ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GAGCGTTGAGTACATGCCCTTCCTCCTGTCGCTGGTGAGCTTCCTCAACGGCTGCTGCTGGACGGCCTACGCGCTCATCCGCTTCGACCTCTACGTCACGgtcagtatcaccggcctctcatgttaacaaaagcgttacagaattaatataattccacctccaagttgagtatagtctcatctcagtttttaaaatacctgcaatgcag

Basic information

species	Zea mays
transcript	GRMZM2G157675_T02
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G157675_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os09g08440.1 (Oryza sativa), 5'ss of exon 1

---GAGCGTTGAGTACATGCCCTTCCTCCTGTCGCTGGTGAGCTTCC-TCAACGGCTGCTGCTGGACGGCCTACGCGCTCATCCGCTTCGACCTCTACGTCACGgtcagtatcaccggcctctcatg--ttaacaaaagcgttacagaattaatataattccacctccaagttgagtatagtctcatctcagtttttaaaatacctgcaatgcag
    | | |||    |||    | |  |    | ||    | | |   |||     ||  |    |  || |  | |  ||| |  ||     | |  ||   |  |    ||| ||||||||  ||    | || | ||| |       | | | |  | || | |||     |  || ||||   |    | |||    |             
CGTCATCTTTGGCACCATCATGTACTCCTCACCACTCACCATCATGAGTCAGGTTGTGAAGACTAAGAGCGTG-GAGTACATGCCATTGCTGTTGTCGGTGgtgagcttcctcaacggcctctgctggaccatcatacgcgctcatccgcttagacatcttcatcaccataccca--atggtcttggcgtgctctttgctctc------------

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|14242996|gb|BG840173.2|BG840173

EST:     GCTGCTGCTGGACGGCCTACGCGCTCATCCGCTTCGACCTNTACGTCACG                         ATCCCGAACGCCCTGGGCGCATTCTTCGGCCTCGTCCAGCTGATCCTCTAC
genomic: GCTGCTGCTGGACGGCCTACGCGCTCATCCGCTTCGACCTCTACGTCACGgtcagtatca ... tgcaatgcagATCCCGAACGCCCTGGGCGCATTCTTCGGCCTCGTCCAGCTGATCCTCTAC

EST: gi|211162570|gb|FL132729.1|FL132729

EST:     GCTGCTGCTGGACGGCCTACGCGCTCATCCGCTTCGACCTCTACGTCACG                         ATCCCGAACGCCCTGGGCGCATTCTTCGGCCTCGTCCAGCTGATCCTCTAC
genomic: GCTGCTGCTGGACGGCCTACGCGCTCATCCGCTTCGACCTCTACGTCACGgtcagtatca ... tgcaatgcagATCCCGAACGCCCTGGGCGCATTCTTCGGCCTCGTCCAGCTGATCCTCTAC

EST: gi|211162573|gb|FL132732.1|FL132732

EST:     GCTGCTGCTGGACGGCCTACGCGCTCATCCGCTTCGACCTCTACGTCACG                         ATCCCGAACGCCCTGGGSGCATTCTTCGGCCTCGTCCAGCTGATCCTCTAC
genomic: GCTGCTGCTGGACGGCCTACGCGCTCATCCGCTTCGACCTCTACGTCACGgtcagtatca ... tgcaatgcagATCCCGAACGCCCTGGGCGCATTCTTCGGCCTCGTCCAGCTGATCCTCTAC

EST: gi|211388914|gb|FL454573.1|FL454573

EST:     GCTGCTGCTGGACGGCCTACGCGCTCATCCGCTTCGACCTCTACGTCACG                         ATCCCGAACGCCCTGGGCGCATTCTTCGGCCTCGTCCAGCTGATCCTCTAC
genomic: GCTGCTGCTGGACGGCCTACGCGCTCATCCGCTTCGACCTCTACGTCACGgtcagtatca ... tgcaatgcagATCCCGAACGCCCTGGGCGCATTCTTCGGCCTCGTCCAGCTGATCCTCTAC

EST: gi|166537343|gb|EG253046.1|EG253046

EST:     GCTGCTGCTGGACGGCCTACGCGCTCATCCGCTTCGACCTCTACGTCACG                         ATCCCGAACGCCCTGGGCGCATTCTTC
genomic: GCTGCTGCTGGACGGCCTACGCGCTCATCCGCTTCGACCTCTACGTCACGgtcagtatca ... tgcaatgcagATCCCGAACGCCCTGGGCGCATTCTTC

EST: gi|211162572|gb|FL132731.1|FL132731

EST:     GCTGCTGCTGGACGGCCTACGCGCTCATCCGCTTCGACCTCTACGTCACG                         ATCCCAAACGCCCTGGGCGCATTCTTCGGACTCATCCAGCTGATCCTCTAC
genomic: GCTGCTGCTGGACGGCCTACGCGCTCATCCGCTTCGACCTCTACGTCACGgtcagtatca ... tgcaatgcagATCCCGAACGCCCTGGGCGCATTCTTCGGCCTCGTCCAGCTGATCCTCTAC

EST: gi|28566554|gb|CB278202.1|CB278202

EST:     GCTGCTGCTGGACGGCCTACGCGCTCATCCGCTTCGACCTCTACGTCACG                         ATCCCGAACGCCCTGGGCGCATTCTTCGGCCTCATCCAGCTGATCCTCTAT
genomic: GCTGCTGCTGGACGGCCTACGCGCTCATCCGCTTCGACCTCTACGTCACGgtcagtatca ... tgcaatgcagATCCCGAACGCCCTGGGCGCATTCTTCGGCCTCGTCCAGCTGATCCTCTAC

EST: gi|17932131|gb|BM269091.1|BM269091

EST:     GCTGCTGATGGACGGCATACGCGCTCATCCGCTTCGACCTCTACGTCACG                         ATCCCGAACGCCCTGGGCGCATTCTTCGGCCTCGTCCAGCTGATCCTCTAC
genomic: GCTGCTGCTGGACGGCCTACGCGCTCATCCGCTTCGACCTCTACGTCACGgtcagtatca ... tgcaatgcagATCCCGAACGCCCTGGGCGCATTCTTCGGCCTCGTCCAGCTGATCCTCTAC

EST: gi|28188031|gb|CB179641.1|CB179641

EST:     GCTGCTGCTGGACGGCCTACGCGCTCATCCGCTTCGACCTCTACGTCACG                         ATCCCGAACGCCCTGGGCGCATTCTTCGGCCTCATCCAGCTGATCCTCTAT
genomic: GCTGCTGCTGGACGGCCTACGCGCTCATCCGCTTCGACCTCTACGTCACGgtcagtatca ... tgcaatgcagATCCCGAACGCCCTGGGCGCATTCTTCGGCCTCGTCCAGCTGATCCTCTAC

EST: gi|37361184|gb|CF602473.1|CF602473

EST:     GCTGCTGCTGGACGGCCTACGCGCTCATCCGCTTCGACCTCTACGTCACG                         ATCCCGAACGCCCTGGGCGCATTCTTCGGCCTCATCCAGCTGATCCTCTAT
genomic: GCTGCTGCTGGACGGCCTACGCGCTCATCCGCTTCGACCTCTACGTCACGgtcagtatca ... tgcaatgcagATCCCGAACGCCCTGGGCGCATTCTTCGGCCTCGTCCAGCTGATCCTCTAC

EST: gi|211148276|gb|FL467068.1|FL467068

EST:     GCTGCTGCTGGACGGCCTACGCGYTCATCCGCTTCGACCTCTACGTCACG                         ATCCCGAACGCCCTGGGCGCATTCTTCGGCCTCGTCCAGCTGATCCTCTAC
genomic: GCTGCTGCTGGACGGCCTACGCGCTCATCCGCTTCGACCTCTACGTCACGgtcagtatca ... tgcaatgcagATCCCGAACGCCCTGGGCGCATTCTTCGGCCTCGTCCAGCTGATCCTCTAC

EST: gi|93014839|gb|EB640359.1|EB640359

EST:     GCTGCTGCTGGACGGCCTACGCGCTCATCCGCTTCGACCTCTACGTCACG                         ATCCCGAACGCCCTGGGCGCATTCTTCGGCCTCGTCCAGCTGATCCTCTAC
genomic: GCTGCTGCTGGACGGCCTACGCGCTCATCCGCTTCGACCTCTACGTCACGgtcagtatca ... tgcaatgcagATCCCGAACGCCCTGGGCGCATTCTTCGGCCTCGTCCAGCTGATCCTCTAC

EST: gi|211124352|gb|FL444992.1|FL444992

EST:     GCTGCTGCTGGACGGCCTACGCGHTMATCCGCTTCGACCTCTACGTCACG                         ATCCCGAACGCCCTGGGCGCATTCTTCGGCCTCGTCCAGCTGATCCTCTAC
genomic: GCTGCTGCTGGACGGCCTACGCGCTCATCCGCTTCGACCTCTACGTCACGgtcagtatca ... tgcaatgcagATCCCGAACGCCCTGGGCGCATTCTTCGGCCTCGTCCAGCTGATCCTCTAC

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 3 RNA-Seq libraries.

Block sizes: 38 (upstream exon), 12 (downstream exon)
Score: 2

GAGCGTTGAGTACATGCCCTTCCTCCTGTCGCTGGTGAGCTTCCTCAACGGCTGCTGCTGGACGGCCTACGCGCTCATCCGCTTCGACCTCTACGTCACGgtcagtatca ... tgcaatgcagATCCCGAACGCCCTGGGCGCATTCTTCGGCCTCGTCCAGCTGATCCTCTACTTCTGCTACTACAAGTCGACCCCCAAGAAGGAGAAGAACGTGGAGCTGC

Block sizes: 41 (upstream exon), 45 (downstream exon)
Score: 7

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 219

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGCGTTGAGTACATGCCCTTCCTCCTGTCGCTGGTGAGCTTCCTCAACGGCTGCTGCTGGACGGCCTACGCGCTCATCCGCTTCGACCTCTACGTCACGgtcagtatcaccggcctctcatgttaacaaaagcgttacagaattaatataattccacctccaagttgagtatagtctcatctcagtttttaaaatacctgcaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA