ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

AGTTGTCCATGTCAATGGGAAGGCCTTGGACAAAGCTGCTAAAGTCACCTTGATCGGTGGTGATGAAGTCATGTTTGTTTCTCTTGGGACACATGCTTATgtatcctttcctaccaccagctactttcttctgtgcttctctgaaatctatttcccttgttggaagtttgctgttaatattcttgatggcatacaagcatccatttggatacgaaattccttaatgtgctggcag

Basic information

species	Zea mays
transcript	GRMZM2G157621_T03
intron #	5
splice site	5'
intron type	U12 (go to U12 genes for details)

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G157621_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os07g47530.2 (Oryza sativa), 5'ss of exon 5

AGTTGTCCATGTCAATGGGAAGGCCTTGGACAAAGCTGCTAAAGTCACCTTGATCGGTGGTGATGAAGTCATGTTTGTTTCTCTTGGGACACATGCTTATgtatcctttcctaccaccagctactttcttctgtgcttctctgaaatctatttcccttgttggaagtttgctgttaatattcttgatgg--catacaagcatccat-ttggatacgaaattccttaatgtgctggcag
|| ||||||||| ||||||||||  || || ||  ||||||| ||||| ||| | || || |||||||| || |||  ||| ||||||| ||||||||||||||||||||  | ||||| ||||  |    |  |  |  ||   |      ||  ||            |   |||| |  ||||| |  || | ||| ||  || ||| ||| |||  |||||||  || | ||||
AGCTGTCCATGTAAATGGGAAGGTATTAGATAAGACTGCTAAGGTCACATTGGTTGGAGGCGATGAAGTTATTTTTAGTTCACTTGGGAGACATGCTTATgtatcctttc--atcaccaactacccttgcataagtgttgcttgtactggcatctgtt------------ccactaatgtaattgattgttcagaaaagtattaatgttgtatatgaagctccttaacatgttcgcag

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|76287386|gb|DV026954.1|DV026954

EST:     TGATCGGTGGTGATGAAGTCATGTTTGTTTCTCTTGGGACACATGCTTAT                         ATATTTCAGCAACTTCTAGAGGAAAAAGCAAGCACACCATCTTT
genomic: TGATCGGTGGTGATGAAGTCATGTTTGTTTCTCTTGGGACACATGCTTATgtatcctttc ... gtgctggcagATATTTCAGCAACTTCTAGAGGAAAAAGCAAGCACACCATCTTT

EST: gi|30705777|gb|CD058918.1|CD058918

EST:     TGATCGGTGGTGATGAAGTCATGTTTGTTTCTCTTGGGACACATGCTTAT                         ATATTTCAGCAACTTCTAGAGGAAAA
genomic: TGATCGGTGGTGATGAAGTCATGTTTGTTTCTCTTGGGACACATGCTTATgtatcctttc ... gtgctggcagATATTTCAGCAACTTCTAGAGGAAAA

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), 49 (downstream exon)
Score: 190

AGTTGTCCATGTCAATGGGAAGGCCTTGGACAAAGCTGCTAAAGTCACCTTGATCGGTGGTGATGAAGTCATGTTTGTTTCTCTTGGGACACATGCTTATgtatcctttc ... gtgctggcagATATTTCAGCAACTTCTAGAGGAAAAAGCAAGCACACCATCTTTGTGTTCAAAATGTGTCATTCAACAAGAACAATATCCAGTTGTCAAAG

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 101

Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 126