ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtatgaataatacttacactgtggctgtcttatgcactccagtttataatttgtatgcttttgtcgtgacttaatgattaatcacgatgtgatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCACGGCCACTTCTTACATTTTCTACAAATTTTGATGAGCAACCTCATTGGAA

Basic information

species	Zea mays
transcript	GRMZM2G168176_T02
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G168176_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g37870.1 (Oryza sativa), 3'ss of exon 3

gtatgaataatacttacactgtggctgtcttatgcactccagtttataatttgtatgcttttgtcgtgacttaatgattaatcacgatgtgatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCACGGCCACTTCTTACATTTTCTACAAATTTTGATGAGCAACCTCATTGGAA
||| | ||   |  ||       |||||  | || ||   || ||||      ||| |  |    ||| || ||||   | |    ||||    ||| |||||||||||||||||||||||||||||| || ||||||||||||||||||||||| ||| | ||||||||||||||||||||||| |||||||| ||| |
gtaagtatgtcaagtatttgtgagctgtaatctgtaca--agattatggacattattccatca--gtgcctaaatgtccagt---aatgtttacatgcagTTCACACCATGGAGGAGTTGAAGCTTACAGGGAACCATCTGAAAGGGTCACGGCCTCTTATAACATTTTCTACAAATTTTGATGAACAACCTCACTGGCA

upper sequence: GRMZM2G168176_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G51310.1 (Glycine max), 3'ss of exon 3

-------------------------------------------------------------------------------------------gtatgaataatacttacactgtggctgtcttatgcactccagtttataatttgtatgcttttgtcgtgacttaa-tgatt-----aatcacgatgtgatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCACGGCCACTTCTTACATTTTCTACAAATTTTGATGAGCAACCTCATTGGAA
                                                                                            |  | ||  | |||      |     | || ||   | |  |   |   |    |  || ||  ||   || | |||||       |  |          |  ||||||||| |||||||| |||||||||||||| || || ||  | || || || ||| || | ||||||||  ||||||||||  |  |  | ||||||||
gtaatagtttcatctgattatagtcataaggttaatacaatatcatttttcttgctatgatgatttagtgttctgatttgtgtatactctaatcggcatttttcttgttggattatgattttttgtgtttctctcactctctcaactatttctgatgtacttttactgatttctgtgtttcctccactgctttccagTTCACACAATGGAGGAATTGAAGCTTACGGGAAATCACCTACAGGGTTCCCGTCCAATTTTGACATTTTCAGCAAATTTTGAAAAAGATGCACATTGGAA

upper sequence: GRMZM2G168176_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT3G15460.1 (Arabidopsis thaliana), 3'ss of exon 3

--------------------------------------gtatgaataatacttacactgtggctgtcttatgcactccagtttat-aatttgtatgcttttgtcgtgacttaatgattaatcacgatgtgatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCACGGCCACTTCTTACATTTTCTACAAATTTTGATGAGCAACCTCATTGGAA
                                         ||| | ||   || | |    || |    |       ||||||| |||||||||  | |    ||    |     | |||  |  | || |||   ||||||||| ||||||||| |||| || || || || ||||||||||| ||||| |||||| | ||||| ||  | ||||||||  |  |  | || |||||
gtaatttgtctccagctcctcttatttggtttcaaaataagtgactgatggatataataatact-ttgggtaatgatgagtttatcaatttgtatcgtctctgagtagtgtttctgtaaatttctgtatggtga---agTTCACACAATGGAGGAGCTGAAACTCACTGGAAATCATCTGAAAGGTTCACGCCCACTTTTGACATTCTCATCCAATTTTGAAAACGATGCACACTGGAA

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|101388447|gb|EB816210.1|EB816210

EST:     GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTG                         TTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC
genomic: GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTGgtatgaataa ... gatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC

EST: gi|211512372|gb|FL212647.1|FL212647

EST:     GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTG                         TTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGNAAGGGTCAC
genomic: GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTGgtatgaataa ... gatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC

EST: gi|148943696|gb|EC888763.2|EC888763

EST:     GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTG                         TTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC
genomic: GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTGgtatgaataa ... gatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC

EST: gi|76289778|gb|DV029346.1|DV029346

EST:     GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTG                         TTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC
genomic: GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTGgtatgaataa ... gatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC

EST: gi|76285403|gb|DV024971.1|DV024971

EST:     GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTG                         TTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC
genomic: GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTGgtatgaataa ... gatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC

EST: gi|71325419|gb|DR799392.1|DR799392

EST:     GATGGTGAAGCCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTG                         TTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC
genomic: GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTGgtatgaataa ... gatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC

EST: gi|71307148|gb|DR789745.1|DR789745

EST:     GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTG                         TTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC
genomic: GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTGgtatgaataa ... gatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC

EST: gi|28930902|gb|CB334263.1|CB334263

EST:     GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTG                         TTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCT
genomic: GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTGgtatgaataa ... gatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCT

EST: gi|89759058|gb|DY688001.1|DY688001

EST:     GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTG                         TTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC
genomic: GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTGgtatgaataa ... gatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC

EST: gi|6827088|gb|AW330731.1|AW330731

EST:     GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTG                         TTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC
genomic: GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTGgtatgaataa ... gatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC

EST: gi|76283913|gb|DV023481.1|DV023481

EST:     GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTG                         TTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC
genomic: GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTGgtatgaataa ... gatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC

EST: gi|78180563|gb|DV550891.1|DV550891

EST:     GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTG                         TTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC
genomic: GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTGgtatgaataa ... gatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC

EST: gi|18659405|gb|BM500320.1|BM500320

EST:     GATGGNGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTG                         TTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC
genomic: GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTGgtatgaataa ... gatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC

EST: gi|32945542|gb|CF050361.1|CF050361

EST:     GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTG                         TTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC
genomic: GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTGgtatgaataa ... gatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC

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: 47 (upstream exon), 49 (downstream exon)
Score: 74

TGCCGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTGgtatgaataa ... gatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCACGGCCACTTCTTACATTTTCTACAAATTTTGATGAGCAACCTCATTGGAA

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 38

Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 75

Block sizes: 40 (upstream exon), 48 (downstream exon)
Score: 22

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ataatttgtatgcttttgtcgtgacttaatgattaatcacgatgtgatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCACGGCCACTTCTTACATTTTCTACAAATTTTGATGAGCAACCTCATTGGAA