ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGAAGAAGCTGAGATTGGCATGTGGGAGGCAGTAACATGGCTTGCGGTTTTAACACTCTGGGTGTCTTTTCTTTCTGAGTACCTAGTTAACGCCATTGAGgtattcttcttctccaattcaacaagaaagaataaaaagtcagcttttattcatctgtagcaagtggaacttgttaaaggtagcttcctacagttgacag...

Basic information

species	Zea mays
transcript	GRMZM2G040017_T02
intron #	7
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G040017_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os04g55940.1 (Oryza sativa), 5'ss of exon 7

TGAAGAAGCTGAGATTGGCATGTGGGAGGCAGTAACATGGCTTGCGGTTTTAACACTCTGGGTGTCTTTTCTTTCTGAGTACCTAGTTAACGCCATTGAGgtattc-ttcttctccaattcaacaagaaag---aataaaaagtcagcttttattcatctgtagcaagtgg-aacttgttaaaggtagcttcctacagttgacag
||||||| | |||||||||||||||||| |  || ||||||| ||| | || ||| | ||||||||| |||||||||| ||||| ||||| ||||||||||||||| ||||  || |||| |  | || ||   || |||||   |||| || || || ||| |||| ||  || |  ||     | || |  || | |||    
TGAAGAATCAGAGATTGGCATGTGGGAGTCCATAGCATGGCTCGCGATGTTGACATTATGGGTGTCTATTCTTTCTGAATACCTGGTTAATGCCATTGAGgtattccttctcttctaatttagaatgacagcacaaaaaaaaagtagctgttcttaatatgt-gcaactgacaaatgattttttttggcctgttaaacttg----

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|149085153|gb|EE174657.2|EE174657

EST:     TAACACTCTGGGTGTCTTTTCTTTCTGAGTACCTAGTTAACGCCATTGAG                         GGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTG
genomic: TAACACTCTGGGTGTCTTTTCTTTCTGAGTACCTAGTTAACGCCATTGAGgtattcttct ... ttgctgttagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTG

EST: gi|211010290|gb|FL457993.1|FL457993

EST:     TTTTCTTTCTGAGTACCTAGTTAACGCCATTGAG                         GGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTCTG
genomic: TTTTCTTTCTGAGTACCTAGTTAACGCCATTGAGgtattcttct ... ttgctgttagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTG

EST: gi|91868897|gb|EB400200.1|EB400200

EST:     TAACACTCTGGGTGTCTTTTCTTTCTGAGTACCTAGTTAACGCCATTGAG                         GGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTG
genomic: TAACACTCTGGGTGTCTTTTCTTTCTGAGTACCTAGTTAACGCCATTGAGgtattcttct ... ttgctgttagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTG

EST: gi|32837305|gb|CD976983.1|CD976983

EST:     TACCTAGTTAACGCCATTGAG                         GGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTCTG
genomic: TACCTAGTTAACGCCATTGAGgtattcttct ... ttgctgttagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTG

EST: gi|60339318|gb|DN206291.1|DN206291

EST:     TAACACTCTGGGTGTCTTTTCTTTCTGAGTACCTAGTTAACGCCATTGAG                         GGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTG
genomic: TAACACTCTGGGTGTCTTTTCTTTCTGAGTACCTAGTTAACGCCATTGAGgtattcttct ... ttgctgttagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTG

EST: gi|32836604|gb|CD976282.1|CD976282

EST:     GTACCTAGTTAACGCCATTGAG                         GGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTCTG
genomic: GTACCTAGTTAACGCCATTGAGgtattcttct ... ttgctgttagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTG

EST: gi|148972711|gb|EE023671.2|EE023671

EST:     TAACACTCTGGGTGTCTTTTCTTTCTGAGTACCTAGTTAACGCCATTGAG                         GGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTG
genomic: TAACACTCTGGGTGTCTTTTCTTTCTGAGTACCTAGTTAACGCCATTGAGgtattcttct ... ttgctgttagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTG

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: 200

TGAAGAAGCTGAGATTGGCATGTGGGAGGCAGTAACATGGCTTGCGGTTTTAACACTCTGGGTGTCTTTTCTTTCTGAGTACCTAGTTAACGCCATTGAGgtattcttct ... ttgctgttagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGCAATGCAGCTGAACATGCAAGTGCAATAATGTTTG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 293

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 339