ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

...nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatggcagGCAAAAACTGGATTAAAGCGATGGTTCTTACAGCGTCCCTGTTTCCGTTCTTGTGTTTCTCAATTGGCTTCGCGCTGAATACAATTGCTATTTTCTACCG

Basic information

species	Zea mays
transcript	GRMZM2G420310_T01
intron #	9
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G420310_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os12g07670.1 (Oryza sativa), 3'ss of exon 9

nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatggcagGCAAAAACTGGATTAAAGCGATGGTTCTTACAGCGTCCCTGTTTCCGTTCTTGTGTTTCTCAATTGGCTTCGCGCTGAATACAATTGCTATTTTCTACCG
                                                                                             |||||||| ||||||||||| || || ||| | |||||||| ||||| ||||| |||||||| ||  |||||||||| |  ||||||||||||||||| ||||||||
ttttttttttgaagtttctagaatttgcatgttgtcatatattatattttcccacttcatgatgtatggttttttgaaccgtaatttccttacatggcagGTAAAAACTGGATAAAGGCTATGATCCTTACAGCATCCCTATTTCCATTCTTGTGCTTTGCAATTGGCTTTGTTCTGAATACAATTGCTATCTTCTACCG

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|67012575|gb|CO441324.1|CO441324

EST:     ATCTTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAATGGTG                         GCAAAAACTGGATTAAAGCGATGGTTCTTACAGCGTCCCTGTTTCCGTTCT
genomic: ATCTTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAATGGTGgtatggttct ... nnnatggcagGCAAAAACTGGATTAAAGCGATGGTTCTTACAGCGTCCCTGTTTCCGTTCT

EST: gi|9028738|gb|BE238778.1|BE238778

EST:     ATCTTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAATGGTG                         GCAAAAACTGGATTAAAGCGATGGTTCTTACAGCGTCCCTGTTTCCGTTCT
genomic: ATCTTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAATGGTGgtatggttct ... nnnatggcagGCAAAAACTGGATTAAAGCGATGGTTCTTACAGCGTCCCTGTTTCCGTTCT

EST: gi|78079181|gb|DV507593.1|DV507593

EST:     ATCTTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAATGGTG                         GCAAAAACTGGATTAAAGCGATGGTTCTTACAGCGTCCCTGTTTCCGTTCT
genomic: ATCTTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAATGGTGgtatggttct ... nnnatggcagGCAAAAACTGGATTAAAGCGATGGTTCTTACAGCGTCCCTGTTTCCGTTCT

EST: gi|21891548|gb|BQ744761.1|BQ744761

EST:     ATCTTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAATGGTG                         GCAAAAACTGGATTAAAGCGATGGTTCTTACAGCGTCCCTGTTTCCGTTCT
genomic: ATCTTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAATGGTGgtatggttct ... nnnatggcagGCAAAAACTGGATTAAAGCGATGGTTCTTACAGCGTCCCTGTTTCCGTTCT

EST: gi|89249565|gb|DY621351.1|DY621351

EST:     ATCTTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAATGGTG                         GCAAAAACTGGATTAAAGCGATGGTTCTTACAGCGTCCCTGTTTCCGTTCT
genomic: ATCTTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAATGGTGgtatggttct ... nnnatggcagGCAAAAACTGGATTAAAGCGATGGTTCTTACAGCGTCCCTGTTTCCGTTCT

EST: gi|9028529|gb|BE238524.1|BE238524

EST:     ATCTTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAATGGTG                         GCAAAAACTGGATTAAAGCGATGGTTCTTACAGCGTCCCTGTTTCCGTTCT
genomic: ATCTTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAATGGTGgtatggttct ... nnnatggcagGCAAAAACTGGATTAAAGCGATGGTTCTTACAGCGTCCCTGTTTCCGTTCT

EST: gi|71327794|gb|DR800533.1|DR800533

EST:     ATCTTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAATGGTG                         GCAAAAACTGGATTAAAGCGATGGTTCTTACAGCGTCCCTGTTTCCGTTCT
genomic: ATCTTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAATGGTGgtatggttct ... nnnatggcagGCAAAAACTGGATTAAAGCGATGGTTCTTACAGCGTCCCTGTTTCCGTTCT

EST: gi|32931030|gb|CF035842.1|CF035842

EST:     ATCTTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAATGGTG                         GCAAAAACTGGATTAAAGCGATGGTTCTTACAGCGTCCCTGTTTCCGTTCT
genomic: ATCTTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAATGGTGgtatggttct ... nnnatggcagGCAAAAACTGGATTAAAGCGATGGTTCTTACAGCGTCCCTGTTTCCGTTCT

EST: gi|67018280|gb|CO447029.1|CO447029

EST:     ATCTTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAATGGTG                         GCAAAAACTGGATTAAAGCGATGGTTCTTACAGCGTCCCTGTTTCCGTTCT
genomic: ATCTTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAATGGTGgtatggttct ... nnnatggcagGCAAAAACTGGATTAAAGCGATGGTTCTTACAGCGTCCCTGTTTCCGTTCT

EST: gi|9953890|gb|BE640473.1|BE640473

EST:     ATCTTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAATGGTG                         GCAAAAACTGGATTAAAGCGATGGTTCTTACAGCGTCCCTGTTTCCGTTCT
genomic: ATCTTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAATGGTGgtatggttct ... nnnatggcagGCAAAAACTGGATTAAAGCGATGGTTCTTACAGCGTCCCTGTTTCCGTTCT

EST: gi|94476145|gb|EB705103.1|EB705103

EST:     ATCTTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAATGGTG                         GCAAAAACTGGATTAAAGCGATGGTTCTTACAGCGTCCCTGTTTCCGTTCT
genomic: ATCTTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAATGGTGgtatggttct ... nnnatggcagGCAAAAACTGGATTAAAGCGATGGTTCTTACAGCGTCCCTGTTTCCGTTCT

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: 268

GCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAATGGTGgtatggttct ... nnnatggcagGCAAAAACTGGATTAAAGCGATGGTTCTTACAGCGTCCCTGTTTCCGTTCTTGTGTTTCTCAATTGGCTTCGCGCTGAATACAATTGCTATTTTCTACCG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 315

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 406