ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

AGCACAATGCTCTGGGCAGAAGGGAGGAAGGAATGGATGCCACTCTCGTCCATCTCTGAGCTACACTCCGCAGTCGCAGCGAAGGATCAATCTGAACAAGgttaaatgttgctgccttgtactgtgcctgtaatggaaattctgtaaggttttcttctcattcactgaacttctgtgcag

Basic information

species	Zea mays
transcript	GRMZM2G171660_T02
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G171660_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os04g41910.1 (Oryza sativa), 5'ss of exon 2

AGCACAATGCTCTGGGCAGAAGGGAGGAAGGAATGGATGCCACTCTCGTCCATCTCTGAGCTACACTCCGCAGTCGCAGCGAAGGATCAATCTGAACAAGgttaaatgttgctgcct--tgtactgtgcctgtaatggaaa-----ttctgtaaggttttcttctcattcactgaacttctgtgcag------
||| ||||||||||||||||||||||||  |||||||||||| | ||||| ||  |||| ||||   | |  ||| ||   ||||||||| ||||  |||||||    || || |||  |||  |  |    ||||  | |      |      | | | ||     ||   | ||  | | ||  |      
AGCTCAATGCTCTGGGCAGAAGGGAGGAGTGAATGGATGCCATTGTCGTCGATTCCTGACCTACTTGCGGTGGTCACAAAAAAGGATCAACCTGATGAAGgttactgatttctaccttctgttttaaggaaataatacagaatacacttcacgtgatctcctgacattttctttaatctttctgatgccccag

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|91054747|gb|EB165165.1|EB165165

EST:     CATCTCTGAGCTACACTCCGCAGTCGCAGCGAAGGATCAATCTGAACAAG                         ATGCTCCAGATGTTGATGATGATTTTGAGAAATTTCAGAAGGAGGTTATCG
genomic: CATCTCTGAGCTACACTCCGCAGTCGCAGCGAAGGATCAATCTGAACAAGgttaaatgtt ... ttctgtgcagATGCTCCAGATGTTGATGATGATTTTGAGAAATTTCAGAAGGAGGTTATCG

EST: gi|149070733|gb|EE159146.2|EE159146

EST:     CATCTCTGAGCTACACTCCGCAGTCGCAGCGAAGGATCAATCTGAACAAG                         ATGCTCCAGATGTTGATGATGATTTTGAGAAATTTCAGAAGGAGGTTATCG
genomic: CATCTCTGAGCTACACTCCGCAGTCGCAGCGAAGGATCAATCTGAACAAGgttaaatgtt ... ttctgtgcagATGCTCCAGATGTTGATGATGATTTTGAGAAATTTCAGAAGGAGGTTATCG

EST: gi|211141165|gb|FL018627.1|FL018627

EST:     CATCTCTGAGCTACACTCCGCAGTCGCAGCGAAGGATCAATCTGAACAAG                         ATGCTCCAGATGTTGATGATGATTTTGAGAAATTTCAGAAGGAGGTTATCG
genomic: CATCTCTGAGCTACACTCCGCAGTCGCAGCGAAGGATCAATCTGAACAAGgttaaatgtt ... ttctgtgcagATGCTCCAGATGTTGATGATGATTTTGAGAAATTTCAGAAGGAGGTTATCG

EST: gi|211475989|gb|FL018621.1|FL018621

EST:     CATCTCTGAGCTACACTCCGCAGTCGCAGCGAAGGATCAATCTGAACAAG                         ATGCTCCAGATGTTGATGATGATTTTGAGAAATTTCAGAAGGAGGTTATCG
genomic: CATCTCTGAGCTACACTCCGCAGTCGCAGCGAAGGATCAATCTGAACAAGgttaaatgtt ... ttctgtgcagATGCTCCAGATGTTGATGATGATTTTGAGAAATTTCAGAAGGAGGTTATCG

EST: gi|50335300|gb|CO530426.1|CO530426

EST:     CATCTCTGAGCTACACTCCGCAGTCGCAGCGAAGGATCAATCTGAACAAG                         ATGCTCCAGATGTTGATGATGATTTTGAGAAATTTCAGAAGGAGGTTATCG
genomic: CATCTCTGAGCTACACTCCGCAGTCGCAGCGAAGGATCAATCTGAACAAGgttaaatgtt ... ttctgtgcagATGCTCCAGATGTTGATGATGATTTTGAGAAATTTCAGAAGGAGGTTATCG

EST: gi|148966210|gb|EE017166.2|EE017166

EST:     CATCTCTGAGCTACACTCCGCAGTCGCAGCGAAGGATCAATCTGAACAAG                         ATGCTCCAGATGTTGATGATGATTTTGAGAAATTTCAGAAGGAGGTTATCG
genomic: CATCTCTGAGCTACACTCCGCAGTCGCAGCGAAGGATCAATCTGAACAAGgttaaatgtt ... ttctgtgcagATGCTCCAGATGTTGATGATGATTTTGAGAAATTTCAGAAGGAGGTTATCG

EST: gi|76909704|gb|DV163493.1|DV163493

EST:     CATCTCTGAGCTACACTCCGCAGTCGCAGCGAAGGATCAATCTGAACAAG                         ATGCTCCAGATGTTGATGATGATTTTGAGAAATTTCAGAAGGAGGTTATCG
genomic: CATCTCTGAGCTACACTCCGCAGTCGCAGCGAAGGATCAATCTGAACAAGgttaaatgtt ... ttctgtgcagATGCTCCAGATGTTGATGATGATTTTGAGAAATTTCAGAAGGAGGTTATCG

EST: gi|211141166|gb|FL018628.1|FL018628

EST:     CATCTCTGAGCTACACTCCGCAGTCGCAGCGAAGGATCAATCTGAACAAG                         ATGCTCCAGATGTTGATGATGATTTTGAGAAATTTCAGAAGGAGGTTATCG
genomic: CATCTCTGAGCTACACTCCGCAGTCGCAGCGAAGGATCAATCTGAACAAGgttaaatgtt ... ttctgtgcagATGCTCCAGATGTTGATGATGATTTTGAGAAATTTCAGAAGGAGGTTATCG

EST: gi|211475990|gb|FL018622.1|FL018622

EST:     CATCTCTGAGCTACACTCCGCAGTCGCAGCGAAGGATCAATCTGAACAAG                         ATGCTCCAGATGTTGATGATGATTTTGAGAAATTTCAGAAGGAGGTTATCG
genomic: CATCTCTGAGCTACACTCCGCAGTCGCAGCGAAGGATCAATCTGAACAAGgttaaatgtt ... ttctgtgcagATGCTCCAGATGTTGATGATGATTTTGAGAAATTTCAGAAGGAGGTTATCG

EST: gi|211141169|gb|FL018631.1|FL018631

EST:     CATCTCTGAGCTACACTCCGCAGTCGCAGCGAAGGATCAATCTGAACAAG                         ATGCTCCAGATGTTGATGATGATTTTGAGAAATTTCAGAAGGAGGT
genomic: CATCTCTGAGCTACACTCCGCAGTCGCAGCGAAGGATCAATCTGAACAAGgttaaatgtt ... ttctgtgcagATGCTCCAGATGTTGATGATGATTTTGAGAAATTTCAGAAGGAGGT

EST: gi|149004610|gb|EE039124.2|EE039124

EST:     CATCTCTGAGCTACACTCCGCAGTCGCAGCGAAGGATCAATCTGAACAAG                         ATGCTCCAGATGTTGATGATGATTTTGAGAAATTTCAGAAGGAGGTTATCG
genomic: CATCTCTGAGCTACACTCCGCAGTCGCAGCGAAGGATCAATCTGAACAAGgttaaatgtt ... ttctgtgcagATGCTCCAGATGTTGATGATGATTTTGAGAAATTTCAGAAGGAGGTTATCG

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: 46 (upstream exon), 45 (downstream exon)
Score: 74

AGCACAATGCTCTGGGCAGAAGGGAGGAAGGAATGGATGCCACTCTCGTCCATCTCTGAGCTACACTCCGCAGTCGCAGCGAAGGATCAATCTGAACAAGgttaaatgtt ... ttctgtgcagATGCTCCAGATGTTGATGATGATTTTGAGAAATTTCAGAAGGAGGTTATCGAAGCCGAGACAGAGGTGAAGGCCTTGAAAGGCAATGATGTGGACCAGCA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 64

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 60