ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaagttaatgaataggattatgcagtgtgtgcttcatgatctatatactgctacatcatatgttatattgcttgtacagGAGTATAACGCAAAGCTCTCTGATTTTGGGCTTGCGAAAGACGGACCTGTAGGTGATAAAACTCATGTTTCTACTCGAGTAATGGGAACCTATGGATATG

Basic information

species	Zea mays
transcript	GRMZM2G132184_T02
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G132184_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 4

-------gtaagttaatgaataggattatgcagtgtgtgcttcatgatctatatactgctacatcatatgttatattgcttgtacagGAGTATAACGCAAAGCTCTCTGATTTTGGGCTTGCGAAAGACGGACCTGTAGGTGATAAAACTCATGTTTCTACTCGAGTAATGGGAACCTATGGATATG
        |||||   ||||| |||||| | | ||    |  || |||  | ||  ||  |  |  ||| ||||  | ||  | ||||| || || ||||| ||||| |||||||||||||| ||||| || ||||||||||| |||||||| || |||||||||||||||||||| ||||| ||||
gtaagttttaagtccttgaattggattacgtattgcacaccacacgattcacatcttgtaattttgtatattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG

upper sequence: GRMZM2G132184_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G02570.1 (Glycine max), 3'ss of exon 4

gtaagttaatgaataggattatgcagtgtgtgcttcatgatctatatactgctacatcatatgttatattgcttgtacagGAGTATAACGCAAAGCTCTCTGATTTTGGGCTTGCGAAAGACGGACCTGTAGGTGATAAAACTCATGTTTCTACTCGAGTAATGGGAACCTATGGATATG
    || | ||   |  | ||      |  ||| |      || | ||    |  |    || || ||  | ||   |||||||| || || |||||||| |||||||| ||||| ||||| || || | |||||||||||| ||||| ||||||||||| |||||||||||||| ||||
----gtaagtgtcaaaaactacaataagattgcatttccccctttttatcagtcta----atattgtaccgatt---cagGAGTACAATGCCAAGCTCTCAGATTTTGGTCTTGCCAAAGATGGTCCAGAAGGTGATAAAACCCATGTGTCTACTCGAGTGATGGGAACCTATGGTTATG

upper sequence: GRMZM2G132184_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA18G16300.1 (Glycine max), 3'ss of exon 5

gtaagt-taatgaataggattatgcagtgtgtgcttcatgatctatatactgctacatcatatgttatattgcttgtacagGAGTATAACGCAAAGCTCTCTGATTTTGGGCTTGCGAAAGACGGACCTGTAGGTGATAAAACTCATGTTTCTACTCGAGTAATGGGAACCTATGGATATG
||||||   |    |   |||||  |   | |   |  | ||   |  | |  |   | |||| ||||  |   | | ||||| || || || |||||||| || ||||| ||||| ||||| || || |  ||||||||||||||||| ||||||||||| |||||||||||||| ||||
gtaagtgccaaattttaaattat-taccatttttcttttcattccttgatt--tgatttatatattattataactattcagGAATACAATGCTAAGCTCTCAGACTTTGGACTTGCAAAAGATGGTCCAGAGGGTGATAAAACTCATGTGTCTACTCGAGTGATGGGAACCTATGGTTATG

upper sequence: GRMZM2G132184_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G40770.1 (Glycine max), 3'ss of exon 4

gtaagttaatgaata--ggattatgcagtgtgtgcttcatgatctatatactgctacatcatatgttatattgcttgtacagGAGTATAACGCAAAGCTCTCTGATTTTGGGCTTGCGAAAGACGGACCTGTAGGTGATAAAACTCATGTTTCTACTCGAGTAATGGGAACCTATGGATATG
||||||     |||      ||||  |   | |   |  | ||   |  | |  |      ||| ||||  |     | ||||| || ||  | |||||||| |||||||| ||||| ||||| || || |  ||||||||||| ||||| ||||||||||| |||||||||||||| ||||
gtaagtggccaaatgttaagttat-taccatctttcttttcattccttgatt--tgatctttatattattataacaattcagGAATACAATTCTAAGCTCTCAGATTTTGGACTTGCAAAAGATGGTCCAGAGGGTGATAAAACCCATGTGTCTACTCGAGTGATGGGAACCTATGGTTATG

upper sequence: GRMZM2G132184_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA01G04930.1 (Glycine max), 3'ss of exon 4

gtaagttaatgaataggattatgcagtgtgtgcttcatgatctatatactgctacatcatatgttatattgcttgtacagGAGTATAACGCAAAGCTCTCTGATTTTGGGCTTGCGAAAGACGGACCTGTAGGTGATAAAACTCATGTTTCTACTCGAGTAATGGGAACCTATGGATATG
    || | ||      | ||      |  ||| | ||   ||   |  || ||  ||  || ||       ||   ||||| || || || |||||||| || ||||| ||||| ||||| || || | |||||||||||| ||||| |||||||| || |||||||||||||| || |
----gtaagtgcccgaaactacaataagattgcat-atttcctcctttttgtta-gtctaatattgccccaatt---cagGACTACAATGCCAAGCTCTCAGACTTTGGTCTTGCCAAAGATGGTCCAGAAGGTGATAAAACCCATGTGTCTACTCGGGTGATGGGAACCTATGGTTACG

upper sequence: GRMZM2G132184_T03 (Zea mays), 3'ss of exon 4
lower sequence: AT3G28690.1 (Arabidopsis thaliana), 3'ss of exon 3

--------gtaagttaatgaataggattatgcagtgtgtgcttcatgatctatatactgctacatcatatgttatattgcttgta---cagGAGTATAACGCAAAGCTCTCTGATTTTGGGCTTGCGAAAGACGGACCTGTAGGTGATAAAACTCATGTTTCTACTCGAGTAATGGGAACCTATGGATATG
        | |||  | | ||   ||| |       | || | | |  ||| |||  |  || ||  ||    | | ||||   |   ||||| ||||| |||||||||||||||||||||||||| ||||| |  || |  |   | ||| | || || || || ||||| |||||||| ||||| ||||
gtatgtctgaaagccacttaacccgataacctcaactctg-tcctttctctctatgtttataaattttagaaaaaaatgctcccattgcagGAATATAATGCAAAGCTCTCTGATTTTGGGCTTGCAAAAGATGCTCCAGACGAGAAAAAATCCCACGTATCAACCCGAGTCATGGGAACTTATGGTTATG

upper sequence: GRMZM2G132184_T03 (Zea mays), 3'ss of exon 4
lower sequence: Vv01s0026g01620.t01 (Vitis vinifera), 3'ss of exon 4

gtaagttaatgaataggattatgcagtgtgtgcttcatgatctatatactgctacatcatatgttatattgcttgtacagGAGTATAACGCAAAGCTCTCTGATTTTGGGCTTGCGAAAGACGGACCTGTAGGTGATAAAACTCATGTTTCTACTCGAGTAATGGGAACCTATGGATATG
|||||| ||| || |   | ||  | |    | ||        ||||  | | |  |  ||| | | ||  ||  | |||||||| || || || || ||||||||||| ||||| ||||| || || |  || ||||| |||||||| ||||| || || |||||||| ||||||||||
gtaagt-aataaaaactgtgata-aattcacgtttgtctcctaatatcattccatcttttatatgacatc-ctatttcagGAGTACAATGCCAAACTTTCTGATTTTGGACTTGCTAAAGATGGTCCCGAGGGAGATAAGACTCATGTATCTACCCGTGTTATGGGAACTTATGGATATG

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|76282950|gb|DV022518.1|DV022518

EST:     GACCAGTCATTTATCGCGATTTTAAAACATCTAATATACTGCTGGATGCG                         GAGTATAACGCAAAGCTCTCTGATTTTGGGCTTGCGAAAGACGGACCTGTA
genomic: GACCAGTCATTTATCGCGATTTTAAAACATCTAATATACTGCTGGATGCGgtaagttaat ... gcttgtacagGAGTATAACGCAAAGCTCTCTGATTTTGGGCTTGCGAAAGACGGACCTGTA

EST: gi|148928770|gb|EC873531.2|EC873531

EST:     GACCAGTCATTTATCGCGATTTTAAAACATCTAATATACTGCTGGATGCG                         GAGTATAACGCAAAGCTCTCTGATTTTGGGCTTGCGAAAGACGGACCTGTA
genomic: GACCAGTCATTTATCGCGATTTTAAAACATCTAATATACTGCTGGATGCGgtaagttaat ... gcttgtacagGAGTATAACGCAAAGCTCTCTGATTTTGGGCTTGCGAAAGACGGACCTGTA

EST: gi|5499049|gb|AI854916.1|AI854916

EST:     GACCAGTCATTTATCGCGATTTTAAAACATCTAACATACTGCTGGATGCG                         GAGTATAACGCANAGCTCTCTGATTNTGNGCTTGCGAAAGACGGACCTGTA
genomic: GACCAGTCATTTATCGCGATTTTAAAACATCTAATATACTGCTGGATGCGgtaagttaat ... gcttgtacagGAGTATAACGCAAAGCTCTCTGATTTTGGGCTTGCGAAAGACGGACCTGTA

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), 48 (downstream exon)
Score: 175

TGCACTCGGAGCAGCAAAGGGTCTGGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTCATTTATCGCGATTTTAAAACATCTAATATACTGCTGGATGCGgtaagttaat ... gcttgtacagGAGTATAACGCAAAGCTCTCTGATTTTGGGCTTGCGAAAGACGGACCTGTAGGTGATAAAACTCATGTTTCTACTCGAGTAATGGGAACCTATGGATATG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 164

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 195

Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 99

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gtgtgtgcttcatgatctatatactgctacatcatatgttatattgcttgtacagGAGTATAACGCAAAGCTCTCTGATTTTGGGCTTGCGAAAGACGGACCTGTAGGTGATAAAACTCATGTTTCTACTCGAGTAATGGGAACCTATGGATATG