ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GAAGGGTAATGAAAAAGCTGTTGTTGCGCGGCATGAAGTAGGTCATGCACTCGTGGGAACTGCTGTAGCAAACCTCCTTCCTGGACAGCCACGTGTGGAGgtttgaacttaagcaattactgatagaacaatctgataaaaaaggatctaatttggctttttaatgttgaatttaacag

Basic information

species	Zea mays
transcript	GRMZM2G072865_T01
intron #	10
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G072865_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os02g43350.1 (Oryza sativa), 5'ss of exon 10

GAAGGGTAATGAAAAAGCTGTTGTTGCGCGGCATGAAGTAGGTCATGCACTCGTGGGAACTGCTGTAGCAAACCTCCTTCCTGGACAGCCACGTGTGGAGgtttgaacttaagcaattactgatagaacaatctgataaaaaa--ggatctaatttggctttttaatgttgaatttaacag------
||||||||||||||| ||||||||||| ||||||||||| ||||||||  | |||||||||||||||||||||||  | || || |||||||||||||||||||||||  |||||| ||  ||||||||| | | | ||||     |   |    |  | ||||| |||||   ||           
GAAGGGTAATGAAAAGGCTGTTGTTGCACGGCATGAAGTTGGTCATGCCGTTGTGGGAACTGCTGTAGCAAACCTATTGCCAGGGCAGCCACGTGTGGAGgtttgaacgcaagcaactatcgatagaacagtttaagaaaatgttcgtcttgggcttacattttagtgttgttcttttttccaccag

upper sequence: GRMZM2G072865_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA14G37090.1 (Glycine max), 5'ss of exon 11

GAAGGGTAATGAAAAAGCTGTTGTTGCGCGGCATGAAGTAGGTCATGCACTCGTGGGAACTGCTGTAGCAAACCTCCTTCCTGGACAGCCACGTGTGGAGgtttgaacttaagcaattactga----tagaacaatctgataaaaaaggatctaatttggctttttaatgttgaatttaacag-------------------
||| || | ||| || ||||| ||||| ||||||||||  ||||||||  | || || ||||| || |||||||| |||||||||||||||||||| |||||   |||    | || | ||      | |  || |   |||    |    |      |   | |  ||| ||  |  | ||                    
GAAAGGAAGTGAGAAGGCTGTAGTTGCACGGCATGAAGCTGGTCATGCTGTGGTAGGTACTGCAGTTGCAAACCTTCTTCCTGGACAGCCACGTGTTGAGgt--aaaccatggaaaatgctctatttttggccatttaaatatgtcaatgccattgcagatatgtagatgatgcttggaccaagttacttgcctgcttgaat

upper sequence: GRMZM2G072865_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA02G39040.1 (Glycine max), 5'ss of exon 11

GAAGGGTAATGAAAAAGCTGTTGTTGCGCGGCATGAAGTAGGTCATGCACTCGTGGGAACTGCTGTAGCAAACCTCCTTCCTGGACAGCCACGTGTGGAGgtttgaacttaagcaattactgatagaacaatctgataaaaaag--gatctaattt--ggctttttaatgttgaatttaacag-------------------
||| || | ||| || ||||| ||||| ||||||||||  ||||||||  | || || ||||| || |||||||| |||||||||||||||||||| |||||   |||    |  | | ||           ||  |||| | |   ||   |||   |   |    ||| ||  | || ||                    
GAAAGGAAGTGAGAAGGCTGTAGTTGCACGGCATGAAGCTGGTCATGCTGTAGTAGGTACTGCAGTTGCAAACCTTCTTCCTGGACAGCCACGTGTTGAGgt--aaaccatggagaatgctctattcttggccttttaaatatgtcaatgccattgcagatatgcagatgatgcttgtaccacatacttgcctgcttgaatt

upper sequence: GRMZM2G072865_T01 (Zea mays), 5'ss of exon 10
lower sequence: Vv06s0004g06120.t01 (Vitis vinifera), 5'ss of exon 10

GAAGGGTAATGAAAAAGCTGTTGTTGCGCGGCATGAAGTAGGTCATGCACTCGTGGGAACTGCTGTAGCAAACCTCCTTCCTGGACAGCCACGTGTGGAGgtttgaacttaagcaattactgatag--aacaat--------ctgataaaaaaggatctaatt-tggctttttaatgttgaatttaacag----------
| |||| | ||| || ||||||||||| ||||||||||  ||||||||| | |||||||||||||| || || || |||||||||||||||||||| |||||  |   ||| |   ||| | | |   || | |        ||| | || |||  || |||| |      |   ||  ||||||   ||          
GCAGGGAAGTGAGAAGGCTGTTGTTGCACGGCATGAAGCTGGTCATGCAGTAGTGGGAACTGCTGTTGCTAATCTTCTTCCTGGACAGCCACGTGTTGAGgtaagttattaggaccttatttacaataaatattttcctttactgcttaacaagtttcaaattatttaacctccctggagaatttggaagacacgtgaga

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|32844110|gb|CD983791.1|CD983791

EST:     TCGTGGGAACTGCTGTAGCAAACCTCCTTCCTGGACAGCCACGTGTGGAG                         AAATTGAGTATATTGCCAAGATCCGGAGGTGCATTAGGCTTCACGTA
genomic: TCGTGGGAACTGCTGTAGCAAACCTCCTTCCTGGACAGCCACGTGTGGAGgtttgaactt ... aatttaacagAAATTGAGTATATTGCCAAGATCTGGAGGTGCATTAGGCTTCACGTA

EST: gi|32926300|gb|CF031112.1|CF031112

EST:     TCGTGGGAACTGCTGTAGCAAACCTCCTTCCTGGACAGCCACGTGTGGAG                         AAGATTGAGATATATTGCCAAGATCCGGAGGTGCATTAGGCTTCACGTA
genomic: TCGTGGGAACTGCTGTAGCAAACCTCCTTCCTGGACAGCCACGTGTGGAGgtttgaactt ... aatttaacagAA-ATTGAG-TATATTGCCAAGATCTGGAGGTGCATTAGGCTTCACGTA

EST: gi|32926533|gb|CF031345.1|CF031345

EST:     TCGTGGGAACTGCTGTAGCAAACCTCCTTCCTGGACAGCCACGTGTGGAG                         AGAATTGAGTATATTGCCAAGATCCGGAGGTGCATTAGGCTTCACGT
genomic: TCGTGGGAACTGCTGTAGCAAACCTCCTTCCTGGACAGCCACGTGTGGAGgtttgaactt ... aatttaacagA-AATTGAGTATATTGCCAAGATCTGGAGGTGCATTAGGCTTCACGT

EST: gi|32926980|gb|CF031792.1|CF031792

EST:     TCGTGGGAACTGCTGTAGCAAACCTCCTTCCTGGACAGCCACGTGTGGAG                         AAATTGAGTATATTGCCAAGATCCGGAGGTGCATTAGGCTTCACGTA
genomic: TCGTGGGAACTGCTGTAGCAAACCTCCTTCCTGGACAGCCACGTGTGGAGgtttgaactt ... aatttaacagAAATTGAGTATATTGCCAAGATCTGGAGGTGCATTAGGCTTCACGTA

EST: gi|32925415|gb|CF030227.1|CF030227

EST:     TCGTGGGAACTGCTGTAGCAAACCTCCTTCCTGGACAGCCACGTGTGGAG                         AAATTGAGTATATTGCCAAGATCCGGAGGTGCATTAGGCTTCACGT
genomic: TCGTGGGAACTGCTGTAGCAAACCTCCTTCCTGGACAGCCACGTGTGGAGgtttgaactt ... aatttaacagAAATTGAGTATATTGCCAAGATCTGGAGGTGCATTAGGCTTCACGT

EST: gi|32844467|gb|CD984148.1|CD984148

EST:     TCGTGGGAACTGCTGTAGCAAACCTCCTTCCTGGACAGCCACGTGTGGAG                         AAATTGAGTATATTGCCAAGATCCGGAGGTGCATTAGGCTTCACGTAC
genomic: TCGTGGGAACTGCTGTAGCAAACCTCCTTCCTGGACAGCCACGTGTGGAGgtttgaactt ... aatttaacagAAATTGAGTATATTGCCAAGATCTGGAGGTGCATTAGGCTTCACGTAC

EST: gi|60338252|gb|DN205225.1|DN205225

EST:     TCGTGGGAACTGCTGTAGCAAACCTCCTTCCTGGACAGCCACGTGTGGAG                         AAATTGAGTATATTGCCAAGATCTGGAGGTGCATTAGGCTTCACGTACACC
genomic: TCGTGGGAACTGCTGTAGCAAACCTCCTTCCTGGACAGCCACGTGTGGAGgtttgaactt ... aatttaacagAAATTGAGTATATTGCCAAGATCTGGAGGTGCATTAGGCTTCACGTACACC

EST: gi|32927000|gb|CF031812.1|CF031812

EST:     TCGTGGGAACTGCTGTAGCAAACCTCCTTCCTGGACAGCCACGTGTGGAG                         AAATTGAGTATATTGCCAAGATCCGGAGGTGCATTAGGCTTCACGTA
genomic: TCGTGGGAACTGCTGTAGCAAACCTCCTTCCTGGACAGCCACGTGTGGAGgtttgaactt ... aatttaacagAAATTGAGTATATTGCCAAGATCTGGAGGTGCATTAGGCTTCACGTA

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: 48 (upstream exon), 47 (downstream exon)
Score: 73

GAAGGGTAATGAAAAAGCTGTTGTTGCGCGGCATGAAGTAGGTCATGCACTCGTGGGAACTGCTGTAGCAAACCTCCTTCCTGGACAGCCACGTGTGGAGgtttgaactt ... aatttaacagAAATTGAGTATATTGCCAAGATCTGGAGGTGCATTAGGCTTCACGTACACCCCTCCCGTCACAGAGGATAGATATTTACTCTTTGTTGATGAACTACGTG

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 90

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 70

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 124

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGGGTAATGAAAAAGCTGTTGTTGCGCGGCATGAAGTAGGTCATGCACTCGTGGGAACTGCTGTAGCAAACCTCCTTCCTGGACAGCCACGTGTGGAGgtttgaacttaagcaattactgatagaacaatctgataaaaaaggatctaatttggctttttaatgttgaatttaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG