ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

...tatgtgcaaacacgtatgtcatacttactgtgttttcttgcaagtatgtttttttggcttcattgatggcttttaacatttgtgtctttgccgtttgcagGAATTCTTCTTGCAGGGAAGATTCATATTTGGGCCTGATGTGAGATCTGTGTTTCTCACTATGATCCTCATCATCGCACCAGTGGTTGTCTTCTGTCTGT

Basic information

species	Zea mays
transcript	GRMZM5G821611_T01
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G821611_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os08g42370.1 (Oryza sativa), 3'ss of exon 1

----tat-gtgc-aaacacgtatgtcatacttactgtgttttcttgcaagtatgtttttttggcttcattgatggcttttaacatttgtgtctttgccgtttgcagGAATTCTTCTTGCAGGGAAGATTCATATTTGGGCCTGATGTGAGATCTGTGTTTCTCACTATGATCCTCATCATCGCACCAGTGGTTGTCTTCTGTCTGT
    ||| |  | ||| ||  || | ||  || || ||  | ||||||| |   |||  | |  |||  ||||||  |    ||||| | | ||||   |||| |||||||||||||||  || || || |||||||||||||||||||||||  | |||||||||||| |||||||| | ||||||||||| | ||||||  |||
tgagtattgcacgaaaaacaaatataatgtttgctatgagtgcttgcaattggatttgatggagttc--tgatggtatc---catttatat-tttgtattttgaagGAATTCTTCTTGCGAGGGAGGTTTATATTTGGGCCTGATGTGAGATCCATATTTCTCACTATGTTCCTCATCGTTGCACCAGTGGTGGCCTTCTGCGTGT

upper sequence: GRMZM5G821611_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os08g42370.3 (Oryza sativa), 3'ss of exon 1

tatgtgcaaacacgtatgtcatacttactgtgttttcttgcaagtatgtttttttggcttcattgatggcttttaacatttgtgtctttgccgtttgcagGAATTCTTCTTGCAGGGAAGATTCATATTTGGGCCTGATGTGAGATCTGTGTTTCTCACTATGATCCTCATCATCGCACCAGTGGTTGTCTTCTGTCTGT----------------------------------------------------------------------------------
                                                                                  | | ||||   |||| |||||||||||||||  || || || |||||||||||||||||||||||  | |||||||||||| |||||||| | ||||||||||| | ||||||  |||                                                                                  
---------------------------------------------------------------------------------atat-tttgtattttgaaggaattcttcttgcgagggaggtttatatttgggcctgatgtgagatccatatttctcactatgttcctcatcgttgcaccagTGGTGGCCTTCTGCGTGTTTGTCGCCAGACACCTCATTGATGACTTTCCCGGTGATTGGGGTATCTCGGTGATGGTTGTGGTGGTTGTCTTCACCGTTTA

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|94472112|gb|EB701070.1|EB701070

EST:     GCGGCGCCGGCGAGCAGCCTAGGCTTTACCAGGTCTGGCGGGGAAGCAAC                         GAATTCTTCTTGCAGGGAAGATTCATATTTGGGCCTGATGTGAGATCTGTG
genomic: GCGGCGCCGGCGAGCAGCCTAGGCTTTACCAGGTCTGGCGGGGAAGCAACgtaagaaatt ... ccgtttgcagGAATTCTTCTTGCAGGGAAGATTCATATTTGGGCCTGATGTGAGATCTGTG

EST: gi|149089592|gb|EE178843.2|EE178843

EST:     GCGGCGCCGGCGAGCAGCCTAGGCTTTACCAGGTCTGGCGGGGAAGCAAC                         GAATTCTTCTTGCAGGGAAGATTCATATTTGGGCCTGATGTGAGATCTGTG
genomic: GCGGCGCCGGCGAGCAGCCTAGGCTTTACCAGGTCTGGCGGGGAAGCAACgtaagaaatt ... ccgtttgcagGAATTCTTCTTGCAGGGAAGATTCATATTTGGGCCTGATGTGAGATCTGTG

EST: gi|149087864|gb|EE177142.2|EE177142

EST:     GCGGCGCCGGCGAGCAGCCTAGGCTTTACCAGGTCTGGCGGGGAAGCAAC                         GAATTCTTCTTGCAGGGAAGATTCATATTTGGGCCTGATGTGAGATCTGTG
genomic: GCGGCGCCGGCGAGCAGCCTAGGCTTTACCAGGTCTGGCGGGGAAGCAACgtaagaaatt ... ccgtttgcagGAATTCTTCTTGCAGGGAAGATTCATATTTGGGCCTGATGTGAGATCTGTG

EST: gi|71313270|gb|DR793166.1|DR793166

EST:     GCGGCGCCGGCGAGCAGCCTAGGCTTTACCAGGTCTGGCGGGGAAGCAAC                         GAATTCTTCTTGCAGGGAAGATTCATATTTGGGCCTGATGTGAGATCTGTG
genomic: GCGGCGCCGGCGAGCAGCCTAGGCTTTACCAGGTCTGGCGGGGAAGCAACgtaagaaatt ... ccgtttgcagGAATTCTTCTTGCAGGGAAGATTCATATTTGGGCCTGATGTGAGATCTGTG

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), 48 (downstream exon)
Score: 78

CCCCCTCCCCTGCGCCGTCGGGATGTACATGCCGCCGCCGCCGCCCACCGGCGGCGCCGGCGAGCAGCCTAGGCTTTACCAGGTCTGGCGGGGAAGCAACgtaagaaatt ... ccgtttgcagGAATTCTTCTTGCAGGGAAGATTCATATTTGGGCCTGATGTGAGATCTGTGTTTCTCACTATGATCCTCATCATCGCACCAGTGGTTGTCTTCTGTCTGT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 122

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 118

Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 120

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

atgtttttttggcttcattgatggcttttaacatttgtgtctttgccgtttgcagGAATTCTTCTTGCAGGGAAGATTCATATTTGGGCCTGATGTGAGATCTGTGTTTCTCACTATGATCCTCATCATCGCACCAGTGGTTGTCTTCTGTCTGT

                         ttttaac  putative branch site (score: 120)
                                       tctttgcc  putative PPT
                         ttttaacattt  TA-rich tract

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatgtgcaaacacgtatgtcatacttactgtgttttcttgcaagtatgtttttttggcttcattgatggcttttaacatttgtgtctttgccgtttgcagGAATTCTTCTTGCAGGGAAGATTCATATTTGGGCCTGATGTGAGATCTGTGTTTCTCACTATGATCCTCATCATCGCACCAGTGGTTGTCTTCTGTCTGT

tatgtgc
- - - -aaacacg
- - - - - - - - - - - - -tactgtg
- - - - - - - - - - - - - - - - - ttcttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -attgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatttg