ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TTGCTGAGCCTAACGGCAAGCGTGTCGTGTTTGTAAATCTTGATGCTTGCATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGACTTAAAGCAAGgtaagagtgatcactcttgaatcttatatcagaaaattgcctctctccctctctctgtttgatcatatatttgtatagcctgatccatcatactttgcac...

Basic information

species	Zea mays
transcript	GRMZM2G180732_T03
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G180732_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g43520.2 (Oryza sativa), 5'ss of exon 2

TTGCTGAGCCTAACGGCAAGCGTGTCGTGTTTGTAAATCTTGATGCTTGCATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGACTTAAAGCAAGgtaagagtgatcactcttgaatcttatatcagaaaattgcctctctccctct-ctctgtttgatcatatatttgtatagcctg-atccatcatactttgcac
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TGGCTGAGCCTAATGGAAAGCGTGTTGTGTTTGTTAATATCGATGCTTGTATGGCATCACAGATTGTGACTATAAAGGTGCTTGAAAGGCTAAAAGCAAGgtaagagttaacatttcttgcgaccttatta-atgcttgcatgtttgttgcaactttatgtgat-atgcgcttatagatcgtgtataaaatgatccatcaac

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|71321470|gb|DR797436.1|DR797436

EST:     ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGACTTAAAGCAAG                         GTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC
genomic: ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGACTTAAAGCAAGgtaagagtga ... aatttggcagGTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC

EST: gi|211192374|gb|FL184214.1|FL184214

EST:     ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGGCTTAAAGCAAG                         GTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC
genomic: ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGACTTAAAGCAAGgtaagagtga ... aatttggcagGTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC

EST: gi|74240745|gb|DT648659.1|DT648659

EST:     ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGACTTAAAGCAAG                         GTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC
genomic: ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGACTTAAAGCAAGgtaagagtga ... aatttggcagGTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC

EST: gi|211189959|gb|FL184194.1|FL184194

EST:     ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGGCTTAAAGCAAG                         GTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC
genomic: ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGACTTAAAGCAAGgtaagagtga ... aatttggcagGTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC

EST: gi|211189960|gb|FL184195.1|FL184195

EST:     ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGACTTAAAGCAAG                         GTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC
genomic: ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGACTTAAAGCAAGgtaagagtga ... aatttggcagGTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC

EST: gi|211192371|gb|FL184211.1|FL184211

EST:     ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGGCTTAAAGCAAG                         GTATGGAGATCTTTATAATGANAATAATGTGGCTATCAGTGGAATCCATAC
genomic: ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGACTTAAAGCAAGgtaagagtga ... aatttggcagGTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC

EST: gi|211192365|gb|FL184205.1|FL184205

EST:     ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGGCTTAAAGCAAG                         GTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC
genomic: ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGACTTAAAGCAAGgtaagagtga ... aatttggcagGTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC

EST: gi|211192367|gb|FL184207.1|FL184207

EST:     TGCTTGAAAGACTTAAAGCAAG                         GTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC
genomic: TGCTTGAAAGACTTAAAGCAAGgtaagagtga ... aatttggcagGTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC

EST: gi|71323344|gb|DR798328.1|DR798328

EST:     ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGACTTAAAGCAAG                         GTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC
genomic: ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGACTTAAAGCAAGgtaagagtga ... aatttggcagGTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC

EST: gi|211189962|gb|FL184197.1|FL184197

EST:     ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGGCTTAAAGCAAG                         GTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC
genomic: ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGACTTAAAGCAAGgtaagagtga ... aatttggcagGTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC

EST: gi|211189967|gb|FL184202.1|FL184202

EST:     ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGGCTTAAAGCAAG                         GTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC
genomic: ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGACTTAAAGCAAGgtaagagtga ... aatttggcagGTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC

EST: gi|211189964|gb|FL184199.1|FL184199

EST:     ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGGCTTAAAGCAAG                         GTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC
genomic: ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGACTTAAAGCAAGgtaagagtga ... aatttggcagGTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC

EST: gi|31363574|gb|CD447931.1|CD447931

EST:     ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGGCTTAAAGCAAG                         GTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC
genomic: ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGACTTAAAGCAAGgtaagagtga ... aatttggcagGTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC

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: 44 (upstream exon), 49 (downstream exon)
Score: 101

TTGCTGAGCCTAACGGCAAGCGTGTCGTGTTTGTAAATCTTGATGCTTGCATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGACTTAAAGCAAGgtaagagtga ... aatttggcagGTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATACGCATGCTGGTCCTGGTGGTTATCTGCAGTATGTAGTTTATATTGTTACA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 223

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 147

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 495

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCTGAGCCTAACGGCAAGCGTGTCGTGTTTGTAAATCTTGATGCTTGCATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGACTTAAAGCAAGgtaagagtgatcactcttgaatcttatatcagaaaattgcctctctccctctctctgtttgatcatatatttgtatagcctgatccatcatactttgcac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cagaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctccctc