttttcttgctcaacaatatgatttgcgaagtta-gcaa-ctatgttcagtcaaactagtccc

upper sequence: GRMZM2G032367_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv14s0171g00330.t01 (Vitis vinifera), 5'ss of exon 3

TTGCTACAATAGCATCTGCTGATGAAGCTGAGCATGGTTTGGCAGCCCCAGATTATCCGTGGCCACATGCTGGCATCATGAGCTCTTATGATCATGCATCgtaagt------caaccatagcttcttcttttcatgaagctttgtttcatatg-atatggcgtgatgtttacaaattcatgtaagccttatttatgaaatatggatt
|||| |||||||||||||||||||| ||||||||||| || | |    || | ||||| ||||| ||  | |||||  | || || ||||| ||||| |||| |||        |   ||   ||    || ||   |  |     | | |   | |   | |||   | |  || | || ||   |  ||||||  |||       
TTGCAACAATAGCATCTGCTGATGAGGCTGAGCATGGATTAGAATGTGCAAACTATCCCTGGCCTCACTCAGGCATTCTCAGTTCATATGACCATGCTTCgtgagtgtctattgaatttaagatcaatcttgcagagaattgatcctaagacacagacaacttgactctcaacaaat-atttatctcaaatttatataatc------

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|91048787|gb|EB159205.1|EB159205

EST:     GATTATCCGTGGCCACATGCTGGCATCATGAGCTCTTATGATCATGCATC                         AATTCGCCGAGGGCATCAAGTTTACACACAAGTTTGTGCTTCTTGTCACTC
genomic: GATTATCCGTGGCCACATGCTGGCATCATGAGCTCTTATGATCATGCATCgtaagtcaac ... tattgcacagAATTCGCCGAGGGCATCAAGTTTACACACAAGTTTGTGCTTCTTGTCACTC

EST: gi|148953376|gb|EE152870.2|EE152870

EST:     GATTATCCGTGGCCACATGCTGGCATCATGAGCTCTTATGATCATGCATC                         AATTCGCCGAGGGCATCAAGTTTACACACAAGTTTGTGCTTCTTGTCACTC
genomic: GATTATCCGTGGCCACATGCTGGCATCATGAGCTCTTATGATCATGCATCgtaagtcaac ... tattgcacagAATTCGCCGAGGGCATCAAGTTTACACACAAGTTTGTGCTTCTTGTCACTC

EST: gi|6127287|gb|AW129812.1|AW129812

EST:     GATTATCCATGGCCACATGCTGGCATCATGAGCTCTTATGATCATGCATC                         AATTCGCCGAGGGCATCAAGTTTACACACAAGTTTGTGCTTCTTGTCACTC
genomic: GATTATCCGTGGCCACATGCTGGCATCATGAGCTCTTATGATCATGCATCgtaagtcaac ... tattgcacagAATTCGCCGAGGGCATCAAGTTTACACACAAGTTTGTGCTTCTTGTCACTC

EST: gi|30705068|gb|CD058657.1|CD058657

EST:     GATTATCCGTGGCCACATGCTGGCATCATGAGCTCTTATGATCATGCATC                         AATTCGCCGAGGGCATCAAGTTTACACACAAGTTTGTGCTTCTTGTCACTC
genomic: GATTATCCGTGGCCACATGCTGGCATCATGAGCTCTTATGATCATGCATCgtaagtcaac ... tattgcacagAATTCGCCGAGGGCATCAAGTTTACACACAAGTTTGTGCTTCTTGTCACTC

EST: gi|101393982|gb|EB818924.1|EB818924

EST:     GATTATCCGTGGCCACATGCTGGCATCATGAGCTCTTATGATCATGCATC                         AATTCGCCGAGGGCATCAAGTTTACACACAAGTTTGTGCTTCTTGTCACTC
genomic: GATTATCCGTGGCCACATGCTGGCATCATGAGCTCTTATGATCATGCATCgtaagtcaac ... tattgcacagAATTCGCCGAGGGCATCAAGTTTACACACAAGTTTGTGCTTCTTGTCACTC

EST: gi|88757330|gb|DY541471.1|DY541471

EST:     GATTATCCGTGGCCACATGCTGGCATCATGAGCTCTTATGATCATGCATC                         AATTCGCCGAGGGCATCAAGTTTACACACAAGTTTGTGCTTCTTGTCACTC
genomic: GATTATCCGTGGCCACATGCTGGCATCATGAGCTCTTATGATCATGCATCgtaagtcaac ... tattgcacagAATTCGCCGAGGGCATCAAGTTTACACACAAGTTTGTGCTTCTTGTCACTC

EST: gi|91878167|gb|EB408124.1|EB408124

EST:     GATTATCCGTGGCCACATGCTGGCATCATGAGCTCTTATGATCATGCATC                         AATTCGCCGAGGGCATCAAGTTTACACACAAGTTTGTGCTTCTTGTCACTC
genomic: GATTATCCGTGGCCACATGCTGGCATCATGAGCTCTTATGATCATGCATCgtaagtcaac ... tattgcacagAATTCGCCGAGGGCATCAAGTTTACACACAAGTTTGTGCTTCTTGTCACTC

EST: gi|32907328|gb|CF012141.1|CF012141

EST:     GATTATCCATGGCCACATGCTGGCATCATGAGCTCTTATGATCATGCATC                         AATTCGCCGAGGGCATCAAGTTTACACACAAGTTTGTGCTTCTTGTCACTC
genomic: GATTATCCGTGGCCACATGCTGGCATCATGAGCTCTTATGATCATGCATCgtaagtcaac ... tattgcacagAATTCGCCGAGGGCATCAAGTTTACACACAAGTTTGTGCTTCTTGTCACTC

EST: gi|91048031|gb|EB158449.1|EB158449

EST:     GATTATCCGTGGCCACATGCTGGCATCATGAGCTCTTATGATCATGCATC                         AATTCGCCGAGGGCATCAAGTTTACACACAAGTTTGTGCTTCTTGTCACTC
genomic: GATTATCCGTGGCCACATGCTGGCATCATGAGCTCTTATGATCATGCATCgtaagtcaac ... tattgcacagAATTCGCCGAGGGCATCAAGTTTACACACAAGTTTGTGCTTCTTGTCACTC

EST: gi|76020657|gb|DT947827.1|DT947827

EST:     GATTATCCGTGGCCACATGCTGGCATCATGAGCTCTTATGATCATGCATC                         AATTCGCCGAGGGCATCAAGTTTACACACAAGTTTGTGCTTCTTGTCACTC
genomic: GATTATCCGTGGCCACATGCTGGCATCATGAGCTCTTATGATCATGCATCgtaagtcaac ... tattgcacagAATTCGCCGAGGGCATCAAGTTTACACACAAGTTTGTGCTTCTTGTCACTC

EST: gi|71327453|gb|DR800341.1|DR800341

EST:     GATTATCCGTGGCCACATGCTGGCATCATGAGCTCTTATGATCATGCATC                         AATTCGCCGAGGGCATCAAGTTTACACACAAGTTTGTGCTTCTTGTCACTC
genomic: GATTATCCGTGGCCACATGCTGGCATCATGAGCTCTTATGATCATGCATCgtaagtcaac ... tattgcacagAATTCGCCGAGGGCATCAAGTTTACACACAAGTTTGTGCTTCTTGTCACTC

EST: gi|71448913|gb|DR829963.1|DR829963

EST:     GATTATCCGTGGCCACATGCTGGCATCATGAGCTCTTATGATCATGCATC                         AATTCGCCGAGGGCATCAAGTTTACACACAAGTTTGTGCTTCTTGTCACTC
genomic: GATTATCCGTGGCCACATGCTGGCATCATGAGCTCTTATGATCATGCATCgtaagtcaac ... tattgcacagAATTCGCCGAGGGCATCAAGTTTACACACAAGTTTGTGCTTCTTGTCACTC

EST: gi|50338207|gb|CO533333.1|CO533333

EST:     GATTATCCGTGGCCACATGCTGGCATCATGAGCTCTTATGATCATGCATC                         AATTCGCCGAGGGCATCAAGTTTACACACAAGTTTGTGCTTCTTGTCACTC
genomic: GATTATCCGTGGCCACATGCTGGCATCATGAGCTCTTATGATCATGCATCgtaagtcaac ... tattgcacagAATTCGCCGAGGGCATCAAGTTTACACACAAGTTTGTGCTTCTTGTCACTC

EST: gi|149084255|gb|EE173682.2|EE173682

EST:     GATTATCCGTGGCCACATGCTGGCATCATGAGCTCTTATGATCATGCATC                         AATTCGCCGAGGGCATCAAGTTTACACACAAGTTTGTGCTTCTTGTCACTC
genomic: GATTATCCGTGGCCACATGCTGGCATCATGAGCTCTTATGATCATGCATCgtaagtcaac ... tattgcacagAATTCGCCGAGGGCATCAAGTTTACACACAAGTTTGTGCTTCTTGTCACTC

EST: gi|149110785|gb|EE190606.2|EE190606

EST:     GATTATCCGTGGCCACATGCTGGCATCATGAGCTCTTATGATCATGCATC                         AATTCGCCGAGGGCATCAAGTTTACACACAAGTTTGTGCTTCTTGTCACTC
genomic: GATTATCCGTGGCCACATGCTGGCATCATGAGCTCTTATGATCATGCATCgtaagtcaac ... tattgcacagAATTCGCCGAGGGCATCAAGTTTACACACAAGTTTGTGCTTCTTGTCACTC

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), 48 (downstream exon)
Score: 175

TTGCTACAATAGCATCTGCTGATGAAGCTGAGCATGGTTTGGCAGCCCCAGATTATCCGTGGCCACATGCTGGCATCATGAGCTCTTATGATCATGCATCgtaagtcaac ... tattgcacagAATTCGCCGAGGGCATCAAGTTTACACACAAGTTTGTGCTTCTTGTCACTCCATGTCCTTGATTTCATACCGTGATTTGGTTGGGGTGGCCTATACTGAG

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 304

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 255

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 259

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCTACAATAGCATCTGCTGATGAAGCTGAGCATGGTTTGGCAGCCCCAGATTATCCGTGGCCACATGCTGGCATCATGAGCTCTTATGATCATGCATCgtaagtcaaccatagcttcttcttttcatgaagctttgtttcatatgatatggcgtgatgtttacaaattcatgtaagccttatttatgaaatatggatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG