ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtatgccttatcttctttgcttttctagatgtttgatatcattgctggggattgggtacatcatttccataaagtgggctgattgttgcactttgactgtcagGTACACTATGGTTTTGGCTGATAACGTGGATGGTGGAGATGACCTTGATCTTATTGTTACCACTATGAATGGCAACGTCTTCTGCTTCTCCACTCAATCA

Basic information

species	Zea mays
transcript	GRMZM2G479744_T01
intron #	6
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G479744_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g61050.1 (Oryza sativa), 3'ss of exon 10

gtatgccttatcttctttgcttttctagatgtttgatatcattgctggggattgggtacatcatttccataaagtgggctgattgttgcactttgactgtcagGTACACTATGGTTTTGGCTGATAACGTGGATGGTGGAGATGACCTTGATCTTATTGTTACCACTATGAATGGCAACGTCTTCTGCTTCTCCACTCAATCA
||||| | | |||| | |||||| | |    ||   ||   |          ||| | ||        | ||||||| || | |  |   | |  | || |||||||| |||||||||||||||||| || ||||||||||||||||| |||||||||||||| || ||||||||||| |||||||||||||||||||  || 
gtatgacatttcttgtctgctttgcaa----ttctgtactctgtacaatttctggattca--------acaaagtgg-ctcacttctttgcat--attgacagGTACAGTATGGTTTTGGCTGATAATGTTGATGGTGGAGATGACCTCGATCTTATTGTTACTACCATGAATGGCAATGTCTTCTGCTTCTCCACTCCCTCT

upper sequence: GRMZM2G479744_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA01G27250.2 (Glycine max), 3'ss of exon 10

gtatgccttatcttctttgcttttctagatgtttgatatcattgctggggattgggtacatcatttccataaagtgggctgattgttgcactttgactgtcagGTACACTATGGTTTTGGCTGATAACGTGGATGGTGGAGATGACCTTGATCTTATTGTTACCACTATGAATGGCAACGTCTTCTGCTTCTCCACTCAATCA
                          |||  ||   || | |  ||   || |  |       |     |    ||   | || ||  || | |  ||  ||| || |  ||||| ||||| || ||||| |||||||| ||||| |||||||| ||||| || |||||||||||||| |||||||||||||| || |  || 
-----------------------gtaagagattctttaacctgtctcttgaatatgctttctgtcctactttcttgaagttat-gtgccattctttcta-cagTTATAGCATGGTCTTGGCAGACAACGTTGATGGTGGGGATGATCTTGATCTAATTGTCACAACTATGAATGGCAATGTCTTCTGCTTCTCAACCCCGTCT

upper sequence: GRMZM2G479744_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA03G14690.1 (Glycine max), 3'ss of exon 12

gtatgccttatcttctttgcttttctagatgtttgatatcattgctggggattgggtacatcatttccataaagtgggctgattgttgcactttgactgtcagGTACACTATGGTTTTGGCTGATAACGTGGATGGTGGAGATGACCTTGATCTTATTGTTACCACTATGAATGGCAACGTCTTCTGCTTCTCCACTCAATCA
             |    | || | ||  ||||  || ||   | |  |  ||  || |   | || | | ||||        |||  || |||   |  |||||| |  ||||| ||||| || || || |||||||| ||||| |||||||| ||||| || || ||||||||||| |||||||||||||| || | ||| 
------------gtaagagattctttaactgtt--atctctcggatatgctttctgttc--tactttcttgaagtta------tgtgccatttttttta-cagGTATAGCATGGTCTTGGCAGACAATGTTGATGGTGGGGATGATCTTGATCTAATTGTCACAACAATGAATGGCAATGTCTTCTGCTTCTCAACCCCATCT

upper sequence: GRMZM2G479744_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT3G09090.2 (Arabidopsis thaliana), 3'ss of exon 10

gtatgccttatcttctttgcttttctagatgtttgatatcattgctggggattgggtacatcatttccataa-agtgggctgattgttgcactttgactgtcagGTACACTATGGTTTTGGCTGATAACGTGGATGGTGGAGATGACCTTGATCTTATTGTTACCACTATGAATGGCAACGTCTTCTGCTTCTCCACTCAATCA
                              ||  |  |   |||||     | ||  || | || ||  ||  | |  |   |    ||   || || |  ||| ||||  ||||| ||||||||||| || || ||||||||||| || |||||||||||  | ||||||||||| |||||||| |||||||| || |  || 
------------------------------gtaagtcacttttgcttcctctcgg-cacgtaatatctttagtattttgaccaccaatgtctttcgagttacagATACAGCATGGTCTTGGCTGATAATGTTGACGGTGGAGATGATCTCGATCTTATTGTCTCAACTATGAATGGAAACGTCTTTTGCTTCTCAACGCCTTCT

upper sequence: GRMZM2G479744_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv08s0007g01790.t01 (Vitis vinifera), 3'ss of exon 10

gtatgccttatcttctttgcttttctagatgtttgatatcattgctggggattgggtacatcatttccataaagtgggctgattgttgcactttgactgtcagGTACACTATGGTTTTGGCTGATAACGTGGATGGTGGAGATGACCTTGATCTTATTGTTACCACTATGAATGGCAACGTCTTCTGCTTCTCCACTCAATCA
   |   ||||| ||    ||  | |  ||||||  | | | || |     |    | ||  ||||   |||| |    | | ||     | || | |  ||| || |  |||||  |||| || || || |||||||||||||| ||||||||||||||||| || ||||||||||| || || ||||| || ||||   | 
--gtaagttatcctcc--actactattcatgtttagttttactgtttaattt----ttcaaaatttgtttaaaata---taaatg-----cctttatta-cagATATAGCATGGTCCTGGCGGACAATGTTGATGGTGGAGATGATCTTGATCTTATTGTTACAACCATGAATGGCAATGTATTTTGCTTTTCAACTCCTGCT

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|211499292|gb|FL279211.1|FL279211

EST:     ATTGAGGGATCGAGTGGCTGTGCAGATGTTGTTGACATTGGAGAGACCTC                         GTACACTATGGTTTTGGCTGATAACGTGGATGGTGGAGATGACCTTGATCT
genomic: ATTGAGGGATCGAGTGGCTGTGCAGATGTTGTTGACATTGGAGAGACCTCgtatgcctta ... tgactgtcagGTACACTATGGTTTTGGCTGATAACGTGGATGGTGGAGATGACCTTGATCT

EST: gi|32860179|gb|CD999860.1|CD999860

EST:     ATTGAGGGATCGAGTGGCTGTGCAGATGTTGTTGACATTGGAGAGACCTC                         GTACACTATGGTTTTGGCTGATAACGTGGATGGTGGAGATGACCTTGATCT
genomic: ATTGAGGGATCGAGTGGCTGTGCAGATGTTGTTGACATTGGAGAGACCTCgtatgcctta ... tgactgtcagGTACACTATGGTTTTGGCTGATAACGTGGATGGTGGAGATGACCTTGATCT

EST: gi|6431890|gb|AW172094.1|AW172094

EST:     ATTGAGGGATCGAGTGGCTGTGCAGATGTTGTTGACATTGGAGAGACCTC                         GTACACTATGGTTTTGGCTGATAACGTGGATGGTGGAGATGACCTTGATCT
genomic: ATTGAGGGATCGAGTGGCTGTGCAGATGTTGTTGACATTGGAGAGACCTCgtatgcctta ... tgactgtcagGTACACTATGGTTTTGGCTGATAACGTGGATGGTGGAGATGACCTTGATCT

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: 217

CAAAAGGGCTAACTCTTGCAACAACGTCCTTTGATGGTTATTTATATTTGATTGAGGGATCGAGTGGCTGTGCAGATGTTGTTGACATTGGAGAGACCTCgtatgcctta ... tgactgtcagGTACACTATGGTTTTGGCTGATAACGTGGATGGTGGAGATGACCTTGATCTTATTGTTACCACTATGAATGGCAACGTCTTCTGCTTCTCCACTCAATCA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 200

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 270

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 248

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ggattgggtacatcatttccataaagtgggctgattgttgcactttgactgtcagGTACACTATGGTTTTGGCTGATAACGTGGATGGTGGAGATGACCTTGATCTTATTGTTACCACTATGAATGGCAACGTCTTCTGCTTCTCCACTCAATCA