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

...ttgtttcctgtatacgatatgttcctcaagtttgcgcctgggcaatgcctgcttaatctggcatcctgatttgttactgctacattttgccctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCACAACTTCGCAACGACATGCGTCTGCCGCGTCCCCAAGCATCTGAGGGAGG

Basic information

species	Zea mays
transcript	GRMZM2G020728_T01
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G020728_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g63890.1 (Oryza sativa), 3'ss of exon 3

ttgtttcctgtatacgatatgttcctcaagtttgcgcctgggcaatgcctgct---taatctggcatcctgatttgttactgctacattttgccctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCACAACTTCGCAACGACATGCGTCTGCCGCGTCCCCAAGCATCTGAGGGAGG
    ||  |  || | | ||       | | ||     |    |  |  ||      | |||   |||   || | | | |||| | |||||     || ||||| ||||| |||||||||||||| || || |||||||||||||| || |||||||| ||||| |||||||||||||| |||||||||||||| || ||||
-cactttttagatgcaa-atccagaagatgcttttttgtcacaagagtttgtcaggcattcttatatca-aatgtatcattgcttctttttgtgtgttttcagCCGGGTTATGAGCGCCTTTGCTGTCTTCGATGCATACAGACACGAGACCACAACTTTGCAACTACATGCGTCTGCCGGGTCCCCAAGCATCTCAGAGAGG

upper sequence: GRMZM2G020728_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g55290.4 (Oryza sativa), 3'ss of exon 3

ttgtttcctgtatacgatatgttcctcaagtttgcgcctgggcaatgcctgct---taatctggcatcctgatttgttactgctacattttgccctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCACAACTTCGCAACGACATGCGTCTGCCGCGTCCCCAAGCATCTGAGGGAGG----
     |  |  || | | ||| |    | | ||     |    |  |  ||      | |||   |||   || | | | |||| | |||||     || |||||||| || |||||||||||||| || || |||||||||||||| || |||||||| ||||| ||||| |||||||| |||||||||||||| || ||||    
-----ttttagatgcaa-atgctgaagatgcttttttgtcacaagagtttgtcaggcattcttatatca-aatgtatcattgcttctttttgtgtgttttcagccagGCTATGAGCGCCTTTGCTGTCTTCGATGCATACAGACACGAGACCACAACTTTGCAACTACATGTGTCTGCCGGGTCCCCAAGCATCTCAGAGAGGAGAA

upper sequence: GRMZM2G020728_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g55290.1 (Oryza sativa), 3'ss of exon 4

ttgtttcctgtatacgatatgttcctcaagtttgcgcctgggcaatgcctgct---taatctggcatcctgatttgttactgctacattttgccctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCACAACTTCGCAACGACATGCGTCTGCCGCGTCCCCAAGCATCTGAGGGAGG
    ||  |  || | | ||| |    | | ||     |    |  |  ||      | |||   |||   || | | | |||| | |||||     || |||||||| || |||||||||||||| || || |||||||||||||| || |||||||| ||||| ||||| |||||||| |||||||||||||| || ||||
-cactttttagatgcaa-atgctgaagatgcttttttgtcacaagagtttgtcaggcattcttatatca-aatgtatcattgcttctttttgtgtgttttcagCCAGGCTATGAGCGCCTTTGCTGTCTTCGATGCATACAGACACGAGACCACAACTTTGCAACTACATGTGTCTGCCGGGTCCCCAAGCATCTCAGAGAGG

upper sequence: GRMZM2G020728_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G11450.1 (Glycine max), 3'ss of exon 4

ttgtttcctgtatacgatatgttcctcaagtttgcgcctgggcaatgcctgcttaatctggcatcctgatttgtta--ctgctacatttt-gccctc--ttgcagCCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCACAACTTCGCAACGACATGCGTCTGCCGCGTCCCCAAGCATCTGAGGGAGG
  ||||    |  || |    ||  |    |||| || |   | |||  |  ||  ||| | ||  ||| |  |||      ||  |||| |  ||   |||||||| ||||| || || |||||||||||  ||||||| ||| ||||||||||||| || || || || || || ||| | || |||||||| || |||||||
--gttttactttcaccaagattttatttcatttgtgcatt--ctatgtgtagttt-tcttggattttgagtacttaaatcattatgtttttggtctgaattgcagCCTGGTTATGAACGTCTTTGCTGCCTGAGGTGCATGCAGCCACGTGATCACAATTTTGCCACCACTTGTGTTTGCAGAGTACCCAAGCAACTTAGGGAGG

upper sequence: GRMZM2G020728_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA05G28440.2 (Glycine max), 3'ss of exon 5

---ttgtttc-ctgtatacgatatgttcctcaagtttgcgcctgggcaatgcctgcttaatctggcatcctgatttgttactgctacat---tttgccctc--ttgcagCCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCACAACTTCGCAACGACATGCGTCTGCCGCGTCCCCAAGCATCTGAGGGAGG
   ||||||  ||||     | || ||  |  | |||| || |         |||  |  ||| | ||  ||| |  |||   |  |||   ||||  ||   |||||||| ||||| || || |||||||||||  ||||||| ||| ||||||||||||| || || || || || || ||| | || |||||||| || |||||||
gtattgttttactgtcactaagattttatttga-tttgtgcat--------tctgtgttttcttggattttgagtaattaaatcatcatgtttttggtctgaattgcagCCTGGTTATGAACGTCTTTGCTGCCTGAGGTGCATGCAGCCACGTGATCACAATTTTGCCACCACTTGTGTTTGCAGAGTTCCCAAGCAACTTAGGGAGG

upper sequence: GRMZM2G020728_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv05s0020g01520.t01 (Vitis vinifera), 3'ss of exon 3

-----ttgtttcctgtatacgatatgttcctcaagtttgcgcctgggcaatgcctgcttaatctggcatcctgatttgttactgctacattttgccctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCACAACTTCGCAACGACATGCGTCTGCCGCGTCCCCAAGCATCTGAGGGAGG
       |  |  | | | |   || |  || ||   |          |     |      ||    |||||   || ||| || ||   |||      |||||||||||||| || || || |||||| |  | ||||| ||  |||| ||||||||||| || || ||||| || ||||| ||||||||||| || |||||||
aaaaacaggctgatatttgcttaatttctctaaaagataaaagcaaagatgaatttacatctccaaaatcct---tttttaatgatatgcttt--tgaattgcagCCAGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCACAACTTTGCCACCACATGTGTGTGCCGGGTCCCCAAGCACCTAAGGGAGG

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|22472254|gb|BU036734.1|BU036734

EST:     GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCAC
genomic: GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCAC

EST: gi|42491834|gb|CK700880.1|CK700880

EST:     GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGACCGC
genomic: GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCAC

EST: gi|16918080|gb|BM073567.1|BM073567

EST:     GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCAC
genomic: GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCAC

EST: gi|78123212|gb|DV541596.1|DV541596

EST:     GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCAC
genomic: GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCAC

EST: gi|5791305|gb|AI978097.1|AI978097

EST:     GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCAC
genomic: GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCAC

EST: gi|78544500|gb|DV621998.1|DV621998

EST:     GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGCTGCCTCCGGAGCATACAGACACGTGATCAC
genomic: GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCAC

EST: gi|89251444|gb|DY623230.1|DY623230

EST:     GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCAC
genomic: GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCAC

EST: gi|22472255|gb|BU036735.1|BU036735

EST:     GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCAC
genomic: GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCAC

EST: gi|211022015|gb|FL261314.1|FL261314

EST:     GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCAC
genomic: GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCAC

EST: gi|26456977|gb|CA828560.1|CA828560

EST:     GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCAC
genomic: GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCAC

EST: gi|37396850|gb|CF635719.1|CF635719

EST:     GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCAC
genomic: GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCAC

EST: gi|211262096|gb|FL418805.1|FL418805

EST:     GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCAC
genomic: GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCAC

EST: gi|26457042|gb|CA828625.1|CA828625

EST:     GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCAC
genomic: GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCAC

EST: gi|20811232|gb|BQ295710.1|BQ295710

EST:     GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCAC
genomic: GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCAC

EST: gi|42491876|gb|CK700922.1|CK700922

EST:     GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGACCAC
genomic: GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCAC

EST: gi|60349541|gb|DN216514.1|DN216514

EST:     GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCAC
genomic: GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCAC

EST: gi|16918867|gb|BM073931.1|BM073931

EST:     GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCAC
genomic: GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCAC

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), 49 (downstream exon)
Score: 387

CGATCTTTATTACAGAAGGAAGGAGATATCACAGGAGCTTTATGAGTTCTGCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCACAACTTCGCAACGACATGCGTCTGCCGCGTCCCCAAGCATCTGAGGGAGG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 258

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 186

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 242

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tgcctgcttaatctggcatcctgatttgttactgctacattttgccctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCACAACTTCGCAACGACATGCGTCTGCCGCGTCCCCAAGCATCTGAGGGAGG

                  tcctgat  putative branch site (score: 242)
                                     cattttgccctctt  putative PPT
                       atttgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtttcctgtatacgatatgttcctcaagtttgcgcctgggcaatgcctgcttaatctggcatcctgatttgttactgctacattttgccctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCACAACTTCGCAACGACATGCGTCTGCCGCGTCCCCAAGCATCTGAGGGAGG

- - - cctgtat
- - - - - - - - - -tgttcct
- - - - - - - - - - - - - - - - -gcgcctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catcctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgctac