ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GAGGAGGCGGCGGAGGCCTTCTTCCGCGCGGCGCCGCCGCTCCGTGACCGCGACCGTCTCGCCGCCAGCCTCGCCGATTTCCTCGCCCGCCACTCCGCCGgcaagtgatccccgatcctccgcttctctccctccctgctctcatctctgtccggctccgggctgggtggctgaaagcctgaaacgaaaaccagatttctgacgcggctgctcctgtcgccaccgatcgcgtgctgcag

Basic information

species	Zea mays
transcript	GRMZM2G008209_T03
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G008209_T03 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os08g07880.1 (Oryza sativa), 5'ss of exon 2

---GAGGAGGCGGCGGAGGCCTTCTTCCGCGCGGCGCCGCCGCTCCGTGACCGCGACCGTCTCGCCGCCAGCCTCGCCGATTTCCTCGCCCGCCACTCCGCCG-
   |  |  | ||||||| ||||||||||||| |||||||||||||| ||||  |||||  ||||||    ||||||||| ||| ||||||||||||||| |  |    |  |||||   ||||| | |  |  |  | | | |||||||||  | ||   |   ||  ||||| |||        | |   | |  | ||  ||  | ||  |                             
GGCGGCGGCGAGGCGGAGTCCTTCTTCCGCGCCGCGCCGCCGCTCCGCGACCAGGACCGCGTCGCCGGGGACCTCGCCGACTTCGTCGCCCGCCACTCCGgcaagtccctcctcccctcgcctcctccttccctctcctccgatctcatctcc-ttcgatgcgtcgcgtggtgggtgagtttgctgatctcgatcgtgtttggtggtg-ggtag-----------------------------

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|91875001|gb|EB404958.1|EB404958

EST:     CGACCGTCTCGCCGCCAGCCTCGCCGATTTCCTCGCCCGCCACTCCGCCG                         GGGGTGGTGGAGTGGTGTGCGTCACCTCCGGCGGCACTACGGTGCCCCTGG
genomic: CGACCGTCTCGCCGCCAGCCTCGCCGATTTCCTCGCCCGCCACTCCGCCGgcaagtgatc ... cgtgctgcagGGGGTGGTGGAGTGGTGTGCGTCACCTCCGGCGGCACTACGGTGCCCCTGG

EST: gi|74243666|gb|DT651580.1|DT651580

EST:     CGACCGTCTCGCCGCCAGCCTCGCCGATTTCCTCGCCCGCCACTCCGCCG                         GGGGTGGTGGAGTGGTGTGCGTCACCTCCGGCGGCACTACGGTGCCCCTGG
genomic: CGACCGTCTCGCCGCCAGCCTCGCCGATTTCCTCGCCCGCCACTCCGCCGgcaagtgatc ... cgtgctgcagGGGGTGGTGGAGTGGTGTGCGTCACCTCCGGCGGCACTACGGTGCCCCTGG

EST: gi|211537797|gb|FL107886.1|FL107886

EST:     CGACCGTCTCGCCGCCAGCCTCGCCGATTTCCTCGCCCGCCACTCAGCCG                         GGGGTGGTGGGAGTGGTGT
genomic: CGACCGTCTCGCCGCCAGCCTCGCCGATTTCCTCGCCCGCCACTCCGCCGgcaagtgatc ... cgtgctgcagGGGGTGGTGG-AGTGGTGT

EST: gi|211537799|gb|FL107888.1|FL107888

EST:     CGACCGTCTCGCCGCNNGCCTCGCCGATTTCCTCGCCCGCCACTCAGCCG                         GGGGTGGTGGAGTGGTGTGCGTCACCTCCGGCGGCACTACGGTG-CCCTGG
genomic: CGACCGTCTCGCCGCCAGCCTCGCCGATTTCCTCGCCCGCCACTCCGCCGgcaagtgatc ... cgtgctgcagGGGGTGGTGGAGTGGTGTGCGTCACCTCCGGCGGCACTACGGTGCCCCTGG

EST: gi|78110995|gb|DV529392.1|DV529392

EST:     CGACCGTCTCGCCGCCAGCCTCGCCGATTTCCTCGCCCGCCACTCCGCCG                         GGGGTGGTGGAGTGGTGTGCGTCACCTCCGGCGGCACTACGGTGCCCCTGG
genomic: CGACCGTCTCGCCGCCAGCCTCGCCGATTTCCTCGCCCGCCACTCCGCCGgcaagtgatc ... cgtgctgcagGGGGTGGTGGAGTGGTGTGCGTCACCTCCGGCGGCACTACGGTGCCCCTGG

EST: gi|91871996|gb|EB401953.1|EB401953

EST:     CGACCGTCTCGCCGCCAGCCTCGCCGATTTCCTCGCCCGCCACTCCGCCG                         GGGGTGGTGGAGTGGTGTGCGTCACCTCCGGCGGCACTACGGTGCCCCTGG
genomic: CGACCGTCTCGCCGCCAGCCTCGCCGATTTCCTCGCCCGCCACTCCGCCGgcaagtgatc ... cgtgctgcagGGGGTGGTGGAGTGGTGTGCGTCACCTCCGGCGGCACTACGGTGCCCCTGG

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: 41 (upstream exon), 47 (downstream exon)
Score: 6

GAGGAGGCGGCGGAGGCCTTCTTCCGCGCGGCGCCGCCGCTCCGTGACCGCGACCGTCTCGCCGCCAGCCTCGCCGATTTCCTCGCCCGCCACTCCGCCGgcaagtgatc ... cgtgctgcagGGGGTGGTGGAGTGGTGTGCGTCACCTCCGGCGGCACTACGGTGCCCCTGGAGCAGCGTTGCGTGCGCTACATCGACAATTTTAGCTCCGGCCAGCGCGG

Block sizes: 45 (upstream exon), 21 (downstream exon)
Score: 2

Block sizes: 39 (upstream exon), 46 (downstream exon)
Score: 8