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

...ctttgtttcctctatataggttatggtcctcaagtttgtggttgtgcagtgccagatctagcatcctcatttcttactgctacattttgtcctcttgcagCCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCACAACTTTGCAACGACTTGTGTCTGCCGAGTCCCCAAGCATCTGAGGGAGG

Basic information

species	Zea mays
transcript	GRMZM2G099007_T01
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G099007_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g55290.4 (Oryza sativa), 3'ss of exon 3

ctttgtttcctctatataggttatggtcctcaagtttgtggttgtgcagtgccagatctagcatcctcatttcttactgctacattttgtcctcttgcagCCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCACAACTTTGCAACGACTTGTGTCTGCCGAGTCCCCAAGCATCTGAGGGAGG----
 |||   | |   ||   |   ||| |  |         |  | ||    ||    |||   |||   || | | | |||| | ||||||    || |||||||| || |||||||||||||| ||||| |||||||||||||| ||||||||||||||||| || ||||||||||| |||||||||||||| || ||||    
ttttagatgcaa-atgctgaagatgcttttttgtcacaagagtttgtcaggc--attcttatatcaa-atgtatcattgcttctttttgtgtgttttcagccagGCTATGAGCGCCTTTGCTGTCTTCGATGCATACAGACACGAGACCACAACTTTGCAACTACATGTGTCTGCCGGGTCCCCAAGCATCTCAGAGAGGAGAA

upper sequence: GRMZM2G099007_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g55290.1 (Oryza sativa), 3'ss of exon 4

ctttgtttcctctatataggttatggtcct-caagtttgtggttgtgcagtgccaga---tctagcatcctcatttcttactgctacattttgtcctcttgcagCCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCACAACTTTGCAACGACTTGTGTCTGCCGAGTCCCCAAGCATCTGAGGGAGG
      ||  |  ||  |  |  ||    | |   |||||          || |||    |||   |||   || | | | |||| | ||||||    || |||||||| || |||||||||||||| ||||| |||||||||||||| ||||||||||||||||| || ||||||||||| |||||||||||||| || ||||
---cactttttagatgcaaatgctgaagatgcttttttgtcacaagagtttgtcaggcattcttatatcaa-atgtatcattgcttctttttgtgtgttttcagCCAGGCTATGAGCGCCTTTGCTGTCTTCGATGCATACAGACACGAGACCACAACTTTGCAACTACATGTGTCTGCCGGGTCCCCAAGCATCTCAGAGAGG

upper sequence: GRMZM2G099007_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g63890.1 (Oryza sativa), 3'ss of exon 3

ctttgtttcctctatataggttatggtcctcaag-tttgtggttgt-gcagtgccagatctagcatcctcatttc-------ttactgctacattttgtcctcttgcagCCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCACAACTTTGCAACGACTTGTGTCTGCCGAGTCCCCAAGCATCTGAGGGAGG
         | || | ||| |     |||  ||| |   |  ||||  ||        ||  |||| || || ||       | | |||| | ||||||    || ||||| || || |||||||||||||| ||||| |||||||||||||| ||||||||||||||||| || || |||||||| |||||||||||||| || ||||
---------cactttttagatgcaaatccagaagatgcttttttgtcacaagagtttgtcaggcattcttatatcaaatgtatcattgcttctttttgtgtgttttcagCCGGGTTATGAGCGCCTTTGCTGTCTTCGATGCATACAGACACGAGACCACAACTTTGCAACTACATGCGTCTGCCGGGTCCCCAAGCATCTCAGAGAGG

upper sequence: GRMZM2G099007_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G11450.1 (Glycine max), 3'ss of exon 4

ctttgtttcctctatataggttatggtcctcaagtttgtggt-tgtgcagtgcc---agatctagcatcctcatttcttactgctacattttgtcctc-ttgcagCCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCACAACTTTGCAACGACTTGTGTCTGCCGAGTCCCCAAGCATCTGAGGGAGG
   | || | |  |   || || |  | |    ||   |  | |||| |||       ||| | |  | || |  || |  || |   ||| |||    |||||||| || || || || |||||||||||  ||||||| ||| ||||||| ||||| ||||| || |||||||| ||| |||| |||||||| || |||||||
--gttttactttcaccaagattttatttcatttgtgcattctatgtgtagttttcttggattttgagtacttaaatcattatgtt---tttggtctgaattgcagCCTGGTTATGAACGTCTTTGCTGCCTGAGGTGCATGCAGCCACGTGATCACAATTTTGCCACCACTTGTGTTTGCAGAGTACCCAAGCAACTTAGGGAGG

upper sequence: GRMZM2G099007_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA05G28440.2 (Glycine max), 3'ss of exon 5

---ctttgtttcctctatataggttatggtcctcaagtttgtggttgtgcagtgccagatctagcatcctcatttcttactgctacattttgtcctc-ttgcagCCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCACAACTTTGCAACGACTTGTGTCTGCCGAGTCCCCAAGCATCTGAGGGAGG
    | | || |    |   || || |  |      ||   |   ||||   |    ||| | |  |  | |  || |  || |   ||| |||    |||||||| || || || || |||||||||||  ||||||| ||| ||||||| ||||| ||||| || |||||||| ||| |||| |||||||| || |||||||
gtattgttttactgtcactaagattttatttgatttgtgcatt-ctgtgttttcttggattttgagtaattaaatcatcatgtt---tttggtctgaattgcagCCTGGTTATGAACGTCTTTGCTGCCTGAGGTGCATGCAGCCACGTGATCACAATTTTGCCACCACTTGTGTTTGCAGAGTTCCCAAGCAACTTAGGGAGG

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|71298627|gb|DR785288.1|DR785288

EST:     GCCTGGACCAGAGCTATGCAGACCGTAACCTGATCGCAAAGTGGAAAAAG                         CCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC
genomic: GCCTGGACCAGAGCTATGCAGACCGTAACCTGATCGCAAAGTGGAAAAAGgtaattatcc ... cctcttgcagCCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC

EST: gi|28986788|gb|CB351310.1|CB351310

EST:     GCCTGGACCAGAGCTATGCAGACCGTAACCTGATCGCAAAGTGGAAAAAG                         CCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC
genomic: GCCTGGACCAGAGCTATGCAGACCGTAACCTGATCGCAAAGTGGAAAAAGgtaattatcc ... cctcttgcagCCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC

EST: gi|71317907|gb|DR795714.1|DR795714

EST:     GCCTGGACCAGAGCTATGCAGACCGTAACCTGATCGCAAAGTGGAAAAAG                         CCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC
genomic: GCCTGGACCAGAGCTATGCAGACCGTAACCTGATCGCAAAGTGGAAAAAGgtaattatcc ... cctcttgcagCCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC

EST: gi|28983213|gb|BQ538564.2|BQ538564

EST:     GCCTGGACCAGAGCTATGCAGACCGTAACCTGATCGCAAAGTGGAAAAAG                         CCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC
genomic: GCCTGGACCAGAGCTATGCAGACCGTAACCTGATCGCAAAGTGGAAAAAGgtaattatcc ... cctcttgcagCCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC

EST: gi|71299366|gb|DR785696.1|DR785696

EST:     GCCTGGACCAGAGCTATGCAGACCGTAACCTGATCGCAAAGTGGAAAAAG                         CCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC
genomic: GCCTGGACCAGAGCTATGCAGACCGTAACCTGATCGCAAAGTGGAAAAAGgtaattatcc ... cctcttgcagCCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC

EST: gi|78090990|gb|DV519364.1|DV519364

EST:     GCCTGGACCAGAGCTATGCAGACCGTAACCTGATCGCAAAGTGGAAAAAG                         CCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC
genomic: GCCTGGACCAGAGCTATGCAGACCGTAACCTGATCGCAAAGTGGAAAAAGgtaattatcc ... cctcttgcagCCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC

EST: gi|76281371|gb|DV020939.1|DV020939

EST:     GCCTGGACCAGAGCTATGCAGACCGTAACCTGATCGCAAAGTGGAAAAAG                         CCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC
genomic: GCCTGGACCAGAGCTATGCAGACCGTAACCTGATCGCAAAGTGGAAAAAGgtaattatcc ... cctcttgcagCCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC

EST: gi|71298624|gb|DR785287.1|DR785287

EST:     GCCTGGACCAGAGCTATGCAGACCGTAACCTGATCGCAAAGTGGAAAAAG                         CCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC
genomic: GCCTGGACCAGAGCTATGCAGACCGTAACCTGATCGCAAAGTGGAAAAAGgtaattatcc ... cctcttgcagCCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC

EST: gi|14883571|gb|BI273423.1|BI273423

EST:     GCCTGGACCAGAGCTATGCAGATCGTAACCTGATCGCAAAGTGGAAAAAG                         CCAGGATACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGACCAC
genomic: GCCTGGACCAGAGCTATGCAGACCGTAACCTGATCGCAAAGTGGAAAAAGgtaattatcc ... cctcttgcagCCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC

EST: gi|71417128|gb|DR803934.1|DR803934

EST:     GCCTGGACCAGAGCTATGCAGACCGTAACCTGATCGCAAAGTGGAAAAAG                         CCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC
genomic: GCCTGGACCAGAGCTATGCAGACCGTAACCTGATCGCAAAGTGGAAAAAGgtaattatcc ... cctcttgcagCCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC

EST: gi|60344260|gb|DN211233.1|DN211233

EST:     GCCTGGACCAGAGCTATGCAGACCGTAACCTGATCGCAAAGTGGAAAAAG                         CCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC
genomic: GCCTGGACCAGAGCTATGCAGACCGTAACCTGATCGCAAAGTGGAAAAAGgtaattatcc ... cctcttgcagCCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC

EST: gi|60357216|gb|DN224189.1|DN224189

EST:     GCCTGGACCAGAGCTATGCAGACCGTAACCTGATCGCAAAGTGGAAAAAG                         CCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC
genomic: GCCTGGACCAGAGCTATGCAGACCGTAACCTGATCGCAAAGTGGAAAAAGgtaattatcc ... cctcttgcagCCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC

EST: gi|60395582|gb|DN228452.1|DN228452

EST:     GCCTGGACCAGAGCTATGCAGACCGTAACCTGATCGCAAAGTGGAAAAAG                         CCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC
genomic: GCCTGGACCAGAGCTATGCAGACCGTAACCTGATCGCAAAGTGGAAAAAGgtaattatcc ... cctcttgcagCCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC

EST: gi|211224314|gb|FK974031.1|FK974031

EST:     GCCTGGACCAGAGCTATGCAGATCGTAACCTGATCGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC
genomic: GCCTGGACCAGAGCTATGCAGACCGTAACCTGATCGCAAAGTGGAAAAAGgtaattatcc ... cctcttgcagCCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC

EST: gi|16916596|gb|BM072910.1|BM072910

EST:     GCCTGGACCAGAGCTATGCAGACCGTAACCTGATCGCAAAGTGGAAAAAG                         CCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC
genomic: GCCTGGACCAGAGCTATGCAGACCGTAACCTGATCGCAAAGTGGAAAAAGgtaattatcc ... cctcttgcagCCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC

EST: gi|91872825|gb|EB402782.1|EB402782

EST:     GCCTGGACCAGAGCTATGCAGACCGTAACCTGATCGCAAAGTGGAAAAAG                         CCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC
genomic: GCCTGGACCAGAGCTATGCAGACCGTAACCTGATCGCAAAGTGGAAAAAGgtaattatcc ... cctcttgcagCCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC

EST: gi|18162287|gb|BM332126.1|BM332126

EST:     GCCTGGACCAAAGCTATGCAGACCGTAACCTGATCGCAAAGTGGAAAAAG                         CCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC
genomic: GCCTGGACCAGAGCTATGCAGACCGTAACCTGATCGCAAAGTGGAAAAAGgtaattatcc ... cctcttgcagCCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC

EST: gi|211440487|gb|FL452482.1|FL452482

EST:     GCCTGGACCAGMGCTATGCAGACCGTAACCTGATCGCAAAGTGGAAAAAG                         CCAGGATACGAGCGCCTTTGCTG-CTTCGGTGCATACAGACACGTGACCAC
genomic: GCCTGGACCAGAGCTATGCAGACCGTAACCTGATCGCAAAGTGGAAAAAGgtaattatcc ... cctcttgcagCCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC

EST: gi|4730779|gb|AI649945.1|AI649945

EST:     GCCTGGACCAGAGCTATGCAGACCGTAACCTGATCGCAAAGTGGAAAAAG                         CCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC
genomic: GCCTGGACCAGAGCTATGCAGACCGTAACCTGATCGCAAAGTGGAAAAAGgtaattatcc ... cctcttgcagCCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC

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: 49 (upstream exon), 48 (downstream exon)
Score: 331

TGATCTTTACTACAGAAGGAAGGAGATATCACGGGAGCTTTATGAGTTCTGCCTGGACCAGAGCTATGCAGACCGTAACCTGATCGCAAAGTGGAAAAAGgtaattatcc ... cctcttgcagCCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCACAACTTTGCAACGACTTGTGTCTGCCGAGTCCCCAAGCATCTGAGGGAGG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 215

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 333

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 200

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gcagtgccagatctagcatcctcatttcttactgctacattttgtcctcttgcagCCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCACAACTTTGCAACGACTTGTGTCTGCCGAGTCCCCAAGCATCTGAGGGAGG

                         ttcttac  putative branch site (score: 200)
                                     cattttgtcctctt  putative PPT
                       atttctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttgtttcctctatataggttatggtcctcaagtttgtggttgtgcagtgccagatctagcatcctcatttcttactgctacattttgtcctcttgcagCCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCACAACTTTGCAACGACTTGTGTCTGCCGAGTCCCCAAGCATCTGAGGGAGG

- - - - - - - - - - - -tggtcct
- - - - - - - - - - - - - - - - - - - - - tgtgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctacat