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

gtaagtggactttattgtttgccactaaatatgtgctatattaatgttgacattttcccttaacttcttttgcctttcgtatcaactggcaattgttaaaatgatacagGTAAATATGTGGCTCCAGAAGTCCTGCGAAATGAAGAGTATGATACCAAAGTGGATGTCTTCTCATTCGCTCTGATACTTCAGGAG

Basic information

species	Zea mays
transcript	GRMZM2G045366_T01
intron #	8
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G045366_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g54480.1 (Oryza sativa), 3'ss of exon 8

gtaagtggactt-tattgt-ttgccactaaatatgtg---ctatattaatgtt----gacattttcccttaacttcttttgcctttcgtatcaactggcaattgtta------aaatgatacagGTAAATATGTGGCTCCAGAAGTCCTGCGAAATGAAGAGTATGATACCAAAGTGGATGTCTTCTCATTCGCTCTGATACTTCAGGAG
|||||   | |  || ||  ||    ||| ||||  |   | || ||| ||||     | ||  || ||||  ||  ||| ||||   | |  ||||  |||||  |      | ||| | ||||||  ||||| |||||||||||||||||||||||||| |||||||| |||||||||||||||||||| ||| |||||||||| |||
gtaagaaaattcatactgaatttgagctatatattagtatccatcttactgttccaaaatatcatcacttacatttgtttaccttctttctgcactgataattggcatgacaaatatgttgcagGTAGGTATGTAGCTCCAGAAGTCCTGCGAAATGAAGAATATGATACTAAAGTGGATGTCTTCTCATTTGCTTTGATACTTCAAGAG

upper sequence: GRMZM2G045366_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g54480.3 (Oryza sativa), 3'ss of exon 8

gtaagtggactt-tattgt-ttgccactaaatatgtg---ctatattaatgtt----gacattttcccttaacttcttttgcctttcgtatcaactggcaattgtt------aaaatgatacagGTAAATATGTGGCTCCAGAAGTCCTGCGAAATGAAGAGTATGATACCAAAGTGGATGTCTTCTCATTCGCTCTGATACTTCAGGAG--------------
|||||   | |  || ||  ||    ||| ||||  |   | || ||| ||||     | ||  || ||||  ||  ||| ||||   | |  ||||  |||||        || ||| | ||||||  ||||| |||||||||||||||||||||||||| |||||||| |||||||||||||||||||| ||| |||||||||| |||              
gtaagaaaattcatactgaatttgagctatatattagtatccatcttactgttccaaaatatcatcacttacatttgtttaccttctttctgcactgataattggcatgacaaatatgttgcagGTAGGTATGTAGCTCCAGAAGTCCTGCGAAATGAAGAATATGATACTAAAGTGGATGTCTTCTCATTTGCTTTGATACTTCAAGAGGTAAAAGTGTTGCT

upper sequence: GRMZM2G045366_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT3G58760.1 (Arabidopsis thaliana), 3'ss of exon 8

----------------------------------------------------------------------------gtaagtggactttattgtttgcca-ctaaatatgtgctatattaatgttgacattttcccttaacttcttttgcctttcgtatcaactggcaattgttaaaatgatacagGTAAATATGTGGCTCCAGAAGTCCTGCGAAATGAAGAGTATGATACCAAAGTGGATGTCTTCTCATTCGCTCTGATACTTCAGGAG
                                                                            |    | |  || ||  |||     |||||  |   ||| |   |   | |   ||    |  |    | |   ||   ||  |         | |||      |  ||||   |||| |||||||||| ||     | ||||||||||||||||| ||||| ||||| ||||| |||||| | ||  | || |||
gtaagtttctttaatctgacgatcttaaaaattcctctgtgaagttgtgtatgttcttgtcttgagctagcttagagctgttagctttaatgttttattgtctaaagctaaactacaaccaatctaatggttattttggaagggtctatgctgatgttactctcttttttcgttctggctaagcagGGCGATATATGGCTCCAGAGGTTTATAGGAATGAAGAGTATGATACAAAAGTAGATGTATTCTCTTTCGCTTTAATCTTACAAGAG

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|60344873|gb|DN211846.1|DN211846

EST:     GAGAAGAAAAGTTAGAGAAGATAAAGCAGTTACTTCTCCAGGCAATGCTT                         GTAAATATGTGGCTCCAGAAGTCCTGCGAAATGAAGAGTATGATACCAAAG
genomic: GAGAAGAAAAGTTAGAGAAGATAAAGCAGTCACTTCTCCAGGCAATGCTTgtaagtggac ... aatgatacagGTAAATATGTGGCTCCAGAAGTCCTGCGAAATGAAGAGTATGATACCAAAG

EST: gi|32858352|gb|CD998033.1|CD998033

EST:     GAGAAGAAAAGTTAGAGAAGATAAAGCAGTTACTTCTCCAGGCAATGCTT                         GTAAATATGTGGCTCCAGAAGTCCTGCGAAATGAAGAGTATGATACCAAAG
genomic: GAGAAGAAAAGTTAGAGAAGATAAAGCAGTCACTTCTCCAGGCAATGCTTgtaagtggac ... aatgatacagGTAAATATGTGGCTCCAGAAGTCCTGCGAAATGAAGAGTATGATACCAAAG

EST: gi|211486462|gb|FL339896.1|FL339896

EST:     GAGAAGAAAAGTTAGAGAAGATAAAGCAGTCACTTCTCCAGGCAATGCTT                         GTAAATATGTGGCTCCAGAAGTCCTGCGAAATGAAGAGTATGATACCAAAG
genomic: GAGAAGAAAAGTTAGAGAAGATAAAGCAGTCACTTCTCCAGGCAATGCTTgtaagtggac ... aatgatacagGTAAATATGTGGCTCCAGAAGTCCTGCGAAATGAAGAGTATGATACCAAAG

EST: gi|76287393|gb|DV026961.1|DV026961

EST:     GAGAAGAAAAGTTAGAGAAGATAAAGCAGTCACTTCTCCAGGCAATGCTT                         GTAAATATGTGGCTCCAGAAGTCCTGCGAAATGAAGAGTATGATACCAAAG
genomic: GAGAAGAAAAGTTAGAGAAGATAAAGCAGTCACTTCTCCAGGCAATGCTTgtaagtggac ... aatgatacagGTAAATATGTGGCTCCAGAAGTCCTGCGAAATGAAGAGTATGATACCAAAG

EST: gi|71760920|gb|DR958857.1|DR958857

EST:     GAGAAGAAAAGTTAGAGAAGATAAAGCAGTCACTTCTCCAGGCAATGCTT                         GTAAATATGTGGCTCCAGAAGTCCTGCGAAATGAAGAGTATGATACCAAAG
genomic: GAGAAGAAAAGTTAGAGAAGATAAAGCAGTCACTTCTCCAGGCAATGCTTgtaagtggac ... aatgatacagGTAAATATGTGGCTCCAGAAGTCCTGCGAAATGAAGAGTATGATACCAAAG

EST: gi|71307029|gb|DR789668.1|DR789668

EST:     GATAAAGCAGTCACTTCTCCAGGCAATGCTT                         GTAAATATGTGGCTCCAGAAGTCCTGCGAAATGAAGAGTATGATACCAAAG
genomic: GATAAAGCAGTCACTTCTCCAGGCAATGCTTgtaagtggac ... aatgatacagGTAAATATGTGGCTCCAGAAGTCCTGCGAAATGAAGAGTATGATACCAAAG

EST: gi|76291779|gb|DV031347.1|DV031347

EST:     AAGAAAAGTTAGAGAAGATAAAGCAGTCACTTCTCCAGGCAATGCTT                         GTAAATATGTGGCTCCAGAAGTCCTGCGAAATGAAGAGTATGATACCAAAG
genomic: AAGAAAAGTTAGAGAAGATAAAGCAGTCACTTCTCCAGGCAATGCTTgtaagtggac ... aatgatacagGTAAATATGTGGCTCCAGAAGTCCTGCGAAATGAAGAGTATGATACCAAAG

EST: gi|76287394|gb|DV026962.1|DV026962

EST:     GAGAAGAAAAGTTAGAGAAGATAAAGCAGTCACTTCTCCAGGCAATGCTT                         GTAAATATGTGGCTCCAGAAGTCCTGCGAA
genomic: GAGAAGAAAAGTTAGAGAAGATAAAGCAGTCACTTCTCCAGGCAATGCTTgtaagtggac ... aatgatacagGTAAATATGTGGCTCCAGAAGTCCTGCGAA

EST: gi|74234286|gb|DT642200.1|DT642200

EST:     GAGAAGAAAAGTTAGAGAAGATAAAGCAGTCACTTCTCCAGGCAATGCTT                         GTAAATATGTGGCTCCAGAAGTCCTGCGAAATGAAGAGTATGATACCAAAG
genomic: GAGAAGAAAAGTTAGAGAAGATAAAGCAGTCACTTCTCCAGGCAATGCTTgtaagtggac ... aatgatacagGTAAATATGTGGCTCCAGAAGTCCTGCGAAATGAAGAGTATGATACCAAAG

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), 48 (downstream exon)
Score: 73

ACTGGACATCTGAAGGTGGCAGATTTTGATCTATGTAAGATGCTAAAATGGAGAAGAAAAGTTAGAGAAGATAAAGCAGTCACTTCTCCAGGCAATGCTTgtaagtggac ... aatgatacagGTAAATATGTGGCTCCAGAAGTCCTGCGAAATGAAGAGTATGATACCAAAGTGGATGTCTTCTCATTCGCTCTGATACTTCAGGAG

Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 66

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 87

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 74

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttcccttaacttcttttgcctttcgtatcaactggcaattgttaaaatgatacagGTAAATATGTGGCTCCAGAAGTCCTGCGAAATGAAGAGTATGATACCAAAGTGGATGTCTTCTCATTCGCTCTGATACTTCAGGAG

   ccttaac  putative branch site (score: 74)
                                    aattgttaaaatgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtggactttattgtttgccactaaatatgtgctatattaatgttgacattttcccttaacttcttttgcctttcgtatcaactggcaattgttaaaatgatacagGTAAATATGTGGCTCCAGAAGTCCTGCGAAATGAAGAGTATGATACCAAAGTGGATGTCTTCTCATTCGCTCTGATACTTCAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA