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

gtctgtatgcatactaccgaccttattgctcgctcgaagttaactttctgtctcatatttctttgtgattgcctaccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGG

Basic information

species	Zea mays
transcript	GRMZM2G051842_T01
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G051842_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g01620.1 (Oryza sativa), 3'ss of exon 5

gtctgtatgcatactaccgaccttattgctcgctcgaagttaactttctgtctcatatttctttgtgattgcctaccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGG
|||||   |||    |  |    ||  |   | ||    ||   |    |   ||  | |  || || ||   ||  |  |||||||| ||||||| |||| |  | || ||| |||||||||| || || ||||||||||||||||| |||||||||||||||||||||||| || ||||
gtctgaccgcagctcattgg---taccgtaaggtctttttttggtacaggcacca-gtctgattttgtttatttattacacagATGGTTCGTGACTATAGGACACAACTCATTGACCTTTTGGAAACTGGCAACATTGACCTTTGCTTTGCCAATGAGGATGAAGCTAGAGAGCTTCTAGG

upper sequence: GRMZM2G051842_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv18s0001g12750.t01 (Vitis vinifera), 3'ss of exon 5

---------------gtctgtatgcatactaccgaccttattgctcgct-cgaagttaactttctgtctcatatttctttgtgattgcctaccatg--cagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGG
                |    |||||    | |   ||| ||      | |   || |   || | |||  ||   | |||   ||   |||| ||  |||||||| ||  ||| |||       ||| |  |  |  || |  | ||  | || || |||||||| ||||||||||||||||| |||||| |  || |
tttgactgcagtatcctactcatgcactggaacagacttgttctgaattgctgggtaaggattgtctcttttaac-cattgcttttttttaccttggccagATGGTTCGGAACTTTAGAGGACCTCTTCTAGAGTTACTGCAATCAGGGGATATAGATCTTTGCTTTGCCAATGAGGATGAAGCAAGAGAGCTGTTAAG

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|29543849|gb|CB604229.1|CB604229

EST:     TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAG                         ATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC
genomic: TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAGgtctgtatgc ... taccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC

EST: gi|31612067|gb|CD568689.1|CD568689

EST:     TTTCAGTATCATTAGATTTGGCCAGTTTTGAG                         ATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC
genomic: TTTCAGTATCATTAGATTTGGCCAGTTTTGAGgtctgtatgc ... taccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC

EST: gi|71762333|gb|DR960270.1|DR960270

EST:     CTTTCAGTATCATTAGATTTGGCCAGTTTTGAG                         ATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC
genomic: CTTTCAGTATCATTAGATTTGGCCAGTTTTGAGgtctgtatgc ... taccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC

EST: gi|78103938|gb|DV522356.1|DV522356

EST:     TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAG                         ATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC
genomic: TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAGgtctgtatgc ... taccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC

EST: gi|211123067|gb|FL031406.1|FL031406

EST:     TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAG                         ATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC
genomic: TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAGgtctgtatgc ... taccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC

EST: gi|29543893|gb|CB604273.1|CB604273

EST:     TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAG                         ATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC
genomic: TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAGgtctgtatgc ... taccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC

EST: gi|78105422|gb|DV523840.1|DV523840

EST:     TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAG                         ATGGTCCGTGACTCTAGGTTTAAGCTTATTAACCTTTTGGAGACCGGTAAC
genomic: TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAGgtctgtatgc ... taccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC

EST: gi|60338856|gb|DN205829.1|DN205829

EST:     TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAG                         ATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC
genomic: TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAGgtctgtatgc ... taccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC

EST: gi|101385265|gb|EB814678.1|EB814678

EST:     TAGATTTGGCCAGTTTTGAG                         ATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC
genomic: TAGATTTGGCCAGTTTTGAGgtctgtatgc ... taccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC

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), 47 (downstream exon)
Score: 246

TGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCTATTAGGATTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAGgtctgtatgc ... taccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGG

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 63

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 105

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 150

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ctcgctcgaagttaactttctgtctcatatttctttgtgattgcctaccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGG

         agttaac  putative branch site (score: 150)
                          atatttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtatgcatactaccgaccttattgctcgctcgaagttaactttctgtctcatatttctttgtgattgcctaccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG