ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GTGTGACCCTCATGCTCAACGTATCATTACTTCGTCCGAGTCTCCTCAGGAGGTCGAAGTTGGCAAGGATATCATATTTACTTACGATGTGGATTTCAAGgtcagaactatgtttgattctttttgtattccaaataagtgattgtagtagctgtagtactaagtgtcctataagtggagcatgaatattgtgttttgctcatttctgagaactactgtaaatttgtag

Basic information

species	Zea mays
transcript	GRMZM2G146951_T01
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G146951_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os08g17370.1 (Oryza sativa), 5'ss of exon 5

GTGTGACCCTCATGCTCAACGTATCATTACTTCGTCCGAGTCTCCTCAGGAGGTCGAAGTTGGCAAGGATATCATATTTACTTACGATGTGGATTTCAAGgtcagaactatgtttgattctttttg-------tattccaaataagtgattgtagtagctgtag--tactaagtgtcctataagtggagcatgaatattgtgtt-ttgctcat---ttctgagaacta--ctgtaaatttgtag
 ||||| ||||||||  ||| ||| ||||| || || || ||||| |||||||| ||||||||||| || || ||||||||||| ||||||||||||||||| |||  |||||    || |||  |       |  || ||  || |||| | |||||||  |   |  | ||||| |  ||  |||||    |||||| ||||       ||   | ||    ||||  |||| |||||| ||
TTGTGATCCTCATGCAAAACATATAATTACATCATCTGATTCTCCCCAGGAGGTTGAAGTTGGCAAAGACATAATATTTACTTATGATGTGGATTTCAAGgtgagatatatgtgcacttttttccgatcgttctgctctaatgaaatgatcgcagtagctagaaattgttcagtgtgcactagatggagtgctaatattttgttaccatctatgcgtccttttgactattctgtcaatttgcag

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|148999936|gb|EE036993.2|EE036993

EST:     AGGTCGAAGTTGGCAAGGATATCATATTTACTTACGATGTGGATTTCAAG                         GAGAGCGACATCAAGTGGGCATCTCGGTGGGACAGCTATCTATTGATGACA
genomic: AGGTCGAAGTTGGCAAGGATATCATATTTACTTACGATGTGGATTTCAAGgtcagaacta ... aaatttgtagGAGAGCGACATCAAGTGGGCATCTCGGTGGGACAGCTATCTATTGATGACA

EST: gi|109637563|gb|EC591108.1|EC591108

EST:     AGGTCGAAGTTGGCAAGGATATCATATTTACTTACGATGTGGATTTCAAG                         GAGAGCGACATCAAGTGGGCATCTCGGTGGGACAGCTATCTATTGATGACA
genomic: AGGTCGAAGTTGGCAAGGATATCATATTTACTTACGATGTGGATTTCAAGgtcagaacta ... aaatttgtagGAGAGCGACATCAAGTGGGCATCTCGGTGGGACAGCTATCTATTGATGACA

EST: gi|149023680|gb|EE045933.2|EE045933

EST:     GGTCGAAGTTGGCAAGGATATCATATTTACTTACGATGTGGATTTTCA-G                         GAGAGCGACATCAAGTGGGCATCTCG
genomic: GGTCGAAGTTGGCAAGGATATCATATTTACTTACGATGTGGATTT-CAAGgtcagaacta ... aaatttgtagGAGAGCGACATCAAGTGGGCATCTCG

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: 386

GTGTGACCCTCATGCTCAACGTATCATTACTTCGTCCGAGTCTCCTCAGGAGGTCGAAGTTGGCAAGGATATCATATTTACTTACGATGTGGATTTCAAGgtcagaacta ... aaatttgtagGAGAGCGACATCAAGTGGGCATCTCGGTGGGACAGCTATCTATTGATGACAGATGATCAGATCCACTGGTTCTCTATTGTGAATTCTCTCATGATTGTTC

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 632

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 723