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

...ttgacaacagcttatgctagtctgaaatcgcatatctgtctattctataatatggatgttatcagacttgctagattgtctgatgttttttttttggcagACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAACCGCATCCTCATGCCGATGATCAACGAGGCCTTCTGGGCTCTGTACACC

Basic information

species	Zea mays
transcript	GRMZM2G106250_T01
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G106250_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g58380.1 (Oryza sativa), 3'ss of exon 3

--ttgacaacagcttatgctagtctgaaatcgcatatctgtctattctataatatggatgttatcagacttgctagattgtctgatgttttttt--tttggcagACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAACCGCATCCTCATGCCGATGATCAACGAGGCCTTCTGGGCTCTGTACACC
        |||  |||    ||| ||||  || | ||| ||  | | ||   |  | | ||  |    |     | |||| |||||  |||||     | |||| || |||||| | || |||||||| ||||| ||||| || |||||||||||||||||||||||||| |||||||||||||| |||||||| || ||||| 
gtcctgttacacatta----agtttgaagccgtaaatccgttcaatgtaatgttggcaagtacttgtccacttgatattgcctgattatttttgaaccttgcagGCTTGGGAAGACGGTAATATGCTCACAAGACTACCCTGGTTTCATCGTGAACCGCATCCTCATGCCAATGATCAACGAGGCGTTCTGGGCACTTTACACT

upper sequence: GRMZM2G106250_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ28731 (Selaginella moellendorffii), 3'ss of exon 3

ttgacaacagcttatgctagtctgaaatcgcatatctgtctattctataatatggatgttatcagacttgctagattgtctgatgttttttttttggcagACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAACCGCATCCTCATGCCGATGATCAACGAGGCCTTCTGGGCTCTGTACACC
                                               ||| | |      | |   |||  ||||   |  | || |        |  ||| |||| ||| | ||  |  |||| |  || | ||| || ||| |||| ||||| |||||||||||||||||||||||||| ||||  || |||  |   
----------------------------------------------gtaaga-gagcagcacccatctta-tagaagctaagctgatcaccccg-gatagATTCGGCAAGACGGTGGTGAGCTCCCGCGACTTCCCGGGCTTCGTCGTCAACCGGATCCTCATGCCGATGATCAACGAGGCGTTCTACGCGCTGCTCGAG

upper sequence: GRMZM2G106250_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ30692 (Selaginella moellendorffii), 3'ss of exon 3

ttgacaacagcttatgctagtctgaaatcgcatatctgtctattctataatatggatgttatcagacttgctagattgtctgatgttttttttttgg-cagACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAACCGCATCCTCATGCCGATGATCAACGAGGCCTTCTGGGCTCTGTACACC
                                                  || | | |  | ||  | |  ||||    || |  |  |      || |||| |||| ||| | ||  |  |||| |  || | ||| || ||| |||| ||||| ||||||||||| |||||||||||||| ||||  || |||  |   
-------------------------------------------------gtaagaaagc-agcacccatcttagagaagctaagctgatcaccccggacagATTCGGCAAGACGGTGGTGAGCTCCCGCGACTTCCCGGGCTTCGTCGTCAACCGGATCCTCATGCCCATGATCAACGAGGCGTTCTACGCGCTGCTCGAG

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|91056169|gb|EB166587.1|EB166587

EST:     GCCGATACGTCAGATGAGGTGTTTGCTGCGGTCAGATCTTTCTCCGAAAG                         ACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAA
genomic: GCCGATACGTCAGATGAGGTGTTTGCTGCGGTCAGATCTTTCTCCGAAAGgtaactaaaa ... tttttggcagACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAA

EST: gi|31359154|gb|CD443511.1|CD443511

EST:     GCCGATACGTCAGATGAGGTGTTTGCTGCTGTCAGATCTTTCTCCGAAAG                         ACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAA
genomic: GCCGATACGTCAGATGAGGTGTTTGCTGCGGTCAGATCTTTCTCCGAAAGgtaactaaaa ... tttttggcagACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAA

EST: gi|60354275|gb|DN221248.1|DN221248

EST:     GCCGATACGTCAGATGAGGTGTTTGCTGCGGTCAGATCTTTCTCCGAAAG                         ACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAA
genomic: GCCGATACGTCAGATGAGGTGTTTGCTGCGGTCAGATCTTTCTCCGAAAGgtaactaaaa ... tttttggcagACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAA

EST: gi|31357729|gb|CD442086.1|CD442086

EST:     GCCGATACGTCAGATGAGGTGTTTGCTGCTGTCAGATCTTTCTCCGAGAG                         ACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAA
genomic: GCCGATACGTCAGATGAGGTGTTTGCTGCGGTCAGATCTTTCTCCGAAAGgtaactaaaa ... tttttggcagACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAA

EST: gi|149070552|gb|EE158955.2|EE158955

EST:     GCCGATACGTCAGATGAGGTGTTTGCTGCGGTCAGATCTTTCTCCGAAAG                         ACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAA
genomic: GCCGATACGTCAGATGAGGTGTTTGCTGCGGTCAGATCTTTCTCCGAAAGgtaactaaaa ... tttttggcagACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAA

EST: gi|89759984|gb|DY688615.1|DY688615

EST:     GCCGATACGTCAGATGAGGTGTTTGCTGCGGTCAGATCTTTCTCCGAAAG                         ACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAA
genomic: GCCGATACGTCAGATGAGGTGTTTGCTGCGGTCAGATCTTTCTCCGAAAGgtaactaaaa ... tttttggcagACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAA

EST: gi|89759982|gb|DY688614.1|DY688614

EST:     CGGTCAGATCTTTCTCCGAAAG                         ACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAA
genomic: CGGTCAGATCTTTCTCCGAAAGgtaactaaaa ... tttttggcagACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAA

EST: gi|91056103|gb|EB166521.1|EB166521

EST:     GCCGATACGTCAGATGAGGTGTTTGCTGCGGTCAGATCTTTCTCCGAAAG                         ACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAA
genomic: GCCGATACGTCAGATGAGGTGTTTGCTGCGGTCAGATCTTTCTCCGAAAGgtaactaaaa ... tttttggcagACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAA

EST: gi|67018075|gb|CO446824.1|CO446824

EST:     GCCGATACGTCAGATGAGGTGTTTGCTGCGGTCAGATCTTTCTCCGAAAG                         ACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAA
genomic: GCCGATACGTCAGATGAGGTGTTTGCTGCGGTCAGATCTTTCTCCGAAAGgtaactaaaa ... tttttggcagACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAA

EST: gi|78093292|gb|DV521666.1|DV521666

EST:     GCCGATACGTCAGATGAGGTGTTTGCTGCGGTCAGATCTTTCTCGGAAAG                         ACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAA
genomic: GCCGATACGTCAGATGAGGTGTTTGCTGCGGTCAGATCTTTCTCCGAAAGgtaactaaaa ... tttttggcagACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAA

EST: gi|71445007|gb|DR826057.1|DR826057

EST:     GCCGATACGTCAGATGAGGTGTTTGCTGCGGTCAGATCTTTCTCCGAAAG                         ACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAA
genomic: GCCGATACGTCAGATGAGGTGTTTGCTGCGGTCAGATCTTTCTCCGAAAGgtaactaaaa ... tttttggcagACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAA

EST: gi|78093293|gb|DV521667.1|DV521667

EST:     GCCGATACGTCAGATGAGGTGTTTGCTGCGGTCAGATCTTTCTCGGAAAG                         ACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAA
genomic: GCCGATACGTCAGATGAGGTGTTTGCTGCGGTCAGATCTTTCTCCGAAAGgtaactaaaa ... tttttggcagACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAA

EST: gi|76290184|gb|DV029752.1|DV029752

EST:     GCCGATACGTCAGATGAGGTGTTTGCTGCGGTCAGATCTTTCTCCGAAAG                         ACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAA
genomic: GCCGATACGTCAGATGAGGTGTTTGCTGCGGTCAGATCTTTCTCCGAAAGgtaactaaaa ... tttttggcagACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAA

EST: gi|76281437|gb|DV021005.1|DV021005

EST:     GCCGATACGTCAGATGAGGTGTTTGCTGCGGTCAGATCTTTCTCCGAAAG                         ACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAA
genomic: GCCGATACGTCAGATGAGGTGTTTGCTGCGGTCAGATCTTTCTCCGAAAGgtaactaaaa ... tttttggcagACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAA

EST: gi|211401737|gb|FL334015.1|FL334015

EST:     GCCGATACGTCAGATGAGGTGTTTGCTGCTGTCAGATCTTTCTCCGAAAG                         GCTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAA
genomic: GCCGATACGTCAGATGAGGTGTTTGCTGCGGTCAGATCTTTCTCCGAAAGgtaactaaaa ... tttttggcagACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAA

EST: gi|149096680|gb|EE182448.2|EE182448

EST:     GCCGATACGTCAGATGAGGTGTTTGCTGCGGTCAGATCTTTCTCCGAAAG                         ACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAA
genomic: GCCGATACGTCAGATGAGGTGTTTGCTGCGGTCAGATCTTTCTCCGAAAGgtaactaaaa ... tttttggcagACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAA

EST: gi|71774114|gb|DR971996.1|DR971996

EST:     GCCGATACGTCAGATGAGGTGTTTGCTGCGGTCAGATCTTTCTCCGAAAG                         ACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAA
genomic: GCCGATACGTCAGATGAGGTGTTTGCTGCGGTCAGATCTTTCTCCGAAAGgtaactaaaa ... tttttggcagACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAA

EST: gi|31360062|gb|CD444419.1|CD444419

EST:     GCCGATACGTCAGATGAGGTGTTTGCTGCTGTCAGATCTTTCTCCGAAAG                         ACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAA
genomic: GCCGATACGTCAGATGAGGTGTTTGCTGCGGTCAGATCTTTCTCCGAAAGgtaactaaaa ... tttttggcagACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAA

EST: gi|76281438|gb|DV021006.1|DV021006

EST:     GCCGATACGTCAGATGAGGTGTTTGCTGCGGTCAGATCTTTCTCCGAAAG                         ACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAA
genomic: GCCGATACGTCAGATGAGGTGTTTGCTGCGGTCAGATCTTTCTCCGAAAGgtaactaaaa ... tttttggcagACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAA

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: 43 (upstream exon), 40 (downstream exon)
Score: 20

ACTTCTTCAACCCTCCTCCGGTAATGAAACTGATCGAGATTATCCGAGGAGCCGATACGTCAGATGAGGTGTTTGCTGCGGTCAGATCTTTCTCCGAAAGgtaactaaaa ... tttttggcagACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAACCGCATCCTCATGCCGATGATCAACGAGGCCTTCTGGGCTCTGTACACC

Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 65

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 64

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 109

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tataatatggatgttatcagacttgctagattgtctgatgttttttttttggcagACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAACCGCATCCTCATGCCGATGATCAACGAGGCCTTCTGGGCTCTGTACACC

                                gtctgat  putative branch site (score: 109)
                                      tgtttttttttt  CT-rich tract
                                   tgatgtttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgacaacagcttatgctagtctgaaatcgcatatctgtctattctataatatggatgttatcagacttgctagattgtctgatgttttttttttggcagACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAACCGCATCCTCATGCCGATGATCAACGAGGCCTTCTGGGCTCTGTACACC

- - caacagc
- - - - - -ttatgct
- - - - - - - - - - - - - - - - - - - - - - - - - -atggatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttgcta