ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GCGAATAAGGAAAGGAATTCCTGATTGTCTCAGAGGACTTGTTTGGCAGTTGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAGgtacccacaaggatccttttttcttccaacttccggcattatatgattgtgatttgcctagttatacctgttactagattgagaaacaggggaacaagtg...

Basic information

species	Zea mays
transcript	GRMZM2G047223_T03
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G047223_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os08g31840.2 (Oryza sativa), 5'ss of exon 3

GCGAATAAGGAAAGGAATTCCTGATTGTCTCAGAGGACTTGTTTGGCAGTTGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAGgtacccacaaggatc------------ctt-------ttttcttccaacttccggcattatatgattgtgatttgcctagtta-tacctgttactagattgagaa-acaggggaacaagtg---------------------------------------------------
  ||||||||||||||||||||||||| || |||||||||||||||||||| |||||||||||  ||||||| || ||||||||||| |||||||| |||||||| | ||  ||             |||       ||||  |  ||  | |   ||||| |  |     | ||     ||| ||  | || ||| |||   |  | |  |    ||| |                                                   
AAGAATAAGGAAAGGAATTCCTGATTGCCTTAGAGGACTTGTTTGGCAGTTAATTTCAGGCAGCAGGGACCTTTTGCTAATGAACCCTGGGGTTTATGAGgtacctataacaattgtgaaagaactgcttgccctgatttttgttgaatgttccctattattttttaactttctgttgtcttagtagttatttctaaattatcaggatattgtcttaagagtcatacatatcttgtcaacattattacatttctatactattttttggacag

upper sequence: GRMZM2G047223_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA19G05360.1 (Glycine max), 5'ss of exon 3

GCGAATAAGGAAAGGAATTCCTGATTGTCTCAGAGGACTTGTTTGGCAGTTGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAGgtacccacaaggatccttttttcttccaacttccggcattatatgattgtgatttgcctagttatacctgttactagattgagaaacaggggaacaagtg
||| ||||||||||||||||| |||||| | || || ||||||||||| ||||| || || ||||| ||||| || || |||||||| || ||||| ||||||   |     ||   |  |  |   || ||  |  ||  | ||      ||||    || |||      | || |  ||           |       
GCGTATAAGGAAAGGAATTCCCGATTGTTTAAGGGGCCTTGTTTGGCAATTGATATCTGGAAGTCGAGACCTATTGCTGATGAACCCTGGAGTTTATGAGgtaattaacttaatttatactgttgaaaaattgtgatatattttgtagaatattttttaagctatgatcagtgcttgtctgttgtttgttatagttcacc

upper sequence: GRMZM2G047223_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA13G07090.1 (Glycine max), 5'ss of exon 2

GCGAATAAGGAAAGGAATTCCTGATTGTCTCAGAGGACTTGTTTGGCAGTTGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAGgtacccacaaggatccttttttcttccaacttccggcattatatgattgtgatttgcctagttatacctgttactagattgagaaacaggggaacaagtg-----
||| |||||||||||||||||||||||  | || || ||||||||||| ||||| || || ||||| ||||| || || |||||||| || ||||| ||||||   |  |   |  ||| | |||  ||     |  || ||||  ||||    |   |  | | |  ||      |||| |      |   | |   ||     
GCGTATAAGGAAAGGAATTCCTGATTGCTTAAGGGGCCTTGTTTGGCAATTGATATCTGGAAGTCGAGACCTGTTGCTGATGAACCCTGGAGTTTATGAGgta---atgaatttaatttatactttgaaaaattgagat-atatt-ttgtagaataaattttaagatatgaacagtgattcaatgcttgtctatcgtttgttatg

upper sequence: GRMZM2G047223_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv14s0083g00540.t01 (Vitis vinifera), 5'ss of exon 3

GCGAATAAGGAAAGGAATTCCTGATTGTCTCAGAGGACTTGTTTGGCAGTTGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAGgtacccacaaggatccttttttcttccaacttccggcatta--tatgattgtgatttgcctagttatacctgt-tactagattgagaaacaggggaacaagtg--
 || ||||| |||||||||||||||||| | || |||||||||||||||||||| ||||| ||||| |||||||| || |||||||| || ||||| ||||||  |       |  | || | |||  | |||      ||    || ||    ||| |    || |   | | | ||| ||| |           |        
ACGTATAAGAAAAGGAATTCCTGATTGTTTAAGGGGACTTGTTTGGCAGTTGATCTCAGGAAGTCGTGACCTCTTGCTGATGAACCCTGGAGTTTATGAGgtatacct-----ttttcttattttctcatttcaaaaggtaaccttggttagatttttctagattttttttatatgctatatttattgctttatttatcttcatt

upper sequence: GRMZM2G047223_T02 (Zea mays), 5'ss of exon 3
lower sequence: PP1S263_22V6.1 (Physcomitrella patens), 5'ss of exon 3

GCGAATAAGGAAAGGAATTCCTGATTGTCTCAGAGGACTTGTTTGGCAGTTGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAGgtacccacaaggatccttttttcttccaacttccggcattata----tgattgtgatttgcctagttatacctgttactagattgagaaacaggggaacaagtg
 ||| |  | || || || || |||||||| ||||| ||||| |||||| ||||||| |||||||||||  |  | || ||||| | ||||||||||||||| | | |    | ||| |||   |  | ||    | ||  ||    | | |||  ||  | ||  | | | ||| | |  ||   ||||     |||| |   
ACGAGTGCGCAAGGGCATCCCCGATTGTCTGAGAGGTCTTGTCTGGCAGCTGATTTCCGGCAGTCGGGATTTGCTGCTCATGAATCAAGGGGTTTACGAGgtgctccctgaaaccctatttctgt--agctgagtgtatcttaacgctcaatgttcttgtcttacattttcatgtcaatttat-atgaaatgctagaactata-

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|78113905|gb|DV532294.1|DV532294

EST:     TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAG                         ACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC
genomic: TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAGgtacccacaa ... ctttgggcagACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC

EST: gi|211004390|gb|FL335892.1|FL335892

EST:     TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAG                         ACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC
genomic: TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAGgtacccacaa ... ctttgggcagACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC

EST: gi|211402149|gb|FL346428.1|FL346428

EST:     TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAG                         ACACTGGTGAT
genomic: TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAGgtacccacaa ... ctttgggcagACACTGGTGAT

EST: gi|211274707|gb|FL354611.1|FL354611

EST:     TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAG                         ACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC
genomic: TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAGgtacccacaa ... ctttgggcagACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC

EST: gi|61118400|gb|DN559361.1|DN559361

EST:     TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAG                         ACACTGGTGATATATGAGACATCGGCCCCTGAATTGGAAATTATTCGTGAC
genomic: TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAGgtacccacaa ... ctttgggcagACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC

EST: gi|91877110|gb|EB407067.1|EB407067

EST:     TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAG                         ACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTC
genomic: TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAGgtacccacaa ... ctttgggcagACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTC

EST: gi|89758012|gb|DY687355.1|DY687355

EST:     TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAG                         ACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC
genomic: TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAGgtacccacaa ... ctttgggcagACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC

EST: gi|89756849|gb|DY686713.1|DY686713

EST:     TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAG                         ACACTGGTGATATATG
genomic: TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAGgtacccacaa ... ctttgggcagACACTGGTGATATATG

EST: gi|91874336|gb|EB404293.1|EB404293

EST:     TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAG                         ACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC
genomic: TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAGgtacccacaa ... ctttgggcagACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC

EST: gi|211241359|gb|FL313117.1|FL313117

EST:     TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAG                         ACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC
genomic: TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAGgtacccacaa ... ctttgggcagACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC

EST: gi|211342758|gb|FL350527.1|FL350527

EST:     TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAG                         ACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC
genomic: TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAGgtacccacaa ... ctttgggcagACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC

EST: gi|78117555|gb|DV535942.1|DV535942

EST:     TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAG                         ACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC
genomic: TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAGgtacccacaa ... ctttgggcagACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC

EST: gi|71771758|gb|DR969695.1|DR969695

EST:     TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAG                         ACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC
genomic: TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAGgtacccacaa ... ctttgggcagACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC

EST: gi|78118515|gb|DV536899.1|DV536899

EST:     TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAG                         ACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC
genomic: TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAGgtacccacaa ... ctttgggcagACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC

EST: gi|211258118|gb|FL346785.1|FL346785

EST:     TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAG                         ACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC
genomic: TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAGgtacccacaa ... ctttgggcagACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC

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: 54

GCGAATAAGGAAAGGAATTCCTGATTGTCTCAGAGGACTTGTTTGGCAGTTGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAGgtacccacaa ... ctttgggcagACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGACATATCACGCACATTTCCATCTCATATATTCTTTCAACAAAGGCATGGTC

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

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 83