ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TTGTCGACAAGACATCCACCATGCAAGACAGCGCCTTTCACTTCCGCAAGCAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCTgtgagtgctgtttctcttccttctatgaatatcgaagacattatatataggtcgatcatttattggtcatctaatttacttcacacagcttagctgttcc...

Basic information

species	Zea mays
transcript	GRMZM2G149843_T02
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G149843_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os10g06540.2 (Oryza sativa), 5'ss of exon 2

TTGTCGACAAGACATCCACCATGCAAGACAGCGCCTTTCACTTCCGCAAGCAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCTgtgagtgctgtttctcttccttctatgaatatcgaagacattatatataggtcgatcatttattggtcatctaatt-tacttcacacagcttagctgttcc
| ||||||||||| ||||||||||||||||| || || ||||||||||||||||||| ||||||| | ||||||||||||||||| |||||||||||||||| |||     ||   ||| |||| |     |        |  ||| ||  ||  ||  || ||   ||   | |   | | | ||     |||  ||   
TCGTCGACAAGACCTCCACCATGCAAGACAGTGCTTTCCACTTCCGCAAGCAATCCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCTgtaagtcaccctttctttctttctttcttgcttactactgtactatctatctct-tctcttctttaccactcactgacagtacccattaactagtggtcag

upper sequence: GRMZM2G149843_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT5G22360.1 (Arabidopsis thaliana), 5'ss of exon 3

TTGTCGACAAGACATCCACCATGCAAGACAGCGCCTTTCACTTCCGCAAGCAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCTgtgagtg-ctgtttctcttcc---ttctatgaatatcgaagacattatatataggtcgatcatttattggtcatctaatttacttcacacagcttagctgttcc
|||| || || ||| | || |||||||| ||| | ||||||||| | |||||||| ||| | || ||  |||||||||||||||| ||||| ||||| |||| ||   || | || ||||    |||| |  ||  |       |  ||  || |     |  |  |      ||||  |   |  || |  ||| || |    
TTGTTGATAAAACAGCAACAATGCAAGATAGCTCGTTTCACTTCAGGAAGCAATCTAAGCGCCTTCGCCGAGCTCTTTGGATGAAAAATGCTAAGCTCCTgtaaggatctctctcacttctagattctcttcattccttttctttgctaactaagagatacgctcttctacattctaggtgtttcaactcgcctttgcag----

upper sequence: GRMZM2G149843_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv06s0080g00800.t01 (Vitis vinifera), 5'ss of exon 3

TTGTCGACAAGACATCCACCATGCAAGACAGCGCCTTTCACTTCCGCAAGCAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCTgtgagtgctgtttctcttccttctatgaatatcgaagacattatatataggtcgatcatttattg-gtcatctaatttacttcacaca-gcttagctgttcc
|||| ||||| ||  | || |||||||||||  | |||||||||   ||||| || ||| |  | ||  |||||||||||||||| |||||||||||  ||||||| |    | ||| |   ||   |  |   |    || | |  |   |  |   || || | |   ||||| |  ||| |  || | ||   ||    
TTGTTGACAAAACTGCAACAATGCAAGACAGTTCTTTTCACTTCAAGAAGCAGTCTAAGCGCTTGCGCCGAGCTCTTTGGATGAAAAATGCCAAGCTCTTgtgagttcctcctttctactgcctcctatcactaagtttatgaaagttgttttcacttttcatggagatttctaaatatcttaaagcatgtttcattgaa--

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|18178773|gb|BM379983.1|BM379983

EST:     CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCT                         AGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC
genomic: CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCTgtgagtgctg ... ttttttgcagAGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC

EST: gi|78090244|gb|DV518618.1|DV518618

EST:     CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCT                         AGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTTTGC
genomic: CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCTgtgagtgctg ... ttttttgcagAGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC

EST: gi|93282853|gb|EB675117.1|EB675117

EST:     CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCT                         AGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC
genomic: CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCTgtgagtgctg ... ttttttgcagAGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC

EST: gi|211395387|gb|FL167591.1|FL167591

EST:     CAATCCAAGAAGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTCCT                         AGTTGTGTGGACAGTTGTCTTAGTAGTGCTGCTCTACT
genomic: CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCTgtgagtgctg ... ttttttgcagAGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACT

EST: gi|78077927|gb|DV506349.1|DV506349

EST:     CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCT                         AGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC
genomic: CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCTgtgagtgctg ... ttttttgcagAGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC

EST: gi|60672326|gb|DN475088.1|DN475088

EST:     CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCT                         AGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC
genomic: CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCTgtgagtgctg ... ttttttgcagAGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC

EST: gi|32859919|gb|CD999600.1|CD999600

EST:     CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCT                         AGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC
genomic: CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCTgtgagtgctg ... ttttttgcagAGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC

EST: gi|60393990|gb|DN226860.1|DN226860

EST:     CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCT                         AGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC
genomic: CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCTgtgagtgctg ... ttttttgcagAGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC

EST: gi|71298112|gb|DR785033.1|DR785033

EST:     CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCT                         AGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCTTTTCTGC
genomic: CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCTgtgagtgctg ... ttttttgcagAGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC

EST: gi|148997924|gb|EE035912.2|EE035912

EST:     CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCT                         AGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC
genomic: CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCTgtgagtgctg ... ttttttgcagAGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC

EST: gi|71448766|gb|DR829816.1|DR829816

EST:     CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCT                         AGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC
genomic: CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCTgtgagtgctg ... ttttttgcagAGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC

EST: gi|211083518|gb|FL102399.1|FL102399

EST:     GAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCT                         AGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC
genomic: GAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCTgtgagtgctg ... ttttttgcagAGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC

EST: gi|60401449|gb|DN234256.1|DN234256

EST:     CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCT                         AGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC
genomic: CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCTgtgagtgctg ... ttttttgcagAGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC

EST: gi|211398003|gb|FL167598.1|FL167598

EST:     AATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAAATGCCA-GCTTCT                         AGTTGTGTTGACA
genomic: AATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAA-TGCCAAGCTTCTgtgagtgctg ... ttttttgcagAGTTGTGTTGACA

EST: gi|94479642|gb|EB708600.1|EB708600

EST:     CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCT                         AGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC
genomic: CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCTgtgagtgctg ... ttttttgcagAGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC

EST: gi|60345692|gb|DN212665.1|DN212665

EST:     CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCT                         AGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC
genomic: CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCTgtgagtgctg ... ttttttgcagAGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC

EST: gi|32803614|gb|CD955850.1|CD955850

EST:     CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCT                         AGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC
genomic: CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCTgtgagtgctg ... ttttttgcagAGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC

EST: gi|76930491|gb|DV172407.1|DV172407

EST:     CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCT                         AGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC
genomic: CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCTgtgagtgctg ... ttttttgcagAGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC

EST: gi|93013841|gb|EB639361.1|EB639361

EST:     CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCT                         AGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC
genomic: CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCTgtgagtgctg ... ttttttgcagAGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC

EST: gi|93282854|gb|EB675118.1|EB675118

EST:     CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCT                         AGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC
genomic: CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCTgtgagtgctg ... ttttttgcagAGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC

EST: gi|60394843|gb|DN227712.1|DN227712

EST:     CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCT                         AGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC
genomic: CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCTgtgagtgctg ... ttttttgcagAGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC

EST: gi|71424443|gb|DR806311.1|DR806311

EST:     CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCT                         AGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTCGATCATTTCTGC
genomic: CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCTgtgagtgctg ... ttttttgcagAGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC

EST: gi|71436666|gb|DR817716.1|DR817716

EST:     CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCT                         AGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC
genomic: CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCTgtgagtgctg ... ttttttgcagAGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC

EST: gi|78090245|gb|DV518619.1|DV518619

EST:     CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCT                         AGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC
genomic: CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCTgtgagtgctg ... ttttttgcagAGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC

EST: gi|88750440|gb|DY534581.1|DY534581

EST:     CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCT                         AGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC
genomic: CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCTgtgagtgctg ... ttttttgcagAGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC

EST: gi|76930492|gb|DV172408.1|DV172408

EST:     CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCT                         AGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC
genomic: CAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCTgtgagtgctg ... ttttttgcagAGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGC

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: 155

TTGTCGACAAGACATCCACCATGCAAGACAGCGCCTTTCACTTCCGCAAGCAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCTgtgagtgctg ... ttttttgcagAGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGCTTTCTGTGGAGGCCTTTCCTTGTCATCATGCAGATCATGAGTAACACAC

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 159

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 211

Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 120

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGTCGACAAGACATCCACCATGCAAGACAGCGCCTTTCACTTCCGCAAGCAATCCAAGAGGCTCCGTAGAGCTCTTTGGATGAAGAATGCCAAGCTTCTgtgagtgctgtttctcttccttctatgaatatcgaagacattatatataggtcgatcatttattggtcatctaatttacttcacacagcttagctgttcc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT