ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GTTCACTGCATGATATGCTCCATCTCTCAGATGATTATAACAAACCACTTAGTTGGAATTCTCGTGTTAAGATTGCGTTGGGCTCTGCACGTGCACTAGAgtaagcaactctgatctctctcccttatgcaactatgatgatagaattttgataaaaaatgtatgttgagcgaattctttttttggtgagtgaaactctactgcgaagcacctcaacctttactcttaccttcctgtag

Basic information

species	Zea mays
transcript	GRMZM2G004572_T01
intron #	12
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G004572_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os10g25090.1 (Oryza sativa), 5'ss of exon 12

GTTCACTGCATGATATGCTCCATCTCTCAGATGATTATAACAAACCACTTAGTTGGAATTCTCGTGTTAAGATTGCGTTGGGCTCTGCACGTGCACTAGAgtaagc---aactctgatctctctcccttatgcaactatgatgatagaattttgataaaaaat-gtatgttgagcgaattctttttttggtgagtgaaactctactgcgaagcacctcaacctttactcttaccttcctgtag
|||| |||||||||||||| || ||| ||||||| |||| ||||||||| || |||||||||||||||||||||||||| || |||||||| |||||||||||||    ||||  |||||||||||||     | || |   ||||   ||   |||||  || || | ||   | | ||  |   |||   |     |    |||                                     
GTTCGCTGCATGATATGCTTCACCTCCCAGATGAATATAGCAAACCACTCAGCTGGAATTCTCGTGTTAAGATTGCGTTAGGTTCTGCACGGGCACTAGAgtaagtgaaaactaagatctctctccct-----atctgttg-gatacttttcaaataaattattgtcttttttccaacttaatgacttgtgaaaattgatctgact-------------------------------------

upper sequence: GRMZM2G004572_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA19G45130.1 (Glycine max), 5'ss of exon 12

GTTCACTGCATGATATGCTCCATCTCTCAGATGATTATAACAAACCACTTAGTTGGAATTCTCGTGTTAAGATTGCGTTGGGCTCTGCACGTGCACTAGAgtaagc-aactctgatctctctcccttatgcaactatgatgatagaattttgataaaaaatgt-atgttgagcga-attctttttttggtgagtgaaactctactgcgaagcacctcaacctttactcttaccttcctgtag
| |||||||||||  | || || || |||||||| ||||  |||||| | |  |||||||| ||||| |||||||| |||||  |||||||||| ||||||||||  |  | ||  ||       |||    | | | |   || | ||| |  |  |||| | |  || |   |   ||  | ||||     |  || |                                          
GATCACTGCATGACTTCCTTCACCTATCAGATGAATATAGTAAACCATTGATATGGAATTCCCGTGTCAAGATTGCTTTGGGGACTGCACGTGCTCTAGAgtaagttagttgtgggctaatgggattagaagattcttacactacattttcgtgaggaaatttcacattaattcatgatcaatatttgaatcatataaat------------------------------------------

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|76014323|gb|DT941493.1|DT941493

EST:     GGCTCTGCACGTGCACTAGA                         GCATCTTCATGAAATTTTTTCTCGATCTATAATTCACAAGAACTTTAAGTC
genomic: GGCTCTGCACGTGCACTAGAgtaagcaact ... cttcctgtagGCATCTTCATGAAATTTGTTCTCCATCTATAATTCACAAGAACTTTAAGTC

EST: gi|60397780|gb|DN230596.1|DN230596

EST:     AGTTGGAATTCTCGTGTTAAGATTGCGTTGGGCTCTGCACGTGCACTAGA                         GCATCTTCATGAAATTTGTTCTCCATCTATAATTCACAAGAACTTTAAGTC
genomic: AGTTGGAATTCTCGTGTTAAGATTGCGTTGGGCTCTGCACGTGCACTAGAgtaagcaact ... cttcctgtagGCATCTTCATGAAATTTGTTCTCCATCTATAATTCACAAGAACTTTAAGTC

EST: gi|74241624|gb|DT649538.1|DT649538

EST:     GCACGTGCACTAGA                         GCATCTTCATGAAATTTGTTCTCCATCTATAATTCACAAGAACTTTAAGTC
genomic: GCACGTGCACTAGAgtaagcaact ... cttcctgtagGCATCTTCATGAAATTTGTTCTCCATCTATAATTCACAAGAACTTTAAGTC

EST: gi|32932312|gb|CF037124.1|CF037124

EST:     AGTTGGAATTCTCGTGTTAAGATTGCGTTGGGCTCTGCACGTGCACTAGA                         GCATCTTCATGAAATTTGTTCTCCATCTATAATTCACAAGAACTTTAAGTC
genomic: AGTTGGAATTCTCGTGTTAAGATTGCGTTGGGCTCTGCACGTGCACTAGAgtaagcaact ... cttcctgtagGCATCTTCATGAAATTTGTTCTCCATCTATAATTCACAAGAACTTTAAGTC

EST: gi|76018776|gb|DT945946.1|DT945946

EST:     TGTTAAGATTGCGTTGGGCTCTGCACGTGCACTAGA                         GCATCTTCATGAAATTTGTTCTCCATCTATAATTCACAAGAACTTTAAGTC
genomic: TGTTAAGATTGCGTTGGGCTCTGCACGTGCACTAGAgtaagcaact ... cttcctgtagGCATCTTCATGAAATTTGTTCTCCATCTATAATTCACAAGAACTTTAAGTC

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: 67

GTTCACTGCATGATATGCTCCATCTCTCAGATGATTATAACAAACCACTTAGTTGGAATTCTCGTGTTAAGATTGCGTTGGGCTCTGCACGTGCACTAGAgtaagcaact ... cttcctgtagGCATCTTCATGAAATTTGTTCTCCATCTATAATTCACAAGAACTTTAAGTCGTCCAATATTTTACTGGACACCGAGCTCAATCCTCACATTTCTGATGCT

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 19

Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 23