ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gtacgtatgttttttgtgttataactgcaaagatagagcaattaccatccagatggtcattgtacggttttgatgtgataactcaccatgttcttaatttctactttattccaaagGTTAAACTGAGGGAAATGAAGCCAGGCATGCTGTCTCGTGAGCTTAAAGATGCTCTTGGTATGCCTGATGGCGCCCCTCCCCCATGGCTTATAAACATGC

Basic information

species	Zea mays
transcript	GRMZM2G132060_T01
intron #	7
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G132060_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA13G25110.2 (Glycine max), 3'ss of exon 8

gtacgtatgttttttgtgttataactgcaaagatagagcaattaccatccagatggtcattgtacggttttgatgtgataactcaccatgttcttaatttctactttattccaaagGTTAAACTGAGGGAAATGAAGCCAGGCATGCTGTCTCGTGAGCTTAAAGATGCTCTTGGTATGCCTGATGGCGCCCCTCCCCCATGGCTTATAAACATGC
          ||||  |   ||   | |   |||  ||  |  |   || ||||  |||  | ||  | |  | || ||||||     | || ||| ||| ||   |  |    |||| ||  |||| || ||||| || |||||| | || | |||  | ||||| ||||||||||||||||| || || ||||| ||||||||||| || ||||
----------ttttgctaagatgtttcccttgatctagtta--agtgtcaagattatca--gcacc-tataaaagttataacttggt-tcttattattttatataatgctgttcagGTAAAGTTGAGAGAGATGAAACCTGGCATGTTATCACATGAATTAAAAGAAGCTCTTGGTATGCCTGAGGGTGCTCCTCCACCATGGCTTATTAATATGC

upper sequence: GRMZM2G132060_T02 (Zea mays), 3'ss of exon 7
lower sequence: AT4G21660.1 (Arabidopsis thaliana), 3'ss of exon 7

gtacgtatgttttttgtgttataactgcaaagatagagcaattaccatccagatggtcattgtacggttttgatgtgataactcaccatgttcttaatttctactttattccaaa--gGTTAAACTGAGGGAAATGAAGCCAGGCATGCTGTCTCGTGAGCTTAAAGATGCTCTTGGTATGCCTGATGGCGCCCCTCCCCCATGGCTTATAAACATGC
    |||  ||  |||||  ||   |    || |  | | || |  |          |||||   |||||   || | |   | |||       ||||| |||   | |   |||  ||||||||||||||||| ||| |||||  |  ||||    ||  | ||||| ||||||||||||||||| ||||| |||||||||||||| || |||||||
----gta-attccttgtgacatgttttttcagctttatctataatta----------cattgcttggtttcattg-gtttgtttacctaaaatctaattactatcatttgggaaatagGTTAAACTGAGGGAAACGAAACCAGGGTTTTTGTCAAACGACTTAAAAGAAGCTCTTGGTATGCCTGAAGGCGCTCCTCCCCCATGGCTGATTAACATGC

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|13382081|gb|BG458756.1|BG458756

EST:     CCAAGCTGTCTAGTCATGGTGATCTGTATTATGAAGGCAAAGAATTTGAG                         GTTAAACTGAGGGAAATGAAGCC
genomic: CCAAGCTGTCTAGTCATGGTGATCTGTATTATGAAGGCAAAGAATTTGAGgtacgtatgt ... tattccaaagGTTAAACTGAGGGAAATGAAGCC

EST: gi|21843267|gb|BQ703848.1|BQ703848

EST:     CCAAGCTGTCTAGTCATGGTGATCTGTATTATGAAGGCAAAGAATTTGAG                         GTTAAACTGAGGGAAATGAAGCCAGGCATGCTGTCTCGNGAGCTTAAAGAT
genomic: CCAAGCTGTCTAGTCATGGTGATCTGTATTATGAAGGCAAAGAATTTGAGgtacgtatgt ... tattccaaagGTTAAACTGAGGGAAATGAAGCCAGGCATGCTGTCTCGTGAGCTTAAAGAT

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: 49 (upstream exon), 49 (downstream exon)
Score: 561

GTTTTGCATGACGCGTTCTTCAAATATCAGACAAAACCCAAGCTGTCTAGTCATGGTGATCTGTATTATGAAGGCAAAGAATTTGAGgtacgtatgt ... tattccaaagGTTAAACTGAGGGAAATGAAGCCAGGCATGCTGTCTCGTGAGCTTAAAGATGCTCTTGGTATGCCTGATGGCGCCCCTCCCCCATGGCTTATAAACATGC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 358

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 463

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 337

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gtacggttttgatgtgataactcaccatgttcttaatttctactttattccaaagGTTAAACTGAGGGAAATGAAGCCAGGCATGCTGTCTCGTGAGCTTAAAGATGCTCTTGGTATGCCTGATGGCGCCCCTCCCCCATGGCTTATAAACATGC