ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

...tgttttaccctagggtgctaatagtattccattttttaatatgcatgcctggcacatgagtatttttgttcaaactttaacggtggctgtctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTAA

Basic information

species	Zea mays
transcript	GRMZM2G122039_T05
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G122039_T05 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g06340.2 (Oryza sativa), 3'ss of exon 2

-tgttttaccctagggtgctaatagtattccattttttaatatgcatgcctggcacatgagtatttttgttcaaactttaacggtggctgtctg-ttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTAA------
   ||| |||||||| |  |||||      |   ||   |     ||||       |||| | |    | | |||   ||| ||||  ||| || ||  ||||| |||||||||||||| ||||| ||||||||||| || |||||||||||||||||||| || || || ||||||||||| |||||||||||||      
ccctttcaccctaggctcataatatcgcgacgacttagcaatgatatgcgctatg-atgaat-tcaacgcttaaatcctaatggtgtttgtatggtttgcagAAGTGCGTCAAGAGAGTGGAGAAGGATGATACTGGGCATAAACACTGCACTGGGCAATATTTCGACTATTGGTCATGCATTGACAAATGTGTAAGTATCT

upper sequence: GRMZM2G122039_T05 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g06340.1 (Oryza sativa), 3'ss of exon 2

-tgttttaccctagggtgctaatagtattccattttttaatatgcatgcctggcacatgagtatttttgttcaaactttaacggtggctgtctg-ttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTAA
   ||| |||||||| |  |||||      |   ||   |     ||||       |||| | |    | | |||   ||| ||||  ||| || ||  ||||| |||||||||||||| ||||| ||||||||||| || |||||||||||||||||||| || || || ||||||||||| |||||||||    
ccctttcaccctaggctcataatatcgcgacgacttagcaatgatatgcgctatg-atgaat-tcaacgcttaaatcctaatggtgtttgtatggtttgcagAAGTGCGTCAAGAGAGTGGAGAAGGATGATACTGGGCATAAACACTGCACTGGGCAATATTTCGACTATTGGTCATGCATTGACAAATGT----

upper sequence: GRMZM2G122039_T05 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G19380.1 (Glycine max), 3'ss of exon 2

tgttttaccctagggtgctaa--tagtattccatttt-ttaatatgcatgcctggcacatgagtatttttgttcaaactttaacggtggctgtctg--ttat--cagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTAA
          ||   ||| ||  |  | |||    || || || |  ||  ||   |  | |||  | ||| |    |   ||  ||   ||| |   ||    |||   ||| | || ||  |  |   ||||||  |||| || |||||||||||||| ||||| |||||||| ||||| || || |||||||||    
-----agtgataaattgccaaatttttgttctgccttatttatttttatttcttcaaattaagt--tcttgcttggccgagaaaagtaattgtttaaattgctacagGCGTGCATTAAAAGGATACATGGTGATGAATCTGGGCAGAAACACTGCACTGGACAATATTTTGATTATTGGTCTTGTATTGACAAATGT----

upper sequence: GRMZM2G122039_T05 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA15G05620.1 (Glycine max), 3'ss of exon 2

tgttttaccctagggtgctaatagtattccattttttaatatgcatgcctggcacatgagtatttttgttcaaactttaacggtggctgtctg--ttat--cagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTAA
   |      ||   ||  ||   | |   ||   ||||| |          || || |   || ||| |    |   ||  ||   ||| ||  ||    |||   ||| | || ||  |  |   ||||||| |||| || |||||||||||||| ||||| |||||||| ||||| || || |||||||||    
---tgagtgataaattgtcaaatttttgttatgccttaattttttatttcttcaaattaa-gttcttgcttggccgagaaaagtaattgtttgaattgctacagGCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACTGGACAATATTTTGATTATTGGTCTTGTATTGACAAATGT----

upper sequence: GRMZM2G122039_T05 (Zea mays), 3'ss of exon 2
lower sequence: AT2G01090.2 (Arabidopsis thaliana), 3'ss of exon 3

-----------------------------------------------------tgttttaccctagggtgctaatagtattccattttttaatatgcatgcctggcacatga----gtatttttgttca----aactttaacg----gtggctgtctgttat-cagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTAA------
                                                     |  |||  | ||| | |  | | | ||| | ||   |  |    ||   |  ||||| |    |  | || || |     |  ||||||     || | |||  ||  | |||   || ||||||||  |  |  |||||||  |||| |||||||| |||||||||||||| ||||||||||||   ||  | |||||||||||||      
gtgaatacgacttgagctgtcactggtcataaccttgttttgcattatacgagtcatttgacatagagagagagttg-attgctttcggtgctgcttatctatctcacatcacatggcttcttagtgctgctcagttttaacatcttgttgttgtgggtggttcagGCGTGTGTCAAGAGGATCCAAGATGATGAGTCTGGCCACAAACATTGCACTGGGCAATATTTTGATTACTGGCATTGTGTTGACAAATGTGTAAGTGTGT

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|211523990|gb|FL156372.1|FL156372

EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT

EST: gi|211526998|gb|FL156385.1|FL156385

EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT

EST: gi|74035153|gb|DT535643.1|DT535643

EST:     TTGAGGAACGATGCNAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT

EST: gi|6671465|gb|AW282244.1|AW282244

EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT

EST: gi|211523995|gb|FL156377.1|FL156377

EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT

EST: gi|211523997|gb|FL156379.1|FL156379

EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT

EST: gi|211526993|gb|FL156380.1|FL156380

EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT

EST: gi|211523991|gb|FL156373.1|FL156373

EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT

EST: gi|211523994|gb|FL156376.1|FL156376

EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT

EST: gi|211526996|gb|FL156383.1|FL156383

EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT

EST: gi|211526995|gb|FL156382.1|FL156382

EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT

EST: gi|33092405|gb|CF052399.1|CF052399

EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT

EST: gi|15499626|gb|BI596139.1|BI596139

EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT

EST: gi|211523996|gb|FL156378.1|FL156378

EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT

EST: gi|211526997|gb|FL156384.1|FL156384

EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT

EST: gi|37395178|gb|CF634869.1|CF634869

EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT

EST: gi|211526994|gb|FL156381.1|FL156381

EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT

EST: gi|32808494|gb|CD960728.1|CD960728

EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTGCGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT

EST: gi|78026630|gb|DV495017.1|DV495017

EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT

EST: gi|211523992|gb|FL156374.1|FL156374

EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT

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: 125

GGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTAA

Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 109

Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 97

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 251

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tgcctggcacatgagtatttttgttcaaactttaacggtggctgtctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTAA