ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GATCGGTCGGCGCCATGTCCAAGGCCAGGGTCTACGCCGACGTCAACGTGCTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGGgtgagtgctatctcgcgcgctctcctctcgcgtcctccgcccctcctgcgcataaccctacctcaagcttcggtttcgcagtgctacgagcgtgcctgta...

Basic information

species	Zea mays
transcript	GRMZM2G143602_T03
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G143602_T03 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os07g02350.1 (Oryza sativa), 5'ss of exon 1

GATCGGTCGGCGCCATGTCCAAGGCCAGGGTCTACGCCGACGTCAACGTGCTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGGgtgagtgc-tatctcgcgcgctctcctctcgcgtcctccgcccctcctgcgcataaccctacctcaagcttcggtttcgcagtgctacgagcgtgcctgta-
    | ||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||| |||||||| |||||||| |||||||||||||||| |  | | |   |    ||  | ||  ||  ||  |  |   |  |   |    ||  | || || |    ||||         ||| | |   
CCCAGATCGGCGCCATGTCCAAGGCCAGGGTCTACACCGACGTCAACGTGCTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtgagtgcctcccactcctacctcgctacctcgctctt-gcttccaccctgtgttgtcgcctctgcatctgcg-tgggtcagtttagattcagtgtcggatg

upper sequence: GRMZM2G143602_T03 (Zea mays), 5'ss of exon 1
lower sequence: PP1S63_208V6.1 (Physcomitrella patens), 5'ss of exon 2

GATCGGTCGGCGCCATGTCCAAGGCCAGGGTCTACGCCGACGTCAACGTGCTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGGgtgagtgctatctcgcgcgctctcctctcgcgtcctccgcccctcctgcgcataaccctacctcaagcttcggtttcgcagtgctacgagcgtgcctgta---
||  |   || |  |||||||||||| | || ||| | || || || || | ||| || || || || |||||||||||||| || ||||||||||||||||   ||||   |  |   ||  |     || |        ||   | |  |   | ||     | |  ||   ||  |   ||| |   ||||   | |   
GACGGCCAGGTGTTATGTCCAAGGCCCGAGTTTACACGGATGTGAATGTTCAGCGGCCGAAAGATTATTGGGATTACGAGGCTCTTACCGTTCAATGGGGgta--tgctccgttactatcttcctcgctgcatttatgattccgtttccctaggtctcttagggatgtctctacttgacgaagct-ctttcgtgtaggaattc

upper sequence: GRMZM2G143602_T03 (Zea mays), 5'ss of exon 1
lower sequence: EFJ28543 (Selaginella moellendorffii), 5'ss of exon 1

GATCGGTCGGCGCCATGTCCAAGGCCAGGGTCTACGCCGACGTCAACGTGCTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGGgtgagtgctatctcgcgcgctctcctc---tcgcgtcctccgcccctcctgcgcataaccctacctcaagcttcggtttcgcagtgctacgagcgtgcctgta
|      ||||||||||||||||||| || | |||||||| || |||||||||||||| |||||||||||||| |||||| | ||| | ||  | ||||||||||   | | |  ||   | |  |    ||  |  |||  |  ||  |  |  |  |                                            
GTGGCCCCGGCGCCATGTCCAAGGCCCGGATATACGCCGATGTGAACGTGCTGCGCCCAAAGGAGTACTGGGACTACGAGTCTCTCTCGGTGGAGTGGGGgtgaggcttttgtttcgtttttttgttggatctagatctcttcttcttgtttgggtggcag------------------------------------------

upper sequence: GRMZM2G143602_T03 (Zea mays), 5'ss of exon 1
lower sequence: EFJ20478 (Selaginella moellendorffii), 5'ss of exon 1

GATCGGTCGGCGCCATGTCCAAGGCCAGGGTCTACGCCGACGTCAACGTGCTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGGgtgagtgctatctcgcgcgctctcctc---tcgcgtcctccgcccctcctgcgcataaccctacctcaagcttcggtttcgcagtgctacgagcgtgcctgta
|      ||||||||||||||||||| || | |||||||| || |||||||||||||| |||||||||||||| |||||| | ||| | ||  | ||||||||||   | | |  ||   | |  |    ||  |  |||  |  || ||  |  |  |                                            
GTGGCCCCGGCGCCATGTCCAAGGCCCGGATATACGCCGATGTGAACGTGCTGCGCCCAAAGGAGTACTGGGACTACGAGTCTCTCTCGGTGGAGTGGGGgtgaggcttttgtttcgtttttttgttggatctagatctcttcttcttctttgggtggcag------------------------------------------

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|211519092|gb|FL312014.1|FL312014

EST:     CTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGGgtgagtgcta ... ctttgatcagTGAGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAAATACAG

EST: gi|211322748|gb|FL352369.1|FL352369

EST:     CTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGGAAAGTCGGGAGAAGAAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGGgtgagtgcta ... ctttgatcagTGAGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAAATACAG

EST: gi|211320448|gb|FL345953.1|FL345953

EST:     CTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGGgtgagtgcta ... ctttgatcagTGAGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAAATACAG

EST: gi|23199704|gb|BU582269.1|BU582269

EST:     CTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGGgtgagtgcta ... ctttgatcagTGAGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAAATACAG

EST: gi|211428133|gb|FL358030.1|FL358030

EST:     CTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAA-TACAG
genomic: CTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGGgtgagtgcta ... ctttgatcagTGAGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAAATACAG

EST: gi|211404409|gb|FL337659.1|FL337659

EST:     CTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGGgtgagtgcta ... ctttgatcagTGAGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAAATACAG

EST: gi|32848629|gb|CD988310.1|CD988310

EST:     ACTGGGATTACGAGGCGCTCACCGTTCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAAATACAG
genomic: ACTGGGATTACGAGGCGCTCACCGTTCAATGGGGgtgagtgcta ... ctttgatcagTGAGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAAATACAG

EST: gi|211532125|gb|FL350196.1|FL350196

EST:     CTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGGgtgagtgcta ... ctttgatcagTGAGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAAATACAG

EST: gi|211367442|gb|FL332752.1|FL332752

EST:     CTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGGgtgagtgcta ... ctttgatcagTGAGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAAATACAG

EST: gi|148979084|gb|EE026504.2|EE026504

EST:     CTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGGgtgagtgcta ... ctttgatcagTGAGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAAATACAG

EST: gi|13388534|gb|BG462212.1|BG462212

EST:     CTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGG                         TGAGCAGGATGACNNNNNNNNNGTCAGGAAGGTCGGGAGAGGAAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGGgtgagtgcta ... ctttgatcagTGAGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAAATACAG

EST: gi|29576768|gb|CB616880.1|CB616880

EST:     CGAGGCGCTCACCGTTCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAAATACAG
genomic: CGAGGCGCTCACCGTTCAATGGGGgtgagtgcta ... ctttgatcagTGAGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAAATACAG

EST: gi|211328912|gb|FL338504.1|FL338504

EST:     CTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGGgtgagtgcta ... ctttgatcagTGAGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAAATACAG

EST: gi|20507676|gb|BQ279725.1|BQ279725

EST:     CTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGGgtgagtgcta ... ctttgatcagTGAGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAAATACAG

EST: gi|26560171|gb|CA832406.1|CA832406

EST:     CTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGG                         GGAAGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAAATACA
genomic: CTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGGgtgagtgcta ... ctttgatcagTG-AGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAAATACA

EST: gi|211244627|gb|FL362238.1|FL362238

EST:     CTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGGgtgagtgcta ... ctttgatcagTGAGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAAATACAG

EST: gi|87156472|gb|DY401261.1|DY401261

EST:     CTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGGgtgagtgcta ... ctttgatcagTGAGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAAATACAG

EST: gi|166616427|gb|EG186990.1|EG186990

EST:     GGATTACGAGGCGCTCACCGTTCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAAATACAG
genomic: GGATTACGAGGCGCTCACCGTTCAATGGGGgtgagtgcta ... ctttgatcagTGAGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAAATACAG

EST: gi|71770653|gb|DR968590.1|DR968590

EST:     CTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGGgtgagtgcta ... ctttgatcagTGAGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAAATACAG

EST: gi|211277424|gb|FL308994.1|FL308994

EST:     CTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGGgtgagtgcta ... ctttgatcagTGAGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAAATACAG

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: 269

GATCGGTCGGCGCCATGTCCAAGGCCAGGGTCTACGCCGACGTCAACGTGCTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGGgtgagtgcta ... ctttgatcagTGAGCAGGATGACTATGAAGTTGTCAGGAAGGTCGGGAGAGGAAAATACAGTGAAGTATTTGAAGGTATTAATGTTAACAATAATGAGAAATGCATCATC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 171

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 297

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 151

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATCGGTCGGCGCCATGTCCAAGGCCAGGGTCTACGCCGACGTCAACGTGCTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGGgtgagtgctatctcgcgcgctctcctctcgcgtcctccgcccctcctgcgcataaccctacctcaagcttcggtttcgcagtgctacgagcgtgcctgta

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