ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TTTATCACTGTTTCTTCTATTCAAGTTTCTCTCAAAAGACTTGGTCAACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCGTAGgttcattttttttttcttgtaacagctttttcagacatgttaagctgtttagttgctctacttatgagtaccgttttatgcag

Basic information

species	Zea mays
transcript	GRMZM2G150251_T02
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G150251_T02 (Zea mays), 5'ss of exon 4
lower sequence: AT2G03120.1 (Arabidopsis thaliana), 5'ss of exon 3

----TTTATCACTGTTTCTTCTATTCAAGTTTCTCTCAAAAGACTTGGTCAACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCGTAGgttcattttttttttcttgtaacagctttttcagacatgttaagctgtttagttgctctact-tatgagtaccgttttatgcag
    | | ||||| ||  |  | ||||||||||||||||| |||||||| || |||||||| || || ||||| ||  |||| || ||||| ||||| ||||| ||   || | |   || ||       |||||   |  |||| | ||||   ||      |    | |  ||    | | |||||
TGCTTCTCTCACTTTTCTTATTGTTCAAGTTTCTCTCAAAGGACTTGGTTAATGCTGTGCTAACAGCTTACTTCTTTGTTCTTGGGATTGTCGCTCTTTCgtatgtc--ttatctaaatcatgccttttgttttttt-atttgtttatctgt--ggtcaagtcatgacacggttatgtgtgtttgcag

upper sequence: GRMZM2G150251_T02 (Zea mays), 5'ss of exon 4
lower sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 4

----TTTATCACTGTTTCTTCTATTCAAGTTTCTCTCAAAAGACTTGGTCAACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCGTAGgttcattttttttttcttgtaacagctttttcag-acatgtta-agctgtttag---ttgctctactta--tgagtaccgttttatgcag-----------------------
     |||||||| || ||||| ||||||||||| |||||||||||||| || ||||| || ||   |||||| ||  | || || ||  | ||||| ||||| |||| ||   | |   |  |   |   |  | |  |  || || |  | |||||   | | |  |  |   |  || |  | |    ||                        
TGCTGTTATCACTATTCCTTCTCTTCAAGTTTCTATCAAAAGACTTGGTTAATGCTGTACTGACATGCTACTTCTTTGTGCTTGGGATCATCGCTCTTTCgtatgttctttccgtatggatcatgctactatgcttaatatttgatataattatttagaaatagtttcatgtggtttggttcattatctcacattatctttcttctattttctgtag

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|60353103|gb|DN220076.1|DN220076

EST:     CTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTC----                         TGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
genomic: CTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCGTAGgttcattttt ... ttttatgcagTGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA

EST: gi|60349110|gb|DN216083.1|DN216083

EST:     CTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTC-T-G                         --CAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
genomic: CTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCGTAGgttcattttt ... ttttatgcagTGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA

EST: gi|76020573|gb|DT947743.1|DT947743

EST:     CTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTC-T-G                         --CAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
genomic: CTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCGTAGgttcattttt ... ttttatgcagTGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA

EST: gi|32837706|gb|CD977384.1|CD977384

EST:     TGTGCTCACTGCCTACTTTTTCATTCTAGGCA-TGNTTGCTCTCTCGTAG                         TGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
genomic: TGTGCTCACTGCCTACTTTTTCATTCTAGGCATTG-TTGCTCTCTCGTAGgttcattttt ... ttttatgcagTGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA

EST: gi|76282341|gb|DV021909.1|DV021909

EST:     CTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTC-T-G                         --CAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
genomic: CTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCGTAGgttcattttt ... ttttatgcagTGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA

EST: gi|211138912|gb|FK978960.1|FK978960

EST:     CTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTC-T-G                         --CAACACTGCTTCCTTCTATAAAAC
genomic: CTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCGTAGgttcattttt ... ttttatgcagTGCAACACTGCTTCCTTCTATAAAAC

EST: gi|30031840|gb|CB833691.1|CB833691

EST:     CTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTC-T-G                         --CAACACTGCTTCCTTCTATAAA
genomic: CTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCGTAGgttcattttt ... ttttatgcagTGCAACACTGCTTCCTTCTATAAA

EST: gi|93282675|gb|EB674939.1|EB674939

EST:     CTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTC-T-G                         --CAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
genomic: CTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCGTAGgttcattttt ... ttttatgcagTGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA

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), 47 (downstream exon)
Score: 114

TTTATCACTGTTTCTTCTATTCAAGTTTCTCTCAAAAGACTTGGTCAACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCGTAGgttcattttt ... ttttatgcagTGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGATAATCTCATTGTCTGGCGTGCTCCACTTTTCCACT

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 38

Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 78