ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GCAGCAGCTTAATGAGCATGCTAAGCTTTCGATGCTTAGGAATGCTACATGGACTCTCTCCAACTTCTGTCGGGGGAAGCCACAACCAAACTTTGATCAGgtatatctgggactatttcttttttgtgttggccaaagttggttctttgattgatattggtgtgttttgttcatgcttgagtag

Basic information

species	Zea mays
transcript	GRMZM2G088088_T01
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G088088_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os05g06350.1 (Oryza sativa), 5'ss of exon 5

GCAGCAGCTTAATGAGCATGCTAAGCTTTCGATGCTTAGGAATGCTACATGGACTCTCTCCAACTTCTGTCGGGGGAAGCCACAACCAAACTTTGATCAGgtata-tctgggactatttcttttttgtgttggccaaagttggttctt-tgattgatattggtgtgtt--ttgttcatgcttgagtag
||| |||||||||||||| || ||||| || ||||| |||||||| |||||||| || || |||||||| || |||||||| || || || ||||| ||||| || |   || |||  |  |  ||   |   |  |  |  ||| || | |||   || | | ||||  || ||  || | ||| ||
GCAACAGCTTAATGAGCACGCCAAGCTCTCAATGCTCAGGAATGCCACATGGACACTGTCAAACTTCTGCCGTGGGAAGCCTCAGCCTAATTTTGAGCAGgtttaattctgggctaccttctactttgatgcactgacctaagtttttatcattaggatggttttgttgattttttgtgttcgagcag

upper sequence: GRMZM2G088088_T01 (Zea mays), 5'ss of exon 5
lower sequence: PP1S165_54V6.1 (Physcomitrella patens), 5'ss of exon 5

-GCAGCAGCTTAATGAGCATGCTAAGCTTTCGATGCTTAGGAATGCTACATGGACTCTCTCCAACTTCTGTCGGGGGAAGCCACAACCAAACTTTGATCAGgtatatc-tgggactatttctttt------ttgtgttggccaaagttggtt-----ctttgattgatattggtgtgttttgttcatgcttgagtag----
 || ||||||||  ||| |  | ||  | || |||||||| || ||||| ||||||||||||||||||||||| || ||||| ||||||   ||||| ||||||| |  || || |||| |  ||      || |  |        || |        || | |||| | |    | ||   |||   |||   |      
TGC-GCAGCTTACGGAGAACACAAAATTGTCTATGCTTAGAAACGCTACCTGGACTCTCTCCAACTTCTGTCGTGGCAAGCCTCAACCACCTTTTGAGCAGgtatgtgatgtgattattacgcttactctattattattattcttattagcaagtgatttcgtttgacagtaagatattcgcttctctcttattttcttcc

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|211452350|gb|FL292615.1|FL292615

EST:     GGACTCTCTCCAACTTCTGTCGGGGGAAGCCACAACCAAACTTTGATCAG                         GTCAAACCAGCATTGCCAGCACTACAGCACCTTATTCACTCTCAGGATGAG
genomic: GGACTCTCTCCAACTTCTGTCGGGGGAAGCCACAACCAAACTTTGATCAGgtatatctgg ... gcttgagtagGTCAAACCAGCATTGCCAGCACTACAGCACCTTATTCACTCTCAGGATGAG

EST: gi|211452354|gb|FL292619.1|FL292619

EST:     GGACTCTCTCCAACTTCTGTCGGGGGAAGCCACAACCAAACTTTGATCAG                         GTCAAACCAGCATTGCCAGCACTACAGCACCTTATTCACTCTCAGGATGAG
genomic: GGACTCTCTCCAACTTCTGTCGGGGGAAGCCACAACCAAACTTTGATCAGgtatatctgg ... gcttgagtagGTCAAACCAGCATTGCCAGCACTACAGCACCTTATTCACTCTCAGGATGAG

EST: gi|211008179|gb|FL253536.1|FL253536

EST:     GGACTCTCTCCAACTTCTGTCGGGGGAAGCCACAACCAAACTTTGATCAG                         GTCAAACCAGCATTGCCAGCACTACAGCACCTTATTCACTCTCAGGATGAA
genomic: GGACTCTCTCCAACTTCTGTCGGGGGAAGCCACAACCAAACTTTGATCAGgtatatctgg ... gcttgagtagGTCAAACCAGCATTGCCAGCACTACAGCACCTTATTCACTCTCAGGATGAG

EST: gi|213179381|gb|FM182985.1|FM182985

EST:     CACAACCAAACTTTGATCAG                         GTCAAACCAGCATTGCCAGCACTACAGCACCTTATTCACTCTCAGGATGAG
genomic: CACAACCAAACTTTGATCAGgtatatctgg ... gcttgagtagGTCAAACCAGCATTGCCAGCACTACAGCACCTTATTCACTCTCAGGATGAG

EST: gi|211452351|gb|FL292616.1|FL292616

EST:     GGACTCTCTCCAACTTCTGTCGGGGGAAGCCACAACCAAACTTTGATCAG                         GTCAAACCAGCATTGCCAGCACTACAGCACCTTATTCACTCTCAGGATGAG
genomic: GGACTCTCTCCAACTTCTGTCGGGGGAAGCCACAACCAAACTTTGATCAGgtatatctgg ... gcttgagtagGTCAAACCAGCATTGCCAGCACTACAGCACCTTATTCACTCTCAGGATGAG

EST: gi|67023557|gb|CO452306.1|CO452306

EST:     GGACTCTCTCCAACTTCTGTCGGGGGAAGCC-CAACCAAACTTTGATCAG                         GTCAAACCAGCATTGCCAGCACTACAGCACCTTATTCACTCTCAGGATGAN
genomic: GGACTCTCTCCAACTTCTGTCGGGGGAAGCCACAACCAAACTTTGATCAGgtatatctgg ... gcttgagtagGTCAAACCAGCATTGCCAGCACTACAGCACCTTATTCACTCTCAGGATGA-

EST: gi|78078677|gb|DV507089.1|DV507089

EST:     GACTCTCTCCAACTTCTGTCGGGGGGAAGC-ACAACCAAACTTTGATCAG                         GTCAAACCAGCATTGCCAGCACTACAGCACCTTATT
genomic: GACTCTCTCCAACTTCTGTCGGGGG-AAGCCACAACCAAACTTTGATCAGgtatatctgg ... gcttgagtagGTCAAACCAGCATTGCCAGCACTACAGCACCTTATT

EST: gi|211049546|gb|FK991525.1|FK991525

EST:     GGACTCTCTCCAACTTCTGTCGGGGGAAGCCACAACCAAACTTTGATCAG                         GTCAAACCAGCATTGCCAGCACTACAGCACCTTATTCACTCTCAGGATGAG
genomic: GGACTCTCTCCAACTTCTGTCGGGGGAAGCCACAACCAAACTTTGATCAGgtatatctgg ... gcttgagtagGTCAAACCAGCATTGCCAGCACTACAGCACCTTATTCACTCTCAGGATGAG

EST: gi|6865203|gb|AW360553.1|AW360553

EST:     GGACTCTCTCCAACTTCTGTCGGGGGAAGCCGCAACCAAACTTTGATCAG                         GTCAAACCAGCATTGCCAGCACTACAGCACCTTATTCACTCTCAGGATGAG
genomic: GGACTCTCTCCAACTTCTGTCGGGGGAAGCCACAACCAAACTTTGATCAGgtatatctgg ... gcttgagtagGTCAAACCAGCATTGCCAGCACTACAGCACCTTATTCACTCTCAGGATGAG

EST: gi|211331752|gb|FL022649.1|FL022649

EST:     GGACTCTCTCCAACTTCTGTCGGGGGAAGCCACAACCAAACTTTGATCAG                         GTCAAACCAGCATTGCCAGCACTACAGCACCTTATTCACTCTCAGGATGAG
genomic: GGACTCTCTCCAACTTCTGTCGGGGGAAGCCACAACCAAACTTTGATCAGgtatatctgg ... gcttgagtagGTCAAACCAGCATTGCCAGCACTACAGCACCTTATTCACTCTCAGGATGAG

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: 532

GCAGCAGCTTAATGAGCATGCTAAGCTTTCGATGCTTAGGAATGCTACATGGACTCTCTCCAACTTCTGTCGGGGGAAGCCACAACCAAACTTTGATCAGgtatatctgg ... gcttgagtagGTCAAACCAGCATTGCCAGCACTACAGCACCTTATTCACTCTCAGGATGAGGAGGTCCTAACTGATGCCTGCTGGGCGCTCTCATACTTGTCTGATGGGA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 515

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 518