ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GTGGTCTGCTGAGTTTGGAACATCAAGAAATGGTTCTTCTGAGCTTCACGTTATGTTAGCAGAATACATATATTCGGAATCTCCAGAGACGgtaacttgctataattcattgtctcataagaatgtggatgtcttctatgtggaagctgcagtttttttgagtcactactgttgttactagtttatttactgcttttatgattttgctccaaggtttaatgtttagtaccttgactgcag

Basic information

species	Zea mays
transcript	GRMZM2G048804_T02
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G048804_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g07100.1 (Oryza sativa), 5'ss of exon 6

GTGGTCTGCTGAGTTTGGAACATCAAGAAATGGTTCTTCTGAGCTTCACGTTATGTTAGCAGAATACATATATTCGGAATCTCCAGAGACGgtaacttgctataattcattg---tctcataagaatgtggatgtcttctatgtg----gaagctgcagtttttttgagtcactactgttgttactagtttatttactgcttttatgattttgctccaaggtttaatgtttagtaccttgactgcag
||||||||||||| ||||  ||||||||| ||| ||| ||||||| || |||||||| || |||||||||||||| ||||||||||| |||||| ||   ||||| | || |   | |  |    |  || || | || | | ||      ||||| | |||| |   |||  | |   |||||||      |||| ||| ||| || |||    | |||                           
GTGGTCTGCTGAGGTTGGGGCATCAAGAAGTGGATCTCCTGAGCTGCATGTTATGTTGGCGGAATACATATATTCTGAATCTCCAGAAACGgta-ctgtttataaattatagaactatttttctgacatgaatatattgtgtttgttttagagctgaaattttat---gtcttttcaactgttactc-----tttaatgcctttgtggtttg---ctaag---------------------------

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|33771157|gb|CF272818.1|CF272818

EST:     AGCTTCACGTTATGTTAGCAGAATACATATATTCGGAATCTCCAGAGACG                         GACATGGCTAAAGTCTCAAGTCATTTTGTTCGTGGAAATGATCCAAAAAAG
genomic: AGCTTCACGTTATGTTAGCAGAATACATATATTCGGAATCTCCAGAGACGgtaacttgct ... ttgactgcagGACATGACTAAAGTCTCAAGTCATTTTGTTCGTGGAAATGATCCAAAAAAG

EST: gi|71773197|gb|DR971110.1|DR971110

EST:     AGCTTCACGTTATGTTAGCAGAATACATATATTCGGAATCTCCAGAGACG                         GACATGACTAAAGTCTCAAGTCATTTTGTTCGTGGAAATGATCCAAAAAAG
genomic: AGCTTCACGTTATGTTAGCAGAATACATATATTCGGAATCTCCAGAGACGgtaacttgct ... ttgactgcagGACATGACTAAAGTCTCAAGTCATTTTGTTCGTGGAAATGATCCAAAAAAG

EST: gi|33467112|gb|CF244161.1|CF244161

EST:     AGCTTCACGTTATGTTAGCAGAATACATATATTCGGAATCTCCAGAGACG                         GACATGACTAAAGTCTCAAGTCATTTT
genomic: AGCTTCACGTTATGTTAGCAGAATACATATATTCGGAATCTCCAGAGACGgtaacttgct ... ttgactgcagGACATGACTAAAGTCTCAAGTCATTTT

EST: gi|113704317|gb|EE681821.1|EE681821

EST:     TTAGCAGAATACATATATTCGGAATTTCCAGAGACG                         GACATGATTAAAGTCTCAAGTTCATTTTGTTCGTGGAAATGATCCAAAAAA
genomic: TTAGCAGAATACATATATTCGGAATCTCCAGAGACGgtaacttgct ... ttgactgcagGACATGACTAAAGTCTCAAG-TCATTTTGTTCGTGGAAATGATCCAAAAAA

EST: gi|74236760|gb|DT644674.1|DT644674

EST:     AGCTTCACGTTATGTTAGCAGAATACATATATTCGGAATCTCCAGAGACG                         GACATGACTAAAGTCTCAAGTCATTTTGTTCGTGGAAATGATCCAAAAAAG
genomic: AGCTTCACGTTATGTTAGCAGAATACATATATTCGGAATCTCCAGAGACGgtaacttgct ... ttgactgcagGACATGACTAAAGTCTCAAGTCATTTTGTTCGTGGAAATGATCCAAAAAAG

EST: gi|32911197|gb|CF016009.1|CF016009

EST:     AGCTTCACGTTATGTTAGCAGAATACATATATTCGGAATCTCCAGAGACG                         GACATGACTAAAGTCTCAAGTCATTTTGTTCGTGGAAATGATCCAAAAAAG
genomic: AGCTTCACGTTATGTTAGCAGAATACATATATTCGGAATCTCCAGAGACGgtaacttgct ... ttgactgcagGACATGACTAAAGTCTCAAGTCATTTTGTTCGTGGAAATGATCCAAAAAAG

EST: gi|31349428|gb|CD433785.1|CD433785

EST:     AGCTTCACGTTATGTTAGCAGAATACATATATTCGGAATCTCCAGAGACG                         GACATGACTAAAGTCTCAAGTCATTTTGTTCGTGGAAATGATCCAAAAAAG
genomic: AGCTTCACGTTATGTTAGCAGAATACATATATTCGGAATCTCCAGAGACGgtaacttgct ... ttgactgcagGACATGACTAAAGTCTCAAGTCATTTTGTTCGTGGAAATGATCCAAAAAAG

EST: gi|32850448|gb|CD990129.1|CD990129

EST:     AGCTTCACGTTATGTTAGCAGAATACATATATTCGGAATCTCCAGAGACG                         GACATGACTAAAGTCTCAAGTCATTTTGTTCGTGGAAATGATCCAAAAAAG
genomic: AGCTTCACGTTATGTTAGCAGAATACATATATTCGGAATCTCCAGAGACGgtaacttgct ... ttgactgcagGACATGACTAAAGTCTCAAGTCATTTTGTTCGTGGAAATGATCCAAAAAAG

EST: gi|74236761|gb|DT644675.1|DT644675

EST:     AGCTTCACGTTATGTTAGCAGAATACATATATTCGGAATCTCCAGAGACG                         GACATGACTAAAGTCTCAAGTCATTTTGTTCGTGGAAATGATCCAAAAAAG
genomic: AGCTTCACGTTATGTTAGCAGAATACATATATTCGGAATCTCCAGAGACGgtaacttgct ... ttgactgcagGACATGACTAAAGTCTCAAGTCATTTTGTTCGTGGAAATGATCCAAAAAAG

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), 46 (downstream exon)
Score: 46

GTGGTCTGCTGAGTTTGGAACATCAAGAAATGGTTCTTCTGAGCTTCACGTTATGTTAGCAGAATACATATATTCGGAATCTCCAGAGACGgtaacttgct ... ttgactgcagGACATGACTAAAGTCTCAAGTCATTTTGTTCGTGGAAATGATCCAAAAAAGTTCGCTTCTATGCTGGTGAACTTTATGGGCAAG

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 100

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 87