ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GTATGATGGAATGGAGCACTACTGCTTAGAAGATGCTCATATTGTCAACCTCTTCTCGTTCTCAAAGGCTTATGGAATGATGGGGTGGCGTGTAGGATACgtgagtgcatcatactcttcatttaccgttttcttatgctttacgcctaccccaacctgcttgcagctagacttttttttgctcctcctcctcctcctgctgttaattaccactgtaccagttagtcacacatgaactgtctgctgcag

Basic information

species	Zea mays
transcript	GRMZM2G107639_T01
intron #	8
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G107639_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os01g08270.1 (Oryza sativa), 5'ss of exon 9

GTATGATGGAATGGAGCACTACTGCTTAGAAGATGCTCATATTGTCAACCTCTTCTCGTTCTCAAAGGCTTATGGAATGATGGGGTGGCGTGTAGGATACgtgagtgcatcatactcttcatttaccgttttcttatgctttacgcctaccccaacctgcttgcagctagacttttttttgctcctcctcctcctcctgctgttaattaccactgtaccagttagtcacacatgaactgtctgctgcag
||||||||||||||||||||| |||||||| | |  ||| ||||||||||||||||| ||||| |||||||| ||||||||||| ||||||||||||||||| |||    |   ||||   | |  |  | |||    || |     |    || |||   |||   ||| |||     ||||  |           |  ||                                               
GTATGATGGAATGGAGCACTATTGCTTAGAGGGTAATCACATTGTCAACCTCTTCTCATTCTCGAAGGCTTACGGAATGATGGGCTGGCGTGTAGGATACgtaagtttgcctctctctctctctctctctctctctctctctctctttctttcatcct--ctgc--ttaggcttgaaaatgctgatgtaagagtcaatattgag---------------------------------------------

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|148950037|gb|EC895569.2|EC895569

EST:     TCTTCTCGTTCTCAAAGGCTTATGGAATGATGGGGTGGCGTGTAGGATAC                         ATTGCATTTCCAAATGAAGCTGATGGCTTCCACGATCAGCTCCTCAAGGTG
genomic: TCTTCTCGTTCTCAAAGGCTTATGGAATGATGGGGTGGCGTGTAGGATACgtgagtgcat ... tctgctgcagATTGCATTTCCAAATGAAGCTGATGGCTTCCACGATCAGCTCCTCAAGGTG

EST: gi|78027605|gb|DV495992.1|DV495992

EST:     ATGGGGTGGCGTGTAGGATAC                         ATTGCATTTCCAAATGAAGCTGATGGCTTCCACGATCAGCTCCTCAAAGTG
genomic: ATGGGGTGGCGTGTAGGATACgtgagtgcat ... tctgctgcagATTGCATTTCCAAATGAAGCTGATGGCTTCCACGATCAGCTCCTCAAGGTG

EST: gi|76017053|gb|DT944223.1|DT944223

EST:     TCTTCTCGTTCTCAAAGGCTTATGGAATGATGGGGTGGCGTGTAGGATAC                         ATTGCATTTCCAAATGAAGCTGATGGCTTCCACGATCAGCTCCTCAAGGTG
genomic: TCTTCTCGTTCTCAAAGGCTTATGGAATGATGGGGTGGCGTGTAGGATACgtgagtgcat ... tctgctgcagATTGCATTTCCAAATGAAGCTGATGGCTTCCACGATCAGCTCCTCAAGGTG

EST: gi|31357857|gb|CD442214.1|CD442214

EST:     TCTTCTCGTTCTCAAAGGCTTATGGAATGATGGGGTGGCGTGTAGGATAC                         ATTGCATTTCCAAATGAAGCTGATGGCTTCCACGATCAGCTCCTCAAAGTG
genomic: TCTTCTCGTTCTCAAAGGCTTATGGAATGATGGGGTGGCGTGTAGGATACgtgagtgcat ... tctgctgcagATTGCATTTCCAAATGAAGCTGATGGCTTCCACGATCAGCTCCTCAAGGTG

EST: gi|149051688|gb|EE155800.2|EE155800

EST:     TCTTCTCGTTCTCAAAGGCTTATGGAATGATGGGGTGGCGTGTAGGATAC                         ATTGCATTTCCAAATGAAGCTGATGGCTTCCACGATCAGCTCCTCAAGGTG
genomic: TCTTCTCGTTCTCAAAGGCTTATGGAATGATGGGGTGGCGTGTAGGATACgtgagtgcat ... tctgctgcagATTGCATTTCCAAATGAAGCTGATGGCTTCCACGATCAGCTCCTCAAGGTG

EST: gi|67011573|gb|CO440322.1|CO440322

EST:     TCTTCTCGTTCTCAAAGGCTTATGGAATGATGGGGTGGCGTGTAGGATAC                         ATTGCATTTCCAAATGAAGCTGATGGCTTCCACGATCAGCTCCTCAAAGTG
genomic: TCTTCTCGTTCTCAAAGGCTTATGGAATGATGGGGTGGCGTGTAGGATACgtgagtgcat ... tctgctgcagATTGCATTTCCAAATGAAGCTGATGGCTTCCACGATCAGCTCCTCAAGGTG

EST: gi|211043539|gb|FL214489.1|FL214489

EST:     TCTTCTCGTTCTCAAAGGCTTATGGAATGATGGGGTGGCGTGTAGGATAC                         ATTGCATTTCCAAATGAAGCTGATGGCTTCCACGATCAGCTCCTCAAAGTG
genomic: TCTTCTCGTTCTCAAAGGCTTATGGAATGATGGGGTGGCGTGTAGGATACgtgagtgcat ... tctgctgcagATTGCATTTCCAAATGAAGCTGATGGCTTCCACGATCAGCTCCTCAAGGTG

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: 236

GTATGATGGAATGGAGCACTACTGCTTAGAAGATGCTCATATTGTCAACCTCTTCTCGTTCTCAAAGGCTTATGGAATGATGGGGTGGCGTGTAGGATACgtgagtgcat ... tctgctgcagATTGCATTTCCAAATGAAGCTGATGGCTTCCACGATCAGCTCCTCAAGGTGCAAGACAACATACCGATCTGCGCCTCCATCATCGGGCAGCGCCTGGCGC

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 521

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 327