ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

...caccatacctgaaaactttattgcattacactgaaatgtagtgttttgttcttatcagatgcctttggtttctgaagttatacacgactttgccttgcagAAGGATTGGAGAGAGAAGCGGGATGAGTTCAAGAAGAAGGTTAGGCAATGTGTCCGCAGGTCTCAGGAAATGCTGTGAAGGAGGAACATGGGGGAGTTGA

Basic information

species	Zea mays
transcript	GRMZM2G007276_T03
intron #	5
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G007276_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g38550.2 (Oryza sativa), 3'ss of exon 5

--caccatacctgaaaactttattgcattac-actgaaatgtagtgttttgttcttatcagatgcctttggtttctgaagttatacacgactttgccttgcagAAGGATTGGAGAGAGAAGCGGGATGAGTTCAAGAAGAAGGTTAGGCAATGTGTCCGCAGGTCTCAGGAAATGCTGTGAAGG---AGGAACATGGGGGAGTTGA
   |  |      |  |||| ||| | | ||  |  ||| ||| | || ||||  ||| |  | |     || |     |  ||    |    ||   ||||||||||||||||||| ||| |||| || |||||||| |||||||| |    ||| || |  || ||||||||||| |||| |   |||| ||   ||| |    
tctagaagtttctagtacttcattccttcactgcaaaaacgta-tattctgtttctattactttctgaacgtgtgctttgaaatttgtggtgctgg--tgcagAAGGATTGGAGAGAAAAGAGGGACGATTTCAAGAAAAAGGTTAGACGCATTGTTCGTAAATCACAGGAAATGCTCTGAAAGATAAGGAGCACAAGGGGGA---

upper sequence: GRMZM2G007276_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA13G40990.1 (Glycine max), 3'ss of exon 5

caccatacctgaaaacttt---attgcattacactgaaatgtagtgttttgttcttatcagatgcctttggtttctgaagttata-cacgactttgccttgcagAAGGATTGGAGAGAGAAGCGGGATGAGTTCAAGAAGAAGGTTAGGCAATGTGTCCGCAGGTCTCAGGAAATGCTGTGAAGGAGGAACATGGGGGAGTTGA-
|   | |  | |||   |    | ||| | |  ||  |  ||     | | || || | |||    |    ||||| |   | |  || ||  ||   ||||||||||| |||||||| | | | ||||| ||||||||||||||||| | |||||| || | ||| || |||||| |||||   |  | | |||          
ctttacagattaaagtgtatgaagtgcttcaatctcgacagtttaaatatattattttgagagagtt----tttcttagactgtgtcatgatcttatgttgcagAAGGAGTGGAGAGATAGGAGAGATGAATTCAAGAAGAAGGTTAGCCGATGTGTGCGGAAGTCACAAGAAATGTTGTGATTTAC-AGCTTGGATTCTCATCT

upper sequence: GRMZM2G007276_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA11G14980.1 (Glycine max), 3'ss of exon 5

caccatacctgaaaactttattgcattacactgaaatgtagtgttttgttcttatc----agatgcctttggtttctgaagttatacacgactttgcc-ttgcagAAGGATTGGAGAGAGAAGCGGGATGAGTTCAAGAAGAAGGTTAGGCAATGTGTCCGCAGGTCTCAGGAAATGCTGTGAAG-GAGGAACATGGGGGAGTTGA
       |||  ||      ||     |   |   ||||  |  ||  | | ||      |  | | |||| ||| |   |   |  | ||  |||   ||||||||||| |||||||| | | ||||||| |||||||| |||||||| | ||| ||  | | ||| || |||||| |||||   |  |   |||    |     
-----ggcctacaagagcctttttgacatttttgtatgtcatccttgatacctagtctgaaagttcttttgatttgttctgacctgtatgatcttggtattgcagAAGGAGTGGAGAGATAGGAGGGATGATTTCAAGAAAAAGGTTAGCCGATGCGTAAGGAAGTCACAAGAAATGTTGTGATTCGTCGCCTATGCCTCATACT-

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|28984547|gb|BQ539151.2|BQ539151

EST:     CAATGCTCTCTAGTCCGAATGACGAGTCTCCAGCAAATATTGAAGCTGCC                         AAGGATTGGAGAGAGAAGCGGGATGAGTTCAAGAAGAAGGTTAGGCAATGT
genomic: CAATGCTCTCTAGTCCGAATGACGAGTCTCCAGCAAATATTGAAGCTGCCgtaagtgcac ... tgccttgcagAAGGATTGGAGAGAGAAGCGGGATGAGTTCAAGAAGAAGGTTAGGCAATGT

EST: gi|6527105|gb|AW216317.1|AW216317

EST:     CAATGCTCTCTAGTCCGAATGCCGAGTCTCCAGCAAATATTGAAGCTGCC                         AAGGATTGGAGAGAGAAGCGGGATGAGTTCAAGAAGAAGGTTAGGCAATGT
genomic: CAATGCTCTCTAGTCCGAATGACGAGTCTCCAGCAAATATTGAAGCTGCCgtaagtgcac ... tgccttgcagAAGGATTGGAGAGAGAAGCGGGATGAGTTCAAGAAGAAGGTTAGGCAATGT

EST: gi|18163967|gb|BM333806.1|BM333806

EST:     CAATGCTCTCTAGTCCGAATGACGAGTCTCCAGCCAATATTGAAGCTGCC                         AAGGATTGGAGAGAGAAGCGGGATGAGTTCAAGAAGAAGGTTAGGCAATGT
genomic: CAATGCTCTCTAGTCCGAATGACGAGTCTCCAGCAAATATTGAAGCTGCCgtaagtgcac ... tgccttgcagAAGGATTGGAGAGAGAAGCGGGATGAGTTCAAGAAGAAGGTTAGGCAATGT

EST: gi|76916346|gb|DV166343.1|DV166343

EST:     GCAAATATTGAAGCTGCC                         AAGGATTGGAGAGAGAAGCGGGATGAGTTCAAGAAGAAGGTTAGGCAATGT
genomic: GCAAATATTGAAGCTGCCgtaagtgcac ... tgccttgcagAAGGATTGGAGAGAGAAGCGGGATGAGTTCAAGAAGAAGGTTAGGCAATGT

EST: gi|45846859|gb|CN070802.1|CN070802

EST:     CAATGCTCTCTAGTCCGAATGACGAGTCTCCAGCAAATATTGAAGCTGCC                         AAGGATTGGAGAGAGAAGCGGGATGAGTTCAAGAAGAAGGTTAGGCAATGT
genomic: CAATGCTCTCTAGTCCGAATGACGAGTCTCCAGCAAATATTGAAGCTGCCgtaagtgcac ... tgccttgcagAAGGATTGGAGAGAGAAGCGGGATGAGTTCAAGAAGAAGGTTAGGCAATGT

EST: gi|18169905|gb|BM339745.1|BM339745

EST:     CAATGCTCTCTAGTCCGAATGACGAGTCTCCAGCAAATATTGAAGCTGCC                         AAGGATTGGAGAGAGAAGCGGGATGAGTTCAAGAAGAAGGTTAGGCAATGT
genomic: CAATGCTCTCTAGTCCGAATGACGAGTCTCCAGCAAATATTGAAGCTGCCgtaagtgcac ... tgccttgcagAAGGATTGGAGAGAGAAGCGGGATGAGTTCAAGAAGAAGGTTAGGCAATGT

EST: gi|16919367|gb|BM074156.1|BM074156

EST:     CAATGCTCTCTAGTCCGAATGACGAGTCTCCAGCAAATATTGAAGCTGCC                         AAGGATTGGAGAGAGAAGCGGGATGAGTTCAAGAAGAAGGTTAGGCAATGT
genomic: CAATGCTCTCTAGTCCGAATGACGAGTCTCCAGCAAATATTGAAGCTGCCgtaagtgcac ... tgccttgcagAAGGATTGGAGAGAGAAGCGGGATGAGTTCAAGAAGAAGGTTAGGCAATGT

EST: gi|211096126|gb|FL442448.1|FL442448

EST:     CGATGCTCTCTAGTCCGAATGAAGAGTTTCCAGCAAATATTGAAGCTGCC                         AAGGATTGGAGAGAGAAGGGGGATGAGTTCAAGAAGAAGGTTAGGCAATGT
genomic: CAATGCTCTCTAGTCCGAATGACGAGTCTCCAGCAAATATTGAAGCTGCCgtaagtgcac ... tgccttgcagAAGGATTGGAGAGAGAAGCGGGATGAGTTCAAGAAGAAGGTTAGGCAATGT

EST: gi|94478519|gb|EB707477.1|EB707477

EST:     CAATGCTCTCTAGTCCGAATGACGAGTCTCCAGCAAATATTGAAGCTGCC                         AAGGATTGGAGAGAGAAGCGGGATGAGTTCAAGAAGAAGGTTAGGCAATGT
genomic: CAATGCTCTCTAGTCCGAATGACGAGTCTCCAGCAAATATTGAAGCTGCCgtaagtgcac ... tgccttgcagAAGGATTGGAGAGAGAAGCGGGATGAGTTCAAGAAGAAGGTTAGGCAATGT

EST: gi|60347046|gb|DN214019.1|DN214019

EST:     CAATGCTCTGTAGTCCGAATGACGAGTCTCCAGCAAATATTGAAGCTGCC                         AAGGATTGGAGAGAGAAGCGGGATGAGTTCAAGAAGAAGGTTAGGCAATGT
genomic: CAATGCTCTCTAGTCCGAATGACGAGTCTCCAGCAAATATTGAAGCTGCCgtaagtgcac ... tgccttgcagAAGGATTGGAGAGAGAAGCGGGATGAGTTCAAGAAGAAGGTTAGGCAATGT

EST: gi|17931724|gb|BM268684.1|BM268684

EST:     CAATGCTCTCTAGTCCGAATGACGAGTCTCCAGCAAATATTGAAGCTGCC                         AAGGATTGGAGAGAGAAGCGGGATGAGTTCAAGAAGAAGGTTAGGCAATGT
genomic: CAATGCTCTCTAGTCCGAATGACGAGTCTCCAGCAAATATTGAAGCTGCCgtaagtgcac ... tgccttgcagAAGGATTGGAGAGAGAAGCGGGATGAGTTCAAGAAGAAGGTTAGGCAATGT

EST: gi|18171105|gb|BM340945.1|BM340945

EST:     CAATGCTCTCTAGTCCGAATGACGAGTCTCCAGCAAATATTGAAGCTGCC                         AAGGATTGGAGAGAGAAGCGGGATGAGTTCAAGAAGAAGGTTAGGCAATGT
genomic: CAATGCTCTCTAGTCCGAATGACGAGTCTCCAGCAAATATTGAAGCTGCCgtaagtgcac ... tgccttgcagAAGGATTGGAGAGAGAAGCGGGATGAGTTCAAGAAGAAGGTTAGGCAATGT

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: 944

GTTGAAAGTATAGTTCTGAGCATCATTTCAATGCTCTCTAGTCCGAATGACGAGTCTCCAGCAAATATTGAAGCTGCCgtaagtgcac ... tgccttgcagAAGGATTGGAGAGAGAAGCGGGATGAGTTCAAGAAGAAGGTTAGGCAATGTGTCCGCAGGTCTCAGGAAATGCTGTGAAGGAGGAACATGGGGGAGTTGA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 818

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1046

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 833

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttgttcttatcagatgcctttggtttctgaagttatacacgactttgccttgcagAAGGATTGGAGAGAGAAGCGGGATGAGTTCAAGAAGAAGGTTAGGCAATGTGTCCGCAGGTCTCAGGAAATGCTGTGAAGGAGGAACATGGGGGAGTTGA

                                          ctttgcctt  CT-rich tract
                             aagttata  TA-rich tract

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caccatacctgaaaactttattgcattacactgaaatgtagtgttttgttcttatcagatgcctttggtttctgaagttatacacgactttgccttgcagAAGGATTGGAGAGAGAAGCGGGATGAGTTCAAGAAGAAGGTTAGGCAATGTGTCCGCAGGTCTCAGGAAATGCTGTGAAGGAGGAACATGGGGGAGTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA