ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

ATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGATCATGCCAAGGTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACGgtaatgccctcagaactactttttgttcagtcgcctaattcatatcagacaatgaacagttttctaattgtgaacttagtttcaacttttgcatattgat...

Basic information

species	Zea mays
transcript	GRMZM2G032944_T02
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G032944_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os07g23169.1 (Oryza sativa), 5'ss of exon 2

ATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGATCATGCCAAGGTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACGgtaatgccctcagaactact-ttttgttcagtcgcctaattcatatcagacaatgaacagttttctaattgtgaacttagtttcaacttttgcatattgat
||||||| ||||||||||| ||||||  || |||||| |||  ||| ||||||||||| ||||| ||||||||||||||||||| |||| ||||| |||||||||| ||||  ||  | | || | || |||     |||   |||  |    || | |      |  ||     |||| |||    | ||  | | | ||
ATTTGCTAAAGGAATTTCCAGAACTTCTTAACAGCAAGGATAGTGCAAAGGTTTTAGAGGTGGGTTGTGGGAATGGAAGCACTGTTGTTCCCATTTTACGgtaatgtcctccaaagcattgttgtatttagtaaaaaaatatctatttgtagttgcaaatgcaaatcgttcaatgcttatttttt-ttgttatagagtaat

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|37417157|gb|CF646231.1|CF646231

EST:     GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACG                         GTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGT
genomic: GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACGgtaatgccct ... gtttcttcagGTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGT

EST: gi|93284543|gb|EB676807.1|EB676807

EST:     GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACG                         GTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT
genomic: GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACGgtaatgccct ... gtttcttcagGTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT

EST: gi|71765663|gb|DR963600.1|DR963600

EST:     GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACG                         GTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT
genomic: GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACGgtaatgccct ... gtttcttcagGTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT

EST: gi|78116629|gb|DV535016.1|DV535016

EST:     GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACG                         GTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT
genomic: GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACGgtaatgccct ... gtttcttcagGTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT

EST: gi|78124012|gb|DV542396.1|DV542396

EST:     GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACG                         GTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT
genomic: GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACGgtaatgccct ... gtttcttcagGTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT

EST: gi|91047980|gb|EB158398.1|EB158398

EST:     GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACG                         GTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT
genomic: GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACGgtaatgccct ... gtttcttcagGTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT

EST: gi|149085005|gb|EE174515.2|EE174515

EST:     GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACG                         GTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT
genomic: GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACGgtaatgccct ... gtttcttcagGTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT

EST: gi|71448268|gb|DR829318.1|DR829318

EST:     GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACG                         GTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT
genomic: GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACGgtaatgccct ... gtttcttcagGTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT

EST: gi|76014696|gb|DT941866.1|DT941866

EST:     GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACG                         GTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT
genomic: GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACGgtaatgccct ... gtttcttcagGTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT

EST: gi|93284224|gb|EB676488.1|EB676488

EST:     GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACG                         GTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT
genomic: GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACGgtaatgccct ... gtttcttcagGTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT

EST: gi|76914812|gb|DV165698.1|DV165698

EST:     GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACG                         GTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT
genomic: GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACGgtaatgccct ... gtttcttcagGTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT

EST: gi|31355055|gb|CD439412.1|CD439412

EST:     GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACG                         GTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT
genomic: GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACGgtaatgccct ... gtttcttcagGTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT

EST: gi|71438631|gb|DR819681.1|DR819681

EST:     GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACG                         GTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT
genomic: GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACGgtaatgccct ... gtttcttcagGTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT

EST: gi|89761751|gb|DY689640.1|DY689640

EST:     GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACG                         GTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT
genomic: GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACGgtaatgccct ... gtttcttcagGTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT

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: 47 (upstream exon), 42 (downstream exon)
Score: 44

ATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGATCATGCCAAGGTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACGgtaatgccct ... gtttcttcagGTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCTTGAGAAGGCATATGAAATTATATCCAATACAAAAGGGATTAATATCAAG

Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 49

Block sizes: 43 (upstream exon), 46 (downstream exon)
Score: 44

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 23

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGATCATGCCAAGGTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACGgtaatgccctcagaactactttttgttcagtcgcctaattcatatcagacaatgaacagttttctaattgtgaacttagtttcaacttttgcatattgat

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT