ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gcaagttcagttttattctggatttatctgaactatgtattgtgctgccttatttagttgctgtcatttgcagGTCCAACTCATGTTTTAGTTGTTCGTGGCTTAGATGAAAATGCTGATGAGGAAATGCTTCGGTACGAATTTGCTAAGCACGCACCATTAAAG

Basic information

species	Zea mays
transcript	GRMZM2G151614_T03
intron #	10
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G151614_T03 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os02g07070.1 (Oryza sativa), 3'ss of exon 10

gcaa-gttcagtttt---attctggatttatctgaactatgtattgtgctgccttatttagttgctgtcatttgcagGTCCAACTCATGTTTTAGTTGTTCGTGGCTTAGATGAAAATGCTGATGAGGAAATGCTTCGGTACGAATTTGCTAAGCACGCACCATTAAAG
|||| | || ||| |   ||| | |  ||||   |||||| |     | ||||||||| ||   ||  ||||| |||||||||||||||||||||||||||||||  | |||||||||||||| |||||||||||||| || |||||||| ||||| |||||  |||||
gcaaagctctgttcttctattgtaggattattaaaactattttgccagttgccttatt-agacactagcattttcagGTCCAACTCATGTTTTAGTTGTTCGTGGTCTGGATGAAAATGCTGACGAGGAAATGCTTCGATATGAATTTGCCAAGCATGCACCTATAAAG

upper sequence: GRMZM2G151614_T03 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA08G35510.1 (Glycine max), 3'ss of exon 8

gcaagttcagttttattctggatttatc-tgaactatgtattgtgctgccttatttagttgctgtcatttgcagGTCCAACTCATGTTTTAGTTGTTCGTGGCTTAGATGAAAATGCTGATGAGGAAATGCTTCGGTACGAATTTGCTAAGCACGCACCATTAAAG
| ||||  |      | ||| |  |  | |  ||| | | |  |||| |  || |||  |           ||||||||||||||||  | ||||| ||||| || |||||||||||||||||||||||||| || || || ||| | || || || ||  | |||
gtaagtataac----tcctgtacctgacattgactttat-taatgct-ctgtaattaactatatgtgcaatcagGTCCAACTCATGTGCTTGTTGTCCGTGGATTGGATGAAAATGCTGATGAGGAAATGCTCCGCTATGAGTTTTCCAAACATGCTCCGATTAAG

upper sequence: GRMZM2G151614_T03 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA16G18030.1 (Glycine max), 3'ss of exon 8

gcaagttcagtttt-attctggatttatctgaactatgtattgtgctgccttatttagttgctgtcatttgcagGTCCAACTCATGTTTTAGTTGTTCGTGGCTTAGATGAAAATGCTGATGAGGAAATGCTTCGGTACGAATTTGCTAAGCACGCACCATTAAAG
| ||||  |  |    | |  ||  |   ||   ||| || ||   ||   || |||  |           |||||||||||||||| || ||||| ||||| || ||||||||||| |||||||||||||| || || || ||| | || || || ||  | |||
gtaagtataactcccgtacctgacattgatgctttat-taatgctttg---taattaactatatgtgcaatcagGTCCAACTCATGTGTTGGTTGTCCGTGGATTGGATGAAAATGCGGATGAGGAAATGCTCCGCTATGAGTTTTCCAAACATGCTCCGATTAAG

upper sequence: GRMZM2G151614_T03 (Zea mays), 3'ss of exon 10
lower sequence: AT3G54230.2 (Arabidopsis thaliana), 3'ss of exon 10

-------------------------------------------------------------------gcaagttcagttttattctggatttatctgaactatgtattgtgctgccttatttag-ttgctgtcatttgcagGTCCAACTCATGTTTTAGTTGTTCGTGGCTTAGATGAAAATGCTGATGAGGAAATGCTTCGGTACGAATTTGCTAAGCACGCACCATTAAAG
                                                                     |||  ||   |  || |   ||| |     | || |||      |    |||  | ||  | || ||| ||||||||||||||||  | ||||| ||||| || |||||| ||||||||||||||||||||||||| |||||| | || || || ||  | |||
gttctgatcagcatttttatttaagatgttttaaatttctttcttgagtcagaaacagtcgcaactgttaaggccatagtctttgtacttttctacatgccatatatacctaagatacattctgcttattttcttttccagGTCCAACTCATGTCCTGGTTGTACGTGGGTTGGATGAAGATGCTGATGAGGAAATGCTTCGGTATGAATTTTCCAAACATGCTCCTATCAAG

upper sequence: GRMZM2G151614_T03 (Zea mays), 3'ss of exon 10
lower sequence: Vv02s0012g00870.t01 (Vitis vinifera), 3'ss of exon 8

gcaagttcagtt--ttattctggatttatctgaactatgtattgtgctgcct-tatttagtt--gctgtcatttg--cagGTCCAACTCATGTTTTAGTTGTTCGTGGCTTAGATGAAAATGCTGATGAGGAAATGCTTCGGTACGAATTTGCTAAGCACGCACCATTAAAG
|   |  || |   ||  | |  |||    || | || | ||| |  |   | || || | |  | ||  || |   ||||||| |  |||||||| |||||||| || || ||||||||||||||||||||||||||||| || |||||| |||| || || ||| | |||
gttggaacactccattgcttttaattggcatgcattaagcattatattcattgtaatttgctaagttgatatgtaatcagGTCCTATCCATGTTTTGGTTGTTCGAGGTTTGGATGAAAATGCTGATGAGGAAATGCTTCGTTATGAATTTTCTAAACATGCTCCAATCAAG

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|32826971|gb|CD966649.1|CD966649

EST:     GATCTGAACTAG                         GTCCAACTCATGTTTTAGTTGTTCGTGGCTTAGATGAAAATGCTGATGAGG
genomic: GATCTGAACTAGgcaagttcag ... tcatttgcagGTCCAACTCATGTTTTAGTTGTTCGTGGCTTAGATGAAAATGCTGATGAGG

EST: gi|32826210|gb|CD965888.1|CD965888

EST:     GATCTGAACTAG                         GTCTAACTCATGTTTTAGTTGTTCGTGGCTTAGATGAAAATGCTGATGAGG
genomic: GATCTGAACTAGgcaagttcag ... tcatttgcagGTCCAACTCATGTTTTAGTTGTTCGTGGCTTAGATGAAAATGCTGATGAGG

EST: gi|33103538|gb|CF063498.1|CF063498

EST:     TGATGCGACAGGTTCCTCTCCACACTTTGGGAGAAAGGGATCTGAACTAG                         GTCCAACTCATGTTTTAGTTGTTCGTGGCTTAGATGAAAATGCTGATGAGG
genomic: TGATGCGACAGGTTCCTCTCCACACTTTGGGAGAAAGGGATCTGAACTAGgcaagttcag ... tcatttgcagGTCCAACTCATGTTTTAGTTGTTCGTGGCTTAGATGAAAATGCTGATGAGG

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: 48 (upstream exon), 49 (downstream exon)
Score: 57

TGCAATGAACCTCGTGCTGAGGATGCTCTACCAGCTGATGCGACAGGTTCCTCTCCACACTTTGGGAGAAAGGGATCTGAACTAGgcaagttcag ... tcatttgcagGTCCAACTCATGTTTTAGTTGTTCGTGGCTTAGATGAAAATGCTGATGAGGAAATGCTTCGGTACGAATTTGCTAAGCACGCACCATTAAAG

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 52

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 37

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 53

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tggatttatctgaactatgtattgtgctgccttatttagttgctgtcatttgcagGTCCAACTCATGTTTTAGTTGTTCGTGGCTTAGATGAAAATGCTGATGAGGAAATGCTTCGGTACGAATTTGCTAAGCACGCACCATTAAAG