ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TTGCACTTATGTTTTGGGAAACAAGGCGTTCAGACTTTGGAGTGTCAATGTCACATCATGTTGCTACTGTTGTTCTGATTGTTCTATCTTACGTGTTCAGgtatgttccttatcttgaataactgttagattttgttattttgtgaatttgcaacatcattcttagtcatcattgcttatttgttaattcctttttctaactcatctcataattcatagacaatttttttaacaatcttctgatcttctccttggtcaaccag

Basic information

species	Zea mays
transcript	GRMZM2G444643_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G444643_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g37080.2 (Oryza sativa), 5'ss of exon 3

TTGCACTTATGTTTTGGGAAACAAGGCGTTCAGACTTTGGAGTGTCAATGTCACATCATGTTGCTACTGTTGTTCTGATTGTTCTATCTTACGTGTTCAGgtatgttccttatcttgaataactgttagattttgttattttgtgaatttgcaacatcatt--cttagtc--atcattgct-tatttgttaattcc------tttttctaactcatct---cataattcat---agacaatttttttaacaatc-----------ttctgatcttctccttggtcaaccag
|||||||||||||||||||||||||||||||||| ||||| ||||||||||||||||||||||| |||||||  ||||| ||| ||||||| ||||||||||      ||  | |||  ||||| |||  ||||||| |||  ||||| || |   |  ||  |||  |   | |||| || |||  |||| |  |        ||  ||  | ||||   |  | || ||   |  || |||| |||||| |            ||||||  || | |||  | ||||||
TTGCACTTATGTTTTGGGAAACAAGGCGTTCAGATTTTGGCGTGTCAATGTCACATCATGTTGCAACTGTTGCGCTGATAGTTTTATCTTATGTGTTCAGgt------ctctttttgtctaacttttaatttttgttgtttcttgaatatgaactttttttaccttgattcaagcattactctatgagttagtagcacagggccttaatattttatcttcactgagtttatttcactcatttttattaacacttaactaatttatttctgaaatttttcttcatgaaccag

upper sequence: GRMZM2G444643_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA16G12080.1 (Glycine max), 5'ss of exon 3

TTGCACTTATGTTTTGGGAAACAAGGCGTTCAGACTTTGGAGTGTCAATGTCACATCATGTTGCTACTGTTGTTCTGATTGTTCTATCTTACGTGTTCAGgtatgttccttatcttgaataactgttagattttgttattttgtgaatttgcaacatcattcttagtcatcattgcttatttgttaattcctttttctaactcatctcataattcatagacaatttttttaacaatcttctgatcttctccttggtcaaccag
||||  | || ||||||||||| ||||| || || ||||||||||| |||   |||||||||||||||||  |||| |||||||| |||||| | || |||||| ||  | ||     |   | |||   | |||| |||    |  |||    | |||   |     | | ||| || ||  ||| ||| ||| ||| | |   ||                                                        
TTGCTTTAATATTTTGGGAAACGAGGCGCTCCGATTTTGGAGTGTCCATGAGTCATCATGTTGCTACTGTAATTCTTATTGTTCTGTCTTACATTTTTAGgtatctttttcattc---acttccgttttgtcttgtcattcaa-gcttttttgtcctcaagttcg---accgttgatt-ttgtttatttcatttgtctgaatttactt-------------------------------------------------------

upper sequence: GRMZM2G444643_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA08G36370.1 (Glycine max), 5'ss of exon 3

TTGCACTTATGTTTTGGGAAACAAGGCGTTCAGACTTTGGAGTGTCAATGTCACATCATGTTGCTACTGTTGTTCTGATTGTTCTATCTTACGTGTTCAGgtatgttccttatcttgaataactgttagattttgttattttgtgaatttgcaacatcattcttagtcatcattgcttattt-gttaattcctttttctaactcatctcataattcatagacaatttttttaacaatcttctgatcttctccttggtcaaccag
||||  | || ||||||||||| ||||| || |||||||||||||| |||   |||||||||||||||||  |||| |||||||| |||||| | ||||||||||||  ||   |    | | ||||   | |||| |||    |  |||    | |||   ||  |||   |||   ||||  || ||| | |||| |                                                                 
TTGCTTTGATATTTTGGGAAACGAGGCGCTCCGACTTTGGAGTGTCCATGAGTCATCATGTTGCTACTGTAATTCTCATTGTTCTGTCTTACATTTTCAGgtatgttttttcattcacttgagtgtttc-tcttgtcattcaa-gcttttttgtcctcaagtttgatcagttttgtagattttatttatttcattttgtctg--------------------------------------------------------------

upper sequence: GRMZM2G444643_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv01s0010g01110.t01 (Vitis vinifera), 5'ss of exon 3

TTGCACTTATGTTTTGGGAAACAAGGCGTTCAGACTTTGGAGTGTCAATGTCACATCATGTTGCTACTGTTGTTCTGATTGTTCTATCTTACGTGTTCAGgtatgttccttatcttgaataactgttagattttgttattttgtgaatttgcaacatcattcttagtcatcattgcttatttgttaattcctttttctaactcatctcataattcatagacaatttttttaacaatcttctgatcttctccttggtcaaccag
||||  | || ||||||||||||||||| || || |||||||||||||||   |||||||| || ||| || |||| ||||| || |||||| | ||||||||||||       | | | || | | ||   ||||   || |    ||   |||| ||    ||  ||| |  |  | |  ||| || ||  |||   ||  || | |      | ||                                            
TTGCTTTGATTTTTTGGGAAACAAGGCGGTCTGATTTTGGAGTGTCAATGGGTCATCATGTGGCAACTTTTATTCTCATTGTGCTGTCTTACATATTCAGgtatgtt-------tggcagaagt-tcag--cttgtagcttggcatgttctgaacacca----taaccatga--ggatgtgggttcataccaattt---acctatttaaagtaaaacag--------------------------------------------

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|211231826|gb|FL279441.1|FL279441

EST:     TCTCATCATGTTGCTACTGTTGTTCTGATTGTTCTATCTTACGTGTTCAG                         ATTTGCTAGAGTTGGCTCTATAGTATTGGCAATTCATGATGCAAGTGACGT
genomic: TCACATCATGTTGCTACTGTTGTTCTGATTGTTCTATCTTACGTGTTCAGgtatgttcct ... ggtcaaccagATTTGCTAGAGTTGGCTCTATAGTATTGGCAATTCATGATGCAAGTGACGT

EST: gi|71767991|gb|DR965928.1|DR965928

EST:     TACGTGTTCAG                         ATTTGCTAGAGTTGGCTCTATAGTATTGGCAATTCATGATGCAAGTGACGT
genomic: TACGTGTTCAGgtatgttcct ... ggtcaaccagATTTGCTAGAGTTGGCTCTATAGTATTGGCAATTCATGATGCAAGTGACGT

EST: gi|78104262|gb|DV522680.1|DV522680

EST:     TCACATCATGTTGCTACTGTTGTTCTGATTGTTCTATCTTACGTGTTCAG                         ATTTGCTAGAGTTGGCTCTATAGTATTGGCAATTCATGATGCAAGTGACGT
genomic: TCACATCATGTTGCTACTGTTGTTCTGATTGTTCTATCTTACGTGTTCAGgtatgttcct ... ggtcaaccagATTTGCTAGAGTTGGCTCTATAGTATTGGCAATTCATGATGCAAGTGACGT

EST: gi|71767992|gb|DR965929.1|DR965929

EST:     TCACATCATGTTGCTACTGTTGTTCTGATTGTTCTATCTTACGTGTTCAG                         ATTTGCTAGAGTTGGCTCTATAGTATTGGCAATTCATGATGCAAGTGACGT
genomic: TCACATCATGTTGCTACTGTTGTTCTGATTGTTCTATCTTACGTGTTCAGgtatgttcct ... ggtcaaccagATTTGCTAGAGTTGGCTCTATAGTATTGGCAATTCATGATGCAAGTGACGT

EST: gi|78086490|gb|DV514883.1|DV514883

EST:     CATGTTGCTACGGTTGTTCTGATTGTTTTATCTTACGTGTTCCG                         ATTTGCTAGAGTTGGCTGTATAGTATTGGCAATTCATGATGCAAGTGACGT
genomic: CATGTTGCTACTGTTGTTCTGATTGTTCTATCTTACGTGTTCAGgtatgttcct ... ggtcaaccagATTTGCTAGAGTTGGCTCTATAGTATTGGCAATTCATGATGCAAGTGACGT

EST: gi|78104263|gb|DV522681.1|DV522681

EST:     TCACATCATGTTGCTACTGTTGTTCTGATTGTTCTATCTTACGTGTTCAG                         ATTTGCTAGAGTTGGCTCTATAGTATTGGCAATTCATGATGCAAGTGACGT
genomic: TCACATCATGTTGCTACTGTTGTTCTGATTGTTCTATCTTACGTGTTCAGgtatgttcct ... ggtcaaccagATTTGCTAGAGTTGGCTCTATAGTATTGGCAATTCATGATGCAAGTGACGT

EST: gi|78086491|gb|DV514884.1|DV514884

EST:     TCACATCATGTTGCTACTGTTGTTCTGATTGTTCTATCTTACGTGTTCAG                         ATTTGCTAGAGTTGGCT
genomic: TCACATCATGTTGCTACTGTTGTTCTGATTGTTCTATCTTACGTGTTCAGgtatgttcct ... ggtcaaccagATTTGCTAGAGTTGGCT

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: 47 (upstream exon), 47 (downstream exon)
Score: 87

TTGCACTTATGTTTTGGGAAACAAGGCGTTCAGACTTTGGAGTGTCAATGTCACATCATGTTGCTACTGTTGTTCTGATTGTTCTATCTTACGTGTTCAGgtatgttcct ... ggtcaaccagATTTGCTAGAGTTGGCTCTATAGTATTGGCAATTCATGATGCAAGTGACGTTTTCCTGGAAGTAGGGAAGATGTCCAAGTACAGCCATTGTGATTGGCTT

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 161

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 146