ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CTGTGCCTCAATTCATTTGATAAAGAAGCAGATCTTGATGTCCTGAACCATCCAATCCTGAACTTCCTCTATTACCTGgtatgaatcctgacggtgtaaaatggtttaccttagattttttttgtaaccaagtggcatttagattttgaaatatcgacttgatcacttctaggaaggc...

Basic information

species	Zea mays
transcript	GRMZM2G003076_T03
intron #	10
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G003076_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os10g39220.1 (Oryza sativa), 5'ss of exon 10

CTGTGCCTCAATTCATTTGATAAAGAAGCAGATCTTGATGTCCTGAACCATCCAATCCTGAACTTCCTCTATTACCTGgtatg-----aatcctgacggtgtaaaatggtttaccttagattttttttgtaaccaagtggcatttagattttgaaatatcgacttgatcacttctaggaaggc
 |||| |||||  |||||||||||| ||| || |||||||| ||||||||||| || ||||| ||| | |||||| |||||||     | || |     |   |  |||| | | || | |  ||| | |   |||      || ||  ||  |  |||  | |  || ||||     ||   
ATGTGTCTCAACACATTTGATAAAGCAGCTGACCTTGATGTTCTGAACCATCCGATTCTGAATTTCTTTTATTACTTGgtatgtcttgattcatttatttcctacttggtatgcttttgttcgtttatattgtcaaa--atgttaagcattcaacttatgcagt--atgacttacgacaact-

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|18166177|gb|BM336016.1|BM336016

EST:     CAGATCTTGATGTCCTGAACCATCCAATCCTGAACTTCCTCTATTACCTG                         CTGGTTGAGATAGTGCCTTCGGCTCTGGTGCTCTTCATTCTACGGAAACTG
genomic: CAGATCTTGATGTCCTGAACCATCCAATCCTGAACTTCCTCTATTACCTGgtatgaatcc ... gcgactgcagCTGGTTGAGATAGTGCCTTCGGCTCTGGTGCTCTTCATTCTACGGAAACTG

EST: gi|16920930|gb|BM074899.1|BM074899

EST:     CAGATCTTGATGTCCTGAACCATCCAATCCTGAACTTCCTCTATTACCTG                         CTGGTTGAGATAGTGCCTTCGGCTCTGGTGCTCTTCATTCTACGGAAACTG
genomic: CAGATCTTGATGTCCTGAACCATCCAATCCTGAACTTCCTCTATTACCTGgtatgaatcc ... gcgactgcagCTGGTTGAGATAGTGCCTTCGGCTCTGGTGCTCTTCATTCTACGGAAACTG

EST: gi|18163841|gb|BM333680.1|BM333680

EST:     CAGATCTTGATGTCCTGAACCATCCAATCCTGAACTTCCTCTATTACCTG                         CTGGTTGAGATAGTGCCTTCGGCTCTGGTGCTCTTCATTCTACGGAAACTG
genomic: CAGATCTTGATGTCCTGAACCATCCAATCCTGAACTTCCTCTATTACCTGgtatgaatcc ... gcgactgcagCTGGTTGAGATAGTGCCTTCGGCTCTGGTGCTCTTCATTCTACGGAAACTG

EST: gi|71319323|gb|DR796414.1|DR796414

EST:     CAGATCTTGATGTCCTGAACCATCCAATCCTGAACTTCCTCTATTACCTG                         CTGGTTGAGATAGTGCCTTCGGCTCTGGTGCTCTTCATTCTACGGAAACTG
genomic: CAGATCTTGATGTCCTGAACCATCCAATCCTGAACTTCCTCTATTACCTGgtatgaatcc ... gcgactgcagCTGGTTGAGATAGTGCCTTCGGCTCTGGTGCTCTTCATTCTACGGAAACTG

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: 39 (upstream exon), 49 (downstream exon)
Score: 31

CTGTGCCTCAATTCATTTGATAAAGAAGCAGATCTTGATGTCCTGAACCATCCAATCCTGAACTTCCTCTATTACCTGgtatgaatcc ... gcgactgcagCTGGTTGAGATAGTGCCTTCGGCTCTGGTGCTCTTCATTCTACGGAAACTGCCTCCAAAACGTGGGATCACACAATATCACCCAATCCATTAGAGAGCAG

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 110

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 147