ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaagtatctcttaaacatgatgcatcgacattttatctgtgaagctaaatccttccaaatttggcttctgagttgaaacattaagtaaaatattggaaggaaatgctaacataacgattatacttaagccctggattagtcctggatactaacagagttttacttcccagGCTGTTGCTGTGAAACAACTTGATCGTAATGGTCTCCAAGGAAACAGGGAATTTCTGGTTGAGGTTCTCATGCTCAGTCTCTTACATCACACTAACCTGG

Basic information

species	Zea mays
transcript	GRMZM2G145709_T01
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G145709_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g71000.1 (Oryza sativa), 3'ss of exon 2

gtaagtatctcttaaac-at---gatgcatcgacattttatctgtgaagctaaatccttccaaatttggcttctgagttgaaacattaagtaaaatattggaaggaaatgctaacataacgattatacttaagccctggattagtcctggatactaacagagttttacttcccagGCTGTTGCTGTGAAACAACTTGATCGTAATGGTCTCCAAGGAAACAGGGAATTTCTGGTTGAGGTTCTCATGCTCAGTCTCTTACATCACACTAACCTGG
|| ||| | |||||| | ||   |||  || || ||||||      |  ||  |   ||     ||  ||   | ||||  || ||| |||||||| |||| || || ||||          || | ||| | |||||||  | |  || |   || ||        |||||||||||||||||||||| ||||||||||| |||||||| |||||||| || ||||| ||||||||||| ||||||||||||||  ||||||||||||||||||
gtcagtctttcttaacctatctagatctattgagattttactaa--atacttgaagtttaggttttcagcgatttagtt--aatattcagtaaaatgttggcag-aattgctg---------ttttgctttatccctggagcactaatgaaatatacca--------cttcccagGCTGTTGCTGTGAAGCAACTTGATCGCAATGGTCTTCAAGGAAATAGAGAATTCCTGGTTGAGGTCCTCATGCTCAGTCTTCTACATCACACTAACCTGG

upper sequence: GRMZM2G145709_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA13G28730.1 (Glycine max), 3'ss of exon 2

gtaagtatctcttaaacatgatgcatcgacattttatctgtgaagctaaatccttccaaatttggcttctgagttgaaacattaagtaaaatattggaaggaaatgctaacataacgattatacttaagccctggattagtcctggatactaacagagttttacttcccagGCTGTTGCTGTGAAACAACTTGATCGTAATGGTCTCCAAGGAAACAGGGAATTTCTGGTTGAGGTTCTCATGCTCAGTCTCTTACATCACACTAACCTGG
                                                         || ||     ||||   | ||   |   ||  | |||||        || ||  |||||        |    | ||    || |  |  ||  | | |   || | | |  ||||  |||||||| ||||| ||||| || |||||||| ||||||||  | || ||| |||| || ||||| |||||||||||||| |||||  | || || |
---------------------------------------------------------aagttatctgtctgctctcaattttcctgttgattattg-----ctctgttactataac--------tctgcctctttcataatttttaatgatgaaatcattct-cgttgcagGTAGTTGCTGTAAAACAGCTTGACCGAAATGGTCTTCAAGGAAATCGAGAGTTTTTGGTGGAAGTTCTTATGCTCAGTCTCTTGCATCATCCAAATCTTG

upper sequence: GRMZM2G145709_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA15G10360.1 (Glycine max), 3'ss of exon 2

gtaagtatctcttaaacatgatgcatcgacattttatctgtgaagctaaatccttccaaatttggcttctgagttgaaacattaagtaaaatattggaaggaaatgctaacataacgattatacttaagcc-ctggattagtcctggatactaacagagttttacttcccagGCTGTTGCTGTGAAACAACTTGATCGTAATGGTCTCCAAGGAAACAGGGAATTTCTGGTTGAGGTTCTCATGCTCAGTCTCTTACATCACACTAACCTGG
                                                                       ||||       |     |||| ||   |   | |  |    |    | ||||  || ||| ||    || || |   || | | |   || | |||| ||||  |||||||| ||||| ||||| || |||||||| ||||||||  | || ||| |||| || ||||| |||||||||||||| |||||  | || || |
----------------------------------------------------------------------aagttatttgtctgctggaaattttcccattgattattgctctg-ttactataactatgcctctttcgtaatcttcattaatgaaatcattct-cttcgcagGTGGTTGCTGTAAAACAGCTTGACCGAAATGGTCTTCAAGGAAATCGAGAGTTTTTGGTGGAAGTTCTTATGCTCAGTCTCTTGCATCATCCAAATCTTG

upper sequence: GRMZM2G145709_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT5G18610.1 (Arabidopsis thaliana), 3'ss of exon 3

gtaagtatctcttaaacatgatgcatcgacattttatctgtgaagctaaatccttccaaatttggcttctgagttgaaacattaagtaaaatattggaaggaaatgctaacataacgattatacttaa-gccctggattagtcctggatactaacagagttt--tacttcccagGCTGTTGCTGTGAAACAACTTGATCGTAATGGTCTCCAAGGAAACAGGGAATTTCTGGTTGAGGTTCTCATGCTCAGTCTCTTACATCACACTAACCTGG
                                                                                                   | |  |  |||  | |   | ||  || |    |  |||| ||| |     ||||  |  |||  || ||  |||   || ||||| ||||| |||||||| || ||||| ||||||||||| || ||||| || |||||||| ||||| || ||  | |||||  | || || |
-------------------------------------------------------------------------------------------------gtgaagttcgtaaattgaatttaatgtttcataatcaagattcgtctt-----ctaattggatttaatattttgcagATAGTAGCTGTTAAACAGCTTGATCGAAACGGTCTACAAGGAAACAGAGAGTTTCTTGTAGAGGTTCTTATGCTGAGCCTTCTGCATCATCCCAATCTTG

upper sequence: GRMZM2G145709_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv05s0020g01770.t01 (Vitis vinifera), 3'ss of exon 2

gtaagtatctcttaaacatgatgcatcgacattttatctgtgaagctaaatccttccaaatttggcttctgagttgaaacattaagtaaaatattggaaggaaatgctaacataacgattatacttaagccctggattagtcctggatactaacagagttttac-ttcccagGCTGTTGCTGTGAAACAACTTGATCGTAATGGTCTCCAAGGAAACAGGGAATTTCTGGTTGAGGTTCTCATGCTCAGTCTCTTACATCACACTAACCTGG
                                                                   |||   || | | ||  | ||    ||||      |||| ||  || ||  |    | |  |   |  |||  |  | | |   ||   | | ||   ||  ||||  |||||||||||||||||||| || ||||| || |||||||| || |||||  |||| |||||||||||||| || |||||||||||| | ||||| |
-----------------------------------------------------------------aatct---tttatatatggaatatgg-attgctgaataatgtta--atcactgtgtctcatctggtatttattgatttttggt-tcaatgaattattgtatttgcagGTAGTTGCTGTGAAACAACTTGACCGAAATGGCCTTCAAGGAAATAGAGAATTCTTGGTGGAGGTTCTCATGCTTAGCCTCTTACATCACCCAAACCTTG

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|149106246|gb|EE291941.2|EE291941

EST:     GAGAGGGAGGTTTTGGTCGTGTATATAAAGGACGCTTGGAGAATGGGCAG                         GCTGTTGCTGTGAAACAACTTGATCGTAATGGTCTCCAAGGAAACAGGGAA
genomic: GAGAGGGAGGTTTTGGTCGTGTATATAAAGGACGCTTGGAGAATGGGCAGgtaagtatct ... tacttcccagGCTGTTGCTGTGAAACAACTTGATCGTAATGGTCTCCAAGGAAACAGGGAA

EST: gi|148990757|gb|EE048618.2|EE048618

EST:     GAGAGGGAGGTTTTGGTCGTGTATATAAAGGACGCTTGGAGAATGGGCAG                         GCTGTTGCTGTGAAACAACTTGATCGTAATGGTCTCCAAGGAAACAGGGAA
genomic: GAGAGGGAGGTTTTGGTCGTGTATATAAAGGACGCTTGGAGAATGGGCAGgtaagtatct ... tacttcccagGCTGTTGCTGTGAAACAACTTGATCGTAATGGTCTCCAAGGAAACAGGGAA

EST: gi|76291614|gb|DV031182.1|DV031182

EST:     GAGAGGGAGGTTTTGGTCGTGTATATAAAGGACGCTTGGAGAATGGGCAG                         GCTGTTGCTGTGAAACAACTTGATCGTAATGGTCTCCAAGGAAACAGGGAA
genomic: GAGAGGGAGGTTTTGGTCGTGTATATAAAGGACGCTTGGAGAATGGGCAGgtaagtatct ... tacttcccagGCTGTTGCTGTGAAACAACTTGATCGTAATGGTCTCCAAGGAAACAGGGAA

EST: gi|89758504|gb|DY687662.1|DY687662

EST:     GAGAGGGAGGTTTTGGTCGTGTATATAAAGGACGCTTGGAGAATGGGCAG                         GCTGTTGCTGTGAAACAACTTGATCGTAATGGTCTCCAAGGAAACAGGGAA
genomic: GAGAGGGAGGTTTTGGTCGTGTATATAAAGGACGCTTGGAGAATGGGCAGgtaagtatct ... tacttcccagGCTGTTGCTGTGAAACAACTTGATCGTAATGGTCTCCAAGGAAACAGGGAA

EST: gi|149015777|gb|EE045476.2|EE045476

EST:     GAGAGGGAGGTTTTGGTCGTGTATATAAAGGACGCTTGGAGAATGGGCAG                         GCTGTTGCTGTGAAACAACTTGATCGTAATGGTCTCCAAGGAAACAGGGAA
genomic: GAGAGGGAGGTTTTGGTCGTGTATATAAAGGACGCTTGGAGAATGGGCAGgtaagtatct ... tacttcccagGCTGTTGCTGTGAAACAACTTGATCGTAATGGTCTCCAAGGAAACAGGGAA

EST: gi|148942135|gb|EC887138.2|EC887138

EST:     GAGAGGGAGGTTTTGGTCGTGTATATAAAGGACGCTTGGAGAATGGGCAG                         GCTGTTGCTGTGAAACAACTTGATCGTAATGGTCTCCAAGGAAACAGGGAA
genomic: GAGAGGGAGGTTTTGGTCGTGTATATAAAGGACGCTTGGAGAATGGGCAGgtaagtatct ... tacttcccagGCTGTTGCTGTGAAACAACTTGATCGTAATGGTCTCCAAGGAAACAGGGAA

EST: gi|148941217|gb|EC886109.2|EC886109

EST:     GAGAGGGAGGTTTTGGTCGTGTATATAAAGGACGCTTGGAGAATGGGCAG                         GCTGTTGCTGTGAAACAACTTGATCGTAATGGTCTCCAAGGAAACAGGGAA
genomic: GAGAGGGAGGTTTTGGTCGTGTATATAAAGGACGCTTGGAGAATGGGCAGgtaagtatct ... tacttcccagGCTGTTGCTGTGAAACAACTTGATCGTAATGGTCTCCAAGGAAACAGGGAA

EST: gi|148938285|gb|EC882589.2|EC882589

EST:     GAGAGGGAGGTTTTGGTCGTGTATATAAAGGACGCTTGGAGAATGGGCAG                         GCTGTTGCTGTGAAACAACTTGATCGTAATGGTCTCCAAGGAAACAGGGAA
genomic: GAGAGGGAGGTTTTGGTCGTGTATATAAAGGACGCTTGGAGAATGGGCAGgtaagtatct ... tacttcccagGCTGTTGCTGTGAAACAACTTGATCGTAATGGTCTCCAAGGAAACAGGGAA

EST: gi|33467045|gb|CF244094.1|CF244094

EST:     GAGAGGGAGGTTTTGGTCGTGTATATAAAGGACGCTTGGAGAATGGGCAG                         GCTGTTGCTGTGAAACAACTTGATCGTAATGGTCTCCAAGGAAACAGGGAA
genomic: GAGAGGGAGGTTTTGGTCGTGTATATAAAGGACGCTTGGAGAATGGGCAGgtaagtatct ... tacttcccagGCTGTTGCTGTGAAACAACTTGATCGTAATGGTCTCCAAGGAAACAGGGAA

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: 372

TCGTGAGCTCGCTGCAGCCACTAAGAACTTCAGGCAAGATTGCCTTTTAGGAGAGGGAGGTTTTGGTCGTGTATATAAAGGACGCTTGGAGAATGGGCAGgtaagtatct ... tacttcccagGCTGTTGCTGTGAAACAACTTGATCGTAATGGTCTCCAAGGAAACAGGGAATTTCTGGTTGAGGTTCTCATGCTCAGTCTCTTACATCACACTAACCTGG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 328

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 283

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 298

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gattatacttaagccctggattagtcctggatactaacagagttttacttcccagGCTGTTGCTGTGAAACAACTTGATCGTAATGGTCTCCAAGGAAACAGGGAATTTCTGGTTGAGGTTCTCATGCTCAGTCTCTTACATCACACTAACCTGG