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

...caaccatattgttgatgcaatttggtgtagttgctttctgtcactttattcattaagttcttgatgaaacagctgatagtatttttcttgtggacaggagATATGCCTCGCTATGATGATCGCTATGGAGGCACGCGCTTGTATGTTGGCAGATTGGCCCCCCGTACTCGTTCTCGTGATTTAGAATATCTCTTCGGCAA

Basic information

species	Zea mays
transcript	GRMZM2G099317_T03
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G099317_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g02880.1 (Oryza sativa), 3'ss of exon 1

-caaccatattgttgatgcaatttggt----gtagttgctttctgtcactttattcattaagttcttgatgaaacagctgatagtatttttcttgtggacaggagATATGCCTCGCTATGATGATCGCTATGGAGGCACGCGCTTGTATGTTGGCAGATTGGCCCCCCGTACTCGTTCTCGTGATTTAGAATATCTCTTCGGCAA
 | || | | ||| |||     || ||    ||| |     ||  ||   | ||||||||  || |  ||   || | || || | ||  | ||||   ||||||||  ||| |||||||||||||| |||||| ||||||||||||||||||| ||| || |  |||| ||||||||||||||  ||||||| |  ||| ||| 
tccacta-actgtagatcttcatttgtaccagtattcatcctccttccaatcattcattagattttgaatagtactgatg-tatttttgctgttgtcttcagGAGAT--GCCGCGCTATGATGATCGTTATGGAAGCACGCGCTTGTATGTTGGTAGACTGTCTTCCCGCACTCGTTCTCGTGACCTAGAATACCATTTCAGCA-

upper sequence: GRMZM2G099317_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g17710.1 (Oryza sativa), 3'ss of exon 1

------caaccatattgttgatgcaatttggtgtagttgctttctgtcactt-tattcattaagttcttgatgaaacagctgatagtatttttcttgtggacaggagATATGCCTCGCTATGATGATCGCTATGGAGGCACGCGCTTGTATGTTGGCAGATTGGCCCCCCGTACTCGTTCTCGTGATTTAGAATATCTCTTCGGCAA
      |||    |||  ||  |||| |     | | |  |||| |||| |  |||||||||  || ||||  |||   |||||  |  ||| ||| ||       || |||||||||||||||||||  |||||| |||| |||||||||||||| ||| || |  | || ||||||||||||||  |||||||||| ||||||| 
actgtacaat-gcatttctg-cgcaagtattcat-gctcttttcagtcattcatattcattagatt-ttga--aaagtactgatgtttctttgcttttgttttcagGAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGTAGACTGTCTTCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCA-

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|211248807|gb|FL007472.1|FL007472

EST:     TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCCAGGAG                       
genomic: TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCC---AGgtacccttct ... tggacagg

EST: gi|211251026|gb|FL007475.1|FL007475

EST:     TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCCAGGAG                       
genomic: TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCC---AGgtacccttct ... tggacagg

EST: gi|148934490|gb|EC878531.2|EC878531

EST:     TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCCAGGAG                       
genomic: TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCC---AGgtacccttct ... tggacagg

EST: gi|76014888|gb|DT942058.1|DT942058

EST:     TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCCAGGAG                       
genomic: TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCC---AGgtacccttct ... tggacagg

EST: gi|71438768|gb|DR819818.1|DR819818

EST:     TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCCAGGAG                       
genomic: TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCC---AGgtacccttct ... tggacagg

EST: gi|148934137|gb|EC878155.2|EC878155

EST:     TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCCAGGAG                       
genomic: TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCC---AGgtacccttct ... tggacagg

EST: gi|74232122|gb|DT640036.1|DT640036

EST:     TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCCAGGAG                       
genomic: TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCC---AGgtacccttct ... tggacagg

EST: gi|211248809|gb|FL007474.1|FL007474

EST:     TCCTTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCCAGGAG                       
genomic: TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCC---AGgtacccttct ... tggacagg

EST: gi|149070621|gb|EE159032.2|EE159032

EST:     CTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCCAGGAG                       
genomic: CTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCC---AGgtacccttct ... tggacagg

EST: gi|211251027|gb|FL007476.1|FL007476

EST:     TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCCAG                         ATATGCCTCGCTATGATGATCGCTATGGAGGCACGCGCTTGTATGTTGGCA
genomic: TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCCAGgtacccttct ... tggacaggagATATGCCTCGCTATGATGATCGCTATGGAGGCACGCGCTTGTATGTTGGCA

EST: gi|211251030|gb|FL007479.1|FL007479

EST:     TCCCTCGTGCCCCGCCGGNTCTCCAGCGCGCCGTCTCTGCCCAGATCCAGGAG                       
genomic: TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCC---AGgtacccttct ... tggacagg

EST: gi|211251028|gb|FL007477.1|FL007477

EST:     TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCCAGGAG                       
genomic: TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCC---AGgtacccttct ... tggacagg

EST: gi|148959184|gb|EE010639.2|EE010639

EST:     TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCCAGGAG                       
genomic: TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCC---AGgtacccttct ... tggacagg

EST: gi|71310802|gb|DR791706.1|DR791706

EST:     TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCCAGGAG                       
genomic: TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCC---AGgtacccttct ... tggacagg

EST: gi|71438958|gb|DR820008.1|DR820008

EST:     TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCCAGGAG                       
genomic: TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCC---AGgtacccttct ... tggacagg

EST: gi|71298912|gb|DR785451.1|DR785451

EST:     TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCCAGGAG                       
genomic: TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCC---AGgtacccttct ... tggacagg

EST: gi|211251031|gb|FL007480.1|FL007480

EST:     TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCCAGGAG                       
genomic: TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCC---AGgtacccttct ... tggacagg

EST: gi|76282712|gb|DV022280.1|DV022280

EST:     TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCCAGGAG                       
genomic: TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCC---AGgtacccttct ... tggacagg

EST: gi|211251033|gb|FL007482.1|FL007482

EST:     TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCCAGGAG                       
genomic: TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCC---AGgtacccttct ... tggacagg

EST: gi|211251036|gb|FL007485.1|FL007485

EST:     TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCCAGGAG                       
genomic: TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCC---AGgtacccttct ... tggacagg

EST: gi|29945034|gb|CB815435.1|CB815435

EST:     TCCCTCG-GCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCCAGGAG                       
genomic: TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCC---AGgtacccttct ... tggacagg

EST: gi|76280523|gb|DV020091.1|DV020091

EST:     TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCCAGGAG                       
genomic: TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCC---AGgtacccttct ... tggacagg

EST: gi|50333687|gb|CO528813.1|CO528813

EST:     CGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCCAGGAG                       
genomic: CGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCC---AGgtacccttct ... tggacagg

EST: gi|211248808|gb|FL007473.1|FL007473

EST:     TCCTTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCCAGGAG                       
genomic: TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCC---AGgtacccttct ... tggacagg

EST: gi|211251029|gb|FL007478.1|FL007478

EST:     TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCCAGGAG                       
genomic: TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCC---AGgtacccttct ... tggacagg

EST: gi|50336824|gb|CO531950.1|CO531950

EST:     TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCCAGGAG                       
genomic: TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCC---AGgtacccttct ... tggacagg

EST: gi|76289551|gb|DV029119.1|DV029119

EST:     TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCCAGGAG                       
genomic: TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCC---AGgtacccttct ... tggacagg

EST: gi|71771421|gb|DR969358.1|DR969358

EST:     TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCCAGGAG                       
genomic: TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCC---AGgtacccttct ... tggacagg

EST: gi|148941832|gb|EC886805.2|EC886805

EST:     TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCCAGGAG                       
genomic: TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCC---AGgtacccttct ... tggacagg

EST: gi|87153453|gb|DY398242.1|DY398242

EST:     GTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCCAGGAG                       
genomic: GTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCC---AGgtacccttct ... tggacagg

EST: gi|89251320|gb|DY623106.1|DY623106

EST:     TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCCAGGAG                       
genomic: TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCC---AGgtacccttct ... tggacagg

EST: gi|87155664|gb|DY400453.1|DY400453

EST:     TCCTTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCCAGGAG                       
genomic: TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCC---AGgtacccttct ... tggacagg

EST: gi|31406034|gb|CD484766.1|CD484766

EST:     TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCCAGGAG                       
genomic: TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCC---AGgtacccttct ... tggacagg

EST: gi|149108516|gb|EE292817.2|EE292817

EST:     TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCCAGGAG                       
genomic: TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCC---AGgtacccttct ... tggacagg

EST: gi|37425051|gb|CF650261.1|CF650261

EST:     TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCCAGGAG                       
genomic: TCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCC---AGgtacccttct ... tggacagg

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 3 RNA-Seq libraries.

Block sizes: 35 (upstream exon), 49 (downstream exon)
Score: 14

GAGGCTAGAATTCGGATCCCTCCCACCACATCCATCCCCTTCCCTTCCCTTCCCTCGTGCCCCGCCGGCTCTCCAGCGCGCCGTCTCTGCCCAGATCCAGgtacccttct ... tggacaggagATATGCCTCGCTATGATGATCGCTATGGAGGCACGCGCTTGTATGTTGGCAGATTGGCCCCCCGTACTCGTTCTCGTGATTTAGAATATCTCTTCGGCAA

Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 8

Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 15

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttattcattaagttcttgatgaaacagctgatagtatttttcttgtggacaggagATATGCCTCGCTATGATGATCGCTATGGAGGCACGCGCTTGTATGTTGGCAGATTGGCCCCCCGTACTCGTTCTCGTGATTTAGAATATCTCTTCGGCAA

                         agctgat  putative branch site (score: 15)
                                    tttttcttgt  putative PPT
                              atagtatttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaccatattgttgatgcaatttggtgtagttgctttctgtcactttattcattaagttcttgatgaaacagctgatagtatttttcttgtggacaggagATATGCCTCGCTATGATGATCGCTATGGAGGCACGCGCTTGTATGTTGGCAGATTGGCCCCCCGTACTCGTTCTCGTGATTTAGAATATCTCTTCGGCAA

- - - - -tgttgat
- - - - - - - - - - tttggtg
- - - - - - - - - - - - - - - -tgctttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acagctg