ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtactcgttcccagcttgcactttaccgtttgtcattgtcaagccagagaagaaccaattttttatggaacatgcatctgcagGTAGCATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCGACTTCTGACAAAGTGAATCGAATTTGCATACCTTACACCTTTGGAAAGT

Basic information

species	Zea mays
transcript	GRMZM2G122039_T05
intron #	3
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 3
lower sequence: LOC_Os11g06340.1 (Oryza sativa), 3'ss of exon 3

--------------------------------gta-ctcgttcccagcttgcactttaccg-----tttgtcattgtcaagccagag-aagaaccaattttttatggaacatgcatctgcagGTAGCATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCGACTTCTGACAAAGTGAATCGA---ATTTGCATA-CCTTACAC-CTTTGGAAAGT-----
                                 || || |  || | |      ||||  |      |   |||    |||| ||   || |||  ||||| | |||    ||||||||||||||||| | || ||| || |||||||||||||||      ||   | ||| |||| ||    ||||| | |    |||||| || ||||   | |  | |||| |     
gtaagtatctgcatgtgtgtgtgcaatatcgcatatctggaaccaaacaaatgatttatggagaagctctgcatatataagctaggttaataacatattttctgtgggg--tgcatctgcaggtagCACCGAAACTCCTTGAGAAGCTCAAATGAT------GACCGGCTGCTACTTTTGGATCAGTGACTTGTTCTATTTGCGTAACCTTGTTCGCACTTGAAACTGAATG

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:     CTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTA-                         G---CATCAWAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCG
genomic: CTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTAAgtactcgttc ... gcatctgcagGTAGCATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCG

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

EST:     CTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTA-                         G---CATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCG
genomic: CTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTAAgtactcgttc ... gcatctgcagGTAGCATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCG

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

EST:     CTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTA-                         G---CATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCG
genomic: CTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTAAgtactcgttc ... gcatctgcagGTAGCATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCG

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

EST:     CTGCACTGGGCAGTACTTTGATTACTGGTCATGCATCGACAAA--TGT--                         GTAGCATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCG
genomic: CTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTAAgtactcgttc ... gcatctgcagGTAGCATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCG

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

EST:     CTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGT----                         ----CATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCG
genomic: CTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTAAgtactcgttc ... gcatctgcagGTAGCATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCG

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

EST:     CTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTA-                         G---CATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCG
genomic: CTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTAAgtactcgttc ... gcatctgcagGTAGCATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCG

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

EST:     CTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTA-                         G---CATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCG
genomic: CTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTAAgtactcgttc ... gcatctgcagGTAGCATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCG

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

EST:     CTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGT----                         ----CATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCG
genomic: CTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTAAgtactcgttc ... gcatctgcagGTAGCATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCG

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

EST:     CTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTA-                         G---CATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCG
genomic: CTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTAAgtactcgttc ... gcatctgcagGTAGCATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCG

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

EST:     CTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGT----                         ----CATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCG
genomic: CTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTAAgtactcgttc ... gcatctgcagGTAGCATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCG

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

EST:     CTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAA--TGT--                         GTAGCATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCG
genomic: CTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTAAgtactcgttc ... gcatctgcagGTAGCATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCG

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

EST:     CTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTA-                         G---CATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCG
genomic: CTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTAAgtactcgttc ... gcatctgcagGTAGCATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCG

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

EST:     CTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTAG                         GTAGCACCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCG
genomic: CTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTAAgtactcgttc ... gcatctgcagGTAGCATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCG

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

EST:     CTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTA-                         G---CATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCG
genomic: CTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTAAgtactcgttc ... gcatctgcagGTAGCATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCG

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

EST:     CTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTA-                         G---CATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCG
genomic: CTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTAAgtactcgttc ... gcatctgcagGTAGCATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCG

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

EST:     CTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTA-                         GCA-C--CAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCG
genomic: CTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTAAgtactcgttc ... gcatctgcagGTAGCATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCG

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

EST:     CTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTA-                         G---CATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCG
genomic: CTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTAAgtactcgttc ... gcatctgcagGTAGCATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCG

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

EST:     CTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAA--TGT--                         GTAGCATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCG
genomic: CTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTAAgtactcgttc ... gcatctgcagGTAGCATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCG

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

EST:     CTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTA-                         G---CATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCG
genomic: CTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTAAgtactcgttc ... gcatctgcagGTAGCATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCG

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: 88

AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTAAgtactcgttc ... gcatctgcagGTAGCATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCGACTTCTGACAAAGTGAATCGAATTTGCATACCTTACACCTTTGGAAAGT

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 165

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 186

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

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tttgtcattgtcaagccagagaagaaccaattttttatggaacatgcatctgcagGTAGCATCAAAGCTCTTTAAGAAGCTCAAATGATTTGTGCGATGTGATGCGACTTCTGACAAAGTGAATCGAATTTGCATACCTTACACCTTTGGAAAGT