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

gtatgcacaaacggttattgaggcactcactactgatgtcagttgtttcctggcacaggattgtactaacgttatgccctcatgcagCTGAAAATGATCCACATGATGGGAAGAGAAAGTGTGAAGCTCTCTGGCCTATTTTCCGTATTTCTCATCAAAGGAGCCGCTACATATATGATCTTTACTA

Basic information

species	Zea mays
transcript	GRMZM2G053801_T01
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G053801_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g63890.1 (Oryza sativa), 3'ss of exon 2

gtatgcacaaacggttattgaggcactcactactgatgtcagttgtt--tcctggcacaggattg-tactaacgttatgccctcatgcagCTGAAAATGATCCACATGATGGGAAGAGAAAGTGTGAAGCTCTCTGGCCTATTTTCCGTATTTCTCATCAAAGGAGCCGCTACATATATGATCTTTACTA
              | |   | || | |  | | |||||   ||| |  | |||       || | ||||||  | ||   |||||| ||||||||||||  |||||||||||||||||||||| ||||| |||||||| |||||||||||||| |||||||| || |||||||||||||||||||| ||
-----------gtatgacatatgctcccctttcagatgtttattgatacttctgctcttatatggatactaatatcatctactcatgtagCTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAATTTTCCGTATTTCCCATCAAAGAAGTCGCTACATATATGATCTTTATTA

upper sequence: GRMZM2G053801_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g55290.1 (Oryza sativa), 3'ss of exon 3

gtatgcacaaacggttattgaggcactcactactgatgtcagttgtt--tcctggcacaggattg-tactaacgttatgccctcatgcagCTGAAAATGATCCACATGATGGGAAGAGAAAGTGTGAAGCTCTCTGGCCTATTTTCCGTATTTCTCATCAAAGGAGCCGCTACATATATGATCTTTACTA
              | |   | || | |  | | |||||   ||| |  | |||       || | ||||||  | ||   |||||||||||||||||||  | |||||||||||||||||||| ||||| |||||||| |||||||||||||| |||||||| || |||||||||||||||||||| ||
-----------gtatgacatatgctcccctttcagatgtttattgatacttctgctcttatatggatactaatatcatctactcatgcagCTGAAAATGACACGCATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAATTTTCCGTATTTCCCATCAAAGAAGTCGCTACATATATGATCTTTATTA

upper sequence: GRMZM2G053801_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA05G28440.2 (Glycine max), 3'ss of exon 3

gtatgcacaaacggttattgaggcactcactac-tgatgtcagttgtttcctggcac--aggattgtactaacgttatgccctc-atg---cagCTGAAAATGATCCACATGATGGGAAGAGAAAGTGTGAAGCTCTCTGGCCTATTTTCCGTATTTCTCATCAAAGGAGCCGCTACATATATGATCTTTACTA
    |    ||   |   | | |  || | ||  |  | | |  |  || |||  |   | ||   || ||   ||||  |||  |||   ||||||| ||||||||||||||||| || ||||| |||||  |  | ||||| || ||    ||| | || || | |||||||||||||| ||| || ||| |
----gttggaattttacatcatgtgcttagtagattttattatgttctttctgaaatcaatgaaattaatagttttatatcctttatgtggcagCTGAGAATGATCCACATGATGGCAAAAGAAAATGTGAGACATTATGGCCAATATTTAAGATTGCACACCAGAAGAGCCGCTACATATTTGACCTCTACCA

upper sequence: GRMZM2G053801_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA07G15700.1 (Glycine max), 3'ss of exon 2

gtatgcacaaacggttattgaggcactcactact---gatgtcagt-tgtttcctggcacaggattgtactaa--cgttatgc---cctcatg---cagCTGAAAATGATCCACATGATGGGAAGAGAAAGTGTGAAGCTCTCTGGCCTATTTTCCGTATTTCTCATCAAAGGAGCCGCTACATATATGATCTTTACTA
    |    ||   |   || |  |||  |   |   ||| | | | ||||   |   | |   ||| ||| |   ||| |||   ||| |||   ||||||| || |||||||||||||| |||||||| |||||  |  | |||||||| ||    ||| | || || | |||||||||||||| ||| || ||  |
----gttggaattttatatgtgatacttgcctttctagattttattgtgttctttctgaaacccttgaacttaattgttttgcattccttatgtggcagCTGAGAACGATCCACATGATGGCAAGAGAAACTGTGAGACATTATGGCCTATATTTAAGATTGCACACCAGAAGAGCCGCTACATATTTGACCTCTATCA

upper sequence: GRMZM2G053801_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv05s0020g01520.t01 (Vitis vinifera), 3'ss of exon 2

-gtatgcacaaacggttat---tgaggcactcactactga---tgtcagttgtttcctgg---cacaggattg----tactaacgttatg---ccctcatgcagCTGAAAATGATCCACATGATGGGAAGAGAAAGTGTGAAGCTCTCTGGCCTATTTTCCGTATTTCTCATCAAAGGAGCCGCTACATATATGATCTTTACTA
  ||| | |      | ||   |   || || | |  ||    ||||  |||||| |||     | |  | |     |   | |||| |    |  |    ||||||||||||| ||||||||||| |||||||| ||||| || || ||||| ||||||   ||  | ||||| | |||||| || || | |||||||||| |
gttattctctttttctcatgcatacagctctgaatgttgtctttgtcgcttgtttgctgaacttataaaactaacaatgacaccgttctatgtcttttgaacagCTGAAAATGACCCACATGATGGTAAGAGAAAATGTGAGGCACTATGGCCGATTTTCAAAATAGCACATCAGAAGAGCCGTTATATTTTTGATCTTTACCA

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|211024557|gb|FL264564.1|FL264564

EST:     GGAGCTTATTGAACCAACCATCCGTGAGTTGGATGCCAAAATGAGAGAAG                         CTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
genomic: GGAGCTTATTGAACCAACCATCCGTGAGTTGGATGCCAAAATGAGAGAAGgtatgcacaa ... cctcatgcagCTGAAAATGATCCACATGATGGGAAGAGAAAGTGTGAAGCTCTCTGGCCTA

EST: gi|211024552|gb|FL264559.1|FL264559

EST:     GGAGCTTATTGAACCAACCATCCGTGAGTTGGATGCCAAAATGAGAGAAG                         CTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
genomic: GGAGCTTATTGAACCAACCATCCGTGAGTTGGATGCCAAAATGAGAGAAGgtatgcacaa ... cctcatgcagCTGAAAATGATCCACATGATGGGAAGAGAAAGTGTGAAGCTCTCTGGCCTA

EST: gi|60349645|gb|DN216618.1|DN216618

EST:     GGAGCTTATTGAACCAACCATCCGTGAGTTGGATGCCAAAATGAGAGAAG                         CTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCGCTCTGGCCTA
genomic: GGAGCTTATTGAACCAACCATCCGTGAGTTGGATGCCAAAATGAGAGAAGgtatgcacaa ... cctcatgcagCTGAAAATGATCCACATGATGGGAAGAGAAAGTGTGAAGCTCTCTGGCCTA

EST: gi|211027007|gb|FL264571.1|FL264571

EST:     GAGCTTATTTGAACCAACCATCCGTGAGTTGGATGCCAAAATGAGAGAAG                         CTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
genomic: GAGCTTA-TTGAACCAACCATCCGTGAGTTGGATGCCAAAATGAGAGAAGgtatgcacaa ... cctcatgcagCTGAAAATGATCCACATGATGGGAAGAGAAAGTGTGAAGCTCTCTGGCCTA

EST: gi|211024549|gb|FL264556.1|FL264556

EST:     GGAGCTTATTGAACCAACCATCCGTGAGTTGGATGCCAAAATGAGAGAAG                         CTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
genomic: GGAGCTTATTGAACCAACCATCCGTGAGTTGGATGCCAAAATGAGAGAAGgtatgcacaa ... cctcatgcagCTGAAAATGATCCACATGATGGGAAGAGAAAGTGTGAAGCTCTCTGGCCTA

EST: gi|211027009|gb|FL264573.1|FL264573

EST:     GGAGCTTATTGAACCAACCATCCGTGAGTTGGATGCCAAAATGAGAGAAG                         CTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
genomic: GGAGCTTATTGAACCAACCATCCGTGAGTTGGATGCCAAAATGAGAGAAGgtatgcacaa ... cctcatgcagCTGAAAATGATCCACATGATGGGAAGAGAAAGTGTGAAGCTCTCTGGCCTA

EST: gi|211224315|gb|FK974032.1|FK974032

EST:     GGAGCTTATTGAACCAACCATCCGTGAGTTGGATGCCAAAATGAGAGAAG                         CTGAAAATGATCCACATGATGG-AAWGAGAAAGTGTGAAGCTCTCTGGCCT
genomic: GGAGCTTATTGAACCAACCATCCGTGAGTTGGATGCCAAAATGAGAGAAGgtatgcacaa ... cctcatgcagCTGAAAATGATCCACATGATGGGAA-GAGAAAGTGTGAAGCTCTCTGGCCT

EST: gi|211027004|gb|FL264568.1|FL264568

EST:     GGAGCTTATTGAACCAACCATCCGTGAGTTGGATGCCAAAATGAGAGAAG                         CTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGG
genomic: GGAGCTTATTGAACCAACCATCCGTGAGTTGGATGCCAAAATGAGAGAAGgtatgcacaa ... cctcatgcagCTGAAAATGATCCACATGATGGGAAGAGAAAGTGTGAAGCTCTCTGG

EST: gi|211224316|gb|FK974033.1|FK974033

EST:     GGAGCTTATTGAACCAACCATCCGTGAGTTGGATGCCAAAATGAGAGAAG                         CTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
genomic: GGAGCTTATTGAACCAACCATCCGTGAGTTGGATGCCAAAATGAGAGAAGgtatgcacaa ... cctcatgcagCTGAAAATGATCCACATGATGGGAAGAGAAAGTGTGAAGCTCTCTGGCCTA

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: 461

GACATCATGCCTAAGATAAAGACAAGTCGTGTCAAGTATCCTGAAGGATGGGAGCTTATTGAACCAACCATCCGTGAGTTGGATGCCAAAATGAGAGAAGgtatgcacaa ... cctcatgcagCTGAAAATGATCCACATGATGGGAAGAGAAAGTGTGAAGCTCTCTGGCCTATTTTCCGTATTTCTCATCAAAGGAGCCGCTACATATATGATCTTTACTA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 255

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 285

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 296

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ctgatgtcagttgtttcctggcacaggattgtactaacgttatgccctcatgcagCTGAAAATGATCCACATGATGGGAAGAGAAAGTGTGAAGCTCTCTGGCCTATTTTCCGTATTTCTCATCAAAGGAGCCGCTACATATATGATCTTTACTA

                               tactaac  putative branch site (score: 296)
                                          tgccctc  putative PPT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcacaaacggttattgaggcactcactactgatgtcagttgtttcctggcacaggattgtactaacgttatgccctcatgcagCTGAAAATGATCCACATGATGGGAAGAGAAAGTGTGAAGCTCTCTGGCCTATTTTCCGTATTTCTCATCAAAGGAGCCGCTACATATATGATCTTTACTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG