ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GAAGGTGAGGTATATGTTGAAGGCGATGACATGGAAGAGATGGATGACATGGAAGACTTTGAAGGCCTCAGTGATGgtaaaaatgttttctgctgaaactttccatgtcatgtcttatggaccttgaatgcttcattatgaactgtgtggggctcttggtctgctagtacgtgcaaggttcagcacttgcatgcaaaggattattgggttatactgttagtgtaatcttcttttttaaaaaaaatgtaaattggttgcag

Basic information

species	Zea mays
transcript	GRMZM2G461793_T01
intron #	7
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G461793_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os07g17040.1 (Oryza sativa), 5'ss of exon 6

---GAAGGTGAGGTATATGTTGAAGGCGATGACATGGAAGAGATGGATGACATGGAAGACTTTGAAGGCCTCAGTGATGgtaaaaatgttttctgctgaaactttccatgtcatgtcttatggaccttgaa--tgcttcattatgaactgtgtggggctcttggtctgctagtacgtgcaaggttcagcacttgcatgcaaaggattattgggttatactgttagtgtaatcttcttttttaaaaaaaatgtaaattggttgcag
   || |  || |  ||||||||||| ||  | ||||| || ||||| || |||||||||||||||||||||  || |||| |  ||| |      ||  |||| |  |   ||   | ||  |  |||||  |  ||      | || |||||       || | ||   | |  |  ||  |   ||| | ||  || ||                                                               
GAAGAGGTGGAAGAGTATGTTGAAGGAGACTATATGGATGACATGGAAGATATGGAAGACTTTGAAGGCCTCCCTGGTGGTGATTATGgt----aatgtgacttccgctagtat---tgatttaatttgaacataattttcagcgtaccgtgtga------tgatgtgaagggaattttaatat---gcattggccagctaata-------------------------------------------------------------

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|71431372|gb|DR812422.1|DR812422

EST:     TGACATGGAAGAGATGGATGACATGGAAGACTTTGAAGGCCTCAGTGATG                         GAGGCACAGATGAAGATGATGTTTTGGATGATCCCGTATCAAAGAAACCCA
genomic: TGACATGGAAGAGATGGATGACATGGAAGACTTTGAAGGCCTCAGTGATGgtaaaaatgt ... ttggttgcagGAGGCACAGATGAAGATGATGTTTTGGATGATCCCGTATCAAAGAAACCCA

EST: gi|33468206|gb|CF245255.1|CF245255

EST:     TGACATGGAAGAGATGGATGACATGGAAGACTTTGAAGGCCTCAGTGATG                         GAGGCACAGATGAAGATGATGTTTTGGATGATCCCGTATCAAAGAAACCCA
genomic: TGACATGGAAGAGATGGATGACATGGAAGACTTTGAAGGCCTCAGTGATGgtaaaaatgt ... ttggttgcagGAGGCACAGATGAAGATGATGTTTTGGATGATCCCGTATCAAAGAAACCCA

EST: gi|211374387|gb|FK951695.1|FK951695

EST:     TGACATGGAAGAGATGGATGACATGGAAGACTTTGAAGGCCTCAGTGATG                         GAGGCACGGATGACGATGATGTTTTGGATGATCCCGTATCAAGGAAATCCA
genomic: TGACATGGAAGAGATGGATGACATGGAAGACTTTGAAGGCCTCAGTGATGgtaaaaatgt ... ttggttgcagGAGGCACAGATGAAGATGATGTTTTGGATGATCCCGTATCAAAGAAACCCA

EST: gi|71322070|gb|DR797725.1|DR797725

EST:     TGACATGGAAGAGATGGATGACATGGAAGACTTTGAAGGCCTCAGTGATG                         GAGGCACAGATGAAGATGATGTTTTGGATGATCCCGTATCAAAGAAACCCA
genomic: TGACATGGAAGAGATGGATGACATGGAAGACTTTGAAGGCCTCAGTGATGgtaaaaatgt ... ttggttgcagGAGGCACAGATGAAGATGATGTTTTGGATGATCCCGTATCAAAGAAACCCA

EST: gi|211371734|gb|FK951691.1|FK951691

EST:     TGACATGGAAGAGATGGATGACATGGAAGACTTTGAAGGCCTCAGTGATG                         GAGGCACGGATGACGATGATGTTTTGGATGATCCCGTATCAAGGAAATCCA
genomic: TGACATGGAAGAGATGGATGACATGGAAGACTTTGAAGGCCTCAGTGATGgtaaaaatgt ... ttggttgcagGAGGCACAGATGAAGATGATGTTTTGGATGATCCCGTATCAAAGAAACCCA

EST: gi|30087565|gb|CB885771.1|CB885771

EST:     TGACATGGAAGAGATGGATGACATGGAAGACTTTGAAGGCCTCAGTGATG                         GAGGCACAGATGAAGATGATGTTTTGGATGATCCCGTATCAAAGAAACCCA
genomic: TGACATGGAAGAGATGGATGACATGGAAGACTTTGAAGGCCTCAGTGATGgtaaaaatgt ... ttggttgcagGAGGCACAGATGAAGATGATGTTTTGGATGATCCCGTATCAAAGAAACCCA

EST: gi|148953457|gb|EE152960.2|EE152960

EST:     TGACATGGAAGAGATGGATGACATGGAAGACTTTGAAGGCCTCAGTGATG                         GAGGCACAGATGAAGATGATGTTTTGGATGATCCCGTATCAAAGAAACCCA
genomic: TGACATGGAAGAGATGGATGACATGGAAGACTTTGAAGGCCTCAGTGATGgtaaaaatgt ... ttggttgcagGAGGCACAGATGAAGATGATGTTTTGGATGATCCCGTATCAAAGAAACCCA

EST: gi|148987549|gb|EE031414.2|EE031414

EST:     TGACATGGAAGAGATGGATGACATGGAAGACTTTGAAGGCCTCAGTGATG                         GAGGCACAGATGAAGATGATGTTTTGGATGATCCCGTATCAAAGAAACCCA
genomic: TGACATGGAAGAGATGGATGACATGGAAGACTTTGAAGGCCTCAGTGATGgtaaaaatgt ... ttggttgcagGAGGCACAGATGAAGATGATGTTTTGGATGATCCCGTATCAAAGAAACCCA

EST: gi|88749612|gb|DY533753.1|DY533753

EST:     TGACATGGAAGAGATGGATGACATGGAAGACTTTGAAGGCCTCAGTGATG                         GAGGCACAGATGAAGATGATGTTTTGGATGATCCCGTATCAAAGAAACCCA
genomic: TGACATGGAAGAGATGGATGACATGGAAGACTTTGAAGGCCTCAGTGATGgtaaaaatgt ... ttggttgcagGAGGCACAGATGAAGATGATGTTTTGGATGATCCCGTATCAAAGAAACCCA

EST: gi|60395012|gb|DN227881.1|DN227881

EST:     TGACATGGAAGAGATGGATGACATGGAAGACTTTGAAGGCCTCAGTGATG                         GAGGCACAGATGAAGATGATGTTTTGGATGATCCCGTATCAAAGAAACCCA
genomic: TGACATGGAAGAGATGGATGACATGGAAGACTTTGAAGGCCTCAGTGATGgtaaaaatgt ... ttggttgcagGAGGCACAGATGAAGATGATGTTTTGGATGATCCCGTATCAAAGAAACCCA

EST: gi|211374384|gb|FK951692.1|FK951692

EST:     TGACATGGAAGAGATGGATGACATGGAAGACTTTGAAGGCCTCAGTGATG                         GAGGCACAGATGAAGATGATGTTTTGGATGATCCCGTATCAAAGAAACCCA
genomic: TGACATGGAAGAGATGGATGACATGGAAGACTTTGAAGGCCTCAGTGATGgtaaaaatgt ... ttggttgcagGAGGCACAGATGAAGATGATGTTTTGGATGATCCCGTATCAAAGAAACCCA

EST: gi|148953458|gb|EE152961.2|EE152961

EST:     TGACATGGAAGAGATGGATGACATGGAAGACTTTGAAGGCCTCAGTGATG                         GAGGCACAGATGAAGATGATGTTTTGGATGA
genomic: TGACATGGAAGAGATGGATGACATGGAAGACTTTGAAGGCCTCAGTGATGgtaaaaatgt ... ttggttgcagGAGGCACAGATGAAGATGATGTTTTGGATGA

EST: gi|91872817|gb|EB402774.1|EB402774

EST:     TGACATGGAAGAGATGGATGACATGGAAGACTTTGAAGGCCTCAGTGATG                         GAGGCACAGATGAAGATGATGTTTTGGATGATCCCGTATCAAAGAAACCCA
genomic: TGACATGGAAGAGATGGATGACATGGAAGACTTTGAAGGCCTCAGTGATGgtaaaaatgt ... ttggttgcagGAGGCACAGATGAAGATGATGTTTTGGATGATCCCGTATCAAAGAAACCCA

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: 46 (upstream exon), 44 (downstream exon)
Score: 63

GAAGGTGAGGTATATGTTGAAGGCGATGACATGGAAGAGATGGATGACATGGAAGACTTTGAAGGCCTCAGTGATGgtaaaaatgt ... ttggttgcagGAGGCACAGATGAAGATGATGTTTTGGATGATCCCGTATCAAAGAAACCCAAGGGATCCTCTTCTTATTCGAAGCAAAATGTCGGGAAAAGGTCTAGGAA

Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 41

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 49

Block sizes: 46 (upstream exon), 42 (downstream exon)
Score: 58

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGGTGAGGTATATGTTGAAGGCGATGACATGGAAGAGATGGATGACATGGAAGACTTTGAAGGCCTCAGTGATGgtaaaaatgttttctgctgaaactttccatgtcatgtcttatggaccttgaatgcttcattatgaactgtgtggggctcttggtctgctagtacgtgcaaggttcagcacttgcatgcaaaggattattgggttatactgttagtgtaatcttcttttttaaaaaaaatgtaaattggttgcag

- - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG