ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

AGATTATGGTTCAAGACAAACTTGAAGCTTTGCAAAATTTGGTTTGATATAGGCGAGTACGGTCGCATGAGCAAGgtccttggatcatttctttcatagtctttgatgcaataaatttgcttgtattattaaattacattcttactggcag

Basic information

species	Zea mays
transcript	GRMZM2G079196_T01
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G079196_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g17180.1 (Oryza sativa), 5'ss of exon 5

AGATTATGGTTCAAGACAAACTTGAAGCTTTGCAAAATTTGGTTTGATATAGGCGAGTACGGTCGCATGAGCAAGgtccttggatca-tttctttcatagtctttgatgcaataaatttgcttgtattattaaattacat-tcttactggcag-------------
||||||||||| ||||||||| ||||||||||||||||||||||||| || || ||||| || || ||||||||||| |||  |  | ||||| |  |    |    | |  || || | ||    | ||||   ||  | | || || | |              
AGATTATGGTTTAAGACAAACCTGAAGCTTTGCAAAATTTGGTTTGACATGGGGGAGTATGGCCGGATGAGCAAGgtgcttatacaagtttctctagtcaattggttttctttacatattctgcagtcattactctaattattttgctcgtaacttcttcctgtag

upper sequence: GRMZM2G079196_T01 (Zea mays), 5'ss of exon 5
lower sequence: PP1S105_216V6.1 (Physcomitrella patens), 5'ss of exon 5

AGATTATGGTTCAAGACAAACTTGAAGCTTTGCAAAATTTGGTTTGATATAGGCGAGTACGGTCGCATGAGCAAGgtcc-ttggat---catttctttca--tagtctttgatg-caataaatttgcttgtattattaaattacattcttac-tggcag----------------
|||||||||||||| || ||||||||| | |||||| | ||||||||||| || || || ||||| |||| ||| ||   ||  ||   |||||  ||||  |||  |    || | |  | |  |    |  ||||| |  |       || ||||                  
AGATTATGGTTCAAAACGAACTTGAAGTTGTGCAAATTGTGGTTTGATATGGGAGAATATGGTCGAATGAACAAAgtaagttaaattaccattttattcagttagaatggattgtcgactagtgagtgcatgctattataacaagcatgcacatggcttatggttttcttatcct

upper sequence: GRMZM2G079196_T01 (Zea mays), 5'ss of exon 5
lower sequence: PP1S90_192V6.1 (Physcomitrella patens), 5'ss of exon 5

AGATTATGGTTCAAGACAAACTTGAAGCTTTGCAAAATTTGGTTTGATATAGGCGAGTACGGTCGCATGAGCAAGgtccttggatcatttctttcatagtctttgatgcaataaatttgcttgtattattaaattacattcttactggcag-------------------------------------------------------------------------------------------------
|| |||||||||||||||||||||||| | || ||| | ||||||||||| || || || ||||| ||||  ||||   |  | ||  | |     | |  ||     |||||  ||    |||  ||||  ||   ||  | | || |||                                                                                                 
AGGTTATGGTTCAAGACAAACTTGAAGTTGTGTAAATTGTGGTTTGATATGGGTGAATATGGTCGAATGAATAAGg---taagttcgctgcc--agttgatttctccacaatatcttcatatgtcctattttatctgataataaatgtcagtcgcttatctcaatgcttttcagttcgagatatatgttcgcagaatatattttttcgtacacaaatgtgagatgcttctaatttcttagaactgcag

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|33093393|gb|CF053387.1|CF053387

EST:     ACGGTCGCATGAGCAAG                         ATATTGAAGGAACTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGAT
genomic: ACGGTCGCATGAGCAAGgtccttggat ... ttactggcagATATTGAAGGAACTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGAT

EST: gi|211287913|gb|FL267057.1|FL267057

EST:     AGCTTTGCAAAATTTGGTTTGATATAGGCGAGTACGGTCGCATGAACAAG                         ATATTGAACGAACTGCATAAATCT
genomic: AGCTTTGCAAAATTTGGTTTGATATAGGCGAGTACGGTCGCATGAGCAAGgtccttggat ... ttactggcagATATTGAAGGAACTGCATAAATCT

EST: gi|76015005|gb|DT942175.1|DT942175

EST:     AGCTTTGCAAAATTTGGTTTGATATAGGCGAGTACGGTCGCATGAGCAAG                         ATATTGAAGGAACTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGAT
genomic: AGCTTTGCAAAATTTGGTTTGATATAGGCGAGTACGGTCGCATGAGCAAGgtccttggat ... ttactggcagATATTGAAGGAACTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGAT

EST: gi|31353952|gb|CD438309.1|CD438309

EST:     AGCTTTGCAAAATTTGGTTTGATATAGGCGAGTACGGTCGCATGAGCAAG                         ATATTGAAGGAACTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGAT
genomic: AGCTTTGCAAAATTTGGTTTGATATAGGCGAGTACGGTCGCATGAGCAAGgtccttggat ... ttactggcagATATTGAAGGAACTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGAT

EST: gi|193502120|gb|AM937931.1|AM937931

EST:     AGCTTTGCAAAATTTGGTTTGGTATAGGCGAGTACGGTCGCATGAGCAAG                         ATATTGAAGGAACTGCATAAATCTTGCCCAAAGGGAAGATGGTTCTGATGA
genomic: AGCTTTGCAAAATTTGGTTTGATATAGGCGAGTACGGTCGCATGAGCAAGgtccttggat ... ttactggcagATATTGAAGGAACTGCATAAATCTTGCC-AAAGGGAAGATGGTTCTGATGA

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: 117

AGATTATGGTTCAAGACAAACTTGAAGCTTTGCAAAATTTGGTTTGATATAGGCGAGTACGGTCGCATGAGCAAGgtccttggat ... ttactggcagATATTGAAGGAACTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGATCAAAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAAATACAAA

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 138

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 149

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 117

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATTATGGTTCAAGACAAACTTGAAGCTTTGCAAAATTTGGTTTGATATAGGCGAGTACGGTCGCATGAGCAAGgtccttggatcatttctttcatagtctttgatgcaataaatttgcttgtattattaaattacattcttactggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG