ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GTCTCTTCACTAGAGGACTTCCTCTTCGTATCGTCATGATTGGTACCCTTACTGGTGCTCAGTGGGGAATTTACGATGCATTCAAAGTGATGGTTGGACTgtgagtgtctctctctactgccttaggaataagtgaatagccaccgcaacatccaaatccttcagagagctcaccaactaattctttgtttcgtttctgtttcag

Basic information

species	Zea mays
transcript	GRMZM2G015401_T01
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G015401_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g52860.1 (Oryza sativa), 5'ss of exon 5

GTCTCTTCACTAGAGGACTTCCTCTTCGTATCGTCATGATTGGTACCCTTACTGGTGCTCAGTGGGGAATTTACGATGCATTCAAAGTGATGGTTGGACTgtgagtgtctctctctactgccttaggaataagtgaatagccaccgcaacatccaaatccttcagagagctcaccaactaattctttgtttcgtttctgtttcag
| || |||||||||||||| || |||||||| || |||||||| || |||||||||||||| ||||| ||||| ||||| || ||||| ||||||||||||| ||| |  || |    |||      | ||| | ||| |  |    |||||  |||  |||  |||   |||   ||| ||      |||  | | | ||||||
GCCTTTTCACTAGAGGACTGCCCCTTCGTATTGTTATGATTGGAACTCTTACTGGTGCTCAATGGGGTATTTATGATGCTTTTAAAGTCATGGTTGGACTgtaagtattccttttgcttgct----aattaatttaattgttag---aacattaaaaggcttttgaggaatcaaggacttatggcccattt-atatat-tttcag

upper sequence: GRMZM2G015401_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA16G05450.1 (Glycine max), 5'ss of exon 6

GTCTCTTCACTAGAGGACTTCCTCTTCGTATCGTCATGATTGGTACCCTTACTGGTGCTCAGTGGGGAATTTACGATGCATTCAAAGTGATGGTTGGACTgtgagtgtctctctctactgccttaggaataagtgaatagccaccgcaacatccaaatccttcagagagctcaccaactaattctttgtttcgtttctgtttcag
||||||| ||  | || ||||| || ||||| || |||||||| || |||||||| || || |||||||| || |||||||||||||||   || ||| ||| ||| |       | ||   ||    ||| |     |  |      | ||     |       ||   | ||   |||||    |   |     || |  |||
GTCTCTTTACCCGTGGTCTTCCCCTCCGTATTGTTATGATTGGAACTCTTACTGGAGCCCAATGGGGAATATATGATGCATTCAAAGTGTCTGTCGGATTgtaagtttacacaattgctagttttatgatagggttccatactttcatatatattgttttccttcagtattgacgttctaatgaaataaatttcccct-tcccag

upper sequence: GRMZM2G015401_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA19G27380.1 (Glycine max), 5'ss of exon 5

GTCTCTTCACTAGAGGACTTCCTCTTCGTATCGTCATGATTGGTACCCTTACTGGTGCTCAGTGGGGAATTTACGATGCATTCAAAGTGATGGTTGGACTgtgagtgtctctctctactgccttaggaataagtgaatagccaccgcaacatccaaatccttcagagagctcaccaactaattctttgtttcgtttctgtttcag
||||||| ||  | || || || || || || || |||||||| || |||||||| || || |||||||| || ||||||||||||||  | || ||| ||| |||   |  | | | |||  |||  |    |      |||      ||| |   | | |||  || |   | ||  |  | |||    | || |        
GTCTCTTTACGCGTGGTCTCCCCCTCCGAATTGTTATGATTGGAACTCTTACTGGAGCCCAATGGGGAATATATGATGCATTCAAAGTCTTCGTCGGATTgtaagt---ttacacaattgc--tagtcaatgatagggttccattctttcattc--cttcatcatgga-cgtgctaatgagattttttcccccttcccag-----

upper sequence: GRMZM2G015401_T01 (Zea mays), 5'ss of exon 5
lower sequence: EFJ31006 (Selaginella moellendorffii), 5'ss of exon 5

GTCTCTTCACTAGAGGACTTCCTCTTCGTATCGTCATGATTGGTACCCTTACTGGTGCTCAGTGGGGAATTTACGATGCATTCAAAGTGATGGTTGGACTgtgagtgtctctctctactgccttaggaataagtgaatagccaccgcaacatccaaatccttcagagagctcaccaactaattctttgtttcgtttctgtttcag
 |||||||||  | || || || || |||||||| |||||||| || || ||||| || ||||||||||| ||||| || ||||||||  | |||||||||| ||| |||| ||||  |  |||  |   || |    |  | |     ||                                                      
CTCTCTTCACCCGGGGGCTACCGCTGCGTATCGTGATGATTGGAACACTCACTGGAGCACAGTGGGGAATCTACGACGCCTTCAAAGTCTTCGTTGGACTgtaagtttctcgctctcatctcttgtggggaaatctcaaatctctattccag-----------------------------------------------------

upper sequence: GRMZM2G015401_T01 (Zea mays), 5'ss of exon 5
lower sequence: EFJ34707 (Selaginella moellendorffii), 5'ss of exon 5

GTCTCTTCACTAGAGGACTTCCTCTTCGTATCGTCATGATTGGTACCCTTACTGGTGCTCAGTGGGGAATTTACGATGCATTCAAAGTGATGGTTGGACTgtgagtgtctctctctactgccttaggaataagtgaatagccaccgcaacatccaaatccttcagagagctcaccaactaattctttgtttcgtttctgtttcag
 |||||||||  | || || || || |||||||| |||||||| || || ||||| || ||||||||||| ||||| || ||||||||  | |||||||||| ||| |||| ||||      |  ||||      |||  | |   ||                                                         
CTCTCTTCACCCGGGGGCTACCGCTGCGTATCGTGATGATTGGAACACTCACTGGAGCACAGTGGGGAATCTACGACGCCTTCAAAGTCTTCGTTGGACTgtaagtttctcgctctctcttgtggggaaatctcaaatctctattccag--------------------------------------------------------

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|148948945|gb|EC894364.2|EC894364

EST:     ACTGGTGCTCAGTGGGGAATTTACGATGCATTCAAAGTGATGGTTGGACT                         CCCAACAACGGGAGGTGTTACACCTGCCCCAGCAGCAGAGGCTGAATTGAA
genomic: ACTGGTGCTCAGTGGGGAATTTACGATGCATTCAAAGTGATGGTTGGACTgtgagtgtct ... tctgtttcagCCCAACAACGGGAGGTGTTACACCTGCCCCAGCAGCAGAGGCTGAATTGAA

EST: gi|8665644|gb|BE186460.1|BE186460

EST:     ACTGGTGCTCAGTGGGGAATTTACGATGCATTCAAAGTGATGGTTGGACT                         CCCAACAACGGGAGGTGTTACACCTGCCCCAGCAGCAGAGGCTGGATTGAA
genomic: ACTGGTGCTCAGTGGGGAATTTACGATGCATTCAAAGTGATGGTTGGACTgtgagtgtct ... tctgtttcagCCCAACAACGGGAGGTGTTACACCTGCCCCAGCAGCAGAGGCTGAATTGAA

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: 48 (upstream exon), 49 (downstream exon)
Score: 416

GTCTCTTCACTAGAGGACTTCCTCTTCGTATCGTCATGATTGGTACCCTTACTGGTGCTCAGTGGGGAATTTACGATGCATTCAAAGTGATGGTTGGACTgtgagtgtct ... tctgtttcagCCCAACAACGGGAGGTGTTACACCTGCCCCAGCAGCAGAGGCTGAATTGAAAGCCAGTGCTTGATTTTTTTTTTCTGTGTTCCCTGAGATCATATTTGGT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 544

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 361