ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GTTAAGCAGATGGTTGTTGCAACACTTGCCGAGTCAGGAATGAATCTTTCGGATGAAATTGTAGAGAGTATAATTGACAAGgtctgttaaagttgtgcatttatgttatggtatatcgaatttatctgtatagtgtagtgcactagcgctactcagaagggcaagcatggtgcagtggtgg...

Basic information

species	Zea mays
transcript	GRMZM2G173424_T02
intron #	7
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G173424_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os12g40510.1 (Oryza sativa), 5'ss of exon 7

GTTAAGCAGATGGTTGTTGCAACACTTGCCGAGTCAGGAATGAATCTTTCGGATGAAATTGTAGAGAGTATAATTGACAAGgtctgttaaagttgtgcatttatgttatggtatatcgaatttatctgtatagtgtagtgcactagcgctactcagaagggcaagcatggtgcagtggtgg-
|||||||||||||||||||| |||||||| ||||| |||||||||||||| ||||||||| ||||||| ||||| || ||||| |||||  ||| | ||||||| || || | | |    ||   |  | || || |  | | |        |   |       | |    | | |  |   
GTTAAGCAGATGGTTGTTGCTACACTTGCTGAGTCTGGAATGAATCTTTCTGATGAAATTATAGAGAGCATAATCGATAAGgtatgttacggtt-tccatttatattttgttgtgtttggttataccctgtattggatggtatttttttagttggtattttgtggtaatcagtaattctcag

upper sequence: GRMZM2G173424_T02 (Zea mays), 5'ss of exon 7
lower sequence: Vv19s0015g01070.t01 (Vitis vinifera), 5'ss of exon 6

GTTAAGCAGATGGTTGTTGCAACACTTGCCGAGTCAGGAATGAATCTTTCGGATGAAATTGTAGAGAGTATAATTGACAAGgt-ctgttaaagttgtgcatttatgttatggtatatcgaatttatctgtatagtgtagtgcactagcgctactcagaagggcaa-gcatggtgcagtggtgg-
|| ||||| ||||| || || |||||||| || || || |||||||||||||||||  || |||| ||||| ||||||||||| ||     |      |||||   | ||   | |||   |  |  | | |  |    |  |    | |   ||| | |   || | |||||| |    |   
GTGAAGCAAATGGTAGTGGCCACACTTGCTGAATCTGGTATGAATCTTTCGGATGATGTTATAGAAAGTATCATTGACAAGgtgctccctcaaccc--catttgactcatttaacatcttgtacag-tatctgatcacctctaaccacccatttcacatgtttaatggatggtgtaagcatcca

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|211119821|gb|FL462978.1|FL462978

EST:     AGTCAGGAATGAATCTTTCGGATGAAATTGTAGAGAGTATAATTGACAAG                         ACATTTGAGGAGGCAGACACAAAGCWTGATGGAAGAATTGACAAGGAAGAG
genomic: AGTCAGGAATGAATCTTTCGGATGAAATTGTAGAGAGTATAATTGACAAGgtctgttaaa ... tcattacaagACATTTGAGGAGGCAGACACAAAGCATGATGGAAGAATTGACAAGGAAGAG

EST: gi|88755366|gb|DY539507.1|DY539507

EST:     AGTCAGGAATGAATCTTTCGGATGAAATTGTAGAGAGTATAATTGACAAG                         ACATTTGAGGAGGCGGACACAAAGCATGATGGAAGAATTGACAAGGAAGAG
genomic: AGTCAGGAATGAATCTTTCGGATGAAATTGTAGAGAGTATAATTGACAAGgtctgttaaa ... tcattacaagACATTTGAGGAGGCAGACACAAAGCATGATGGAAGAATTGACAAGGAAGAG

EST: gi|74244689|gb|DT652603.1|DT652603

EST:     AGTCAGGAATGAATCTTTCGGATGAAATTGTAGAGAGTATAATTGACAAG                         ACATTTGAGGAGGCAGACACAAAGCATGATGGAAGAATTGACAAGGAAGAG
genomic: AGTCAGGAATGAATCTTTCGGATGAAATTGTAGAGAGTATAATTGACAAGgtctgttaaa ... tcattacaagACATTTGAGGAGGCAGACACAAAGCATGATGGAAGAATTGACAAGGAAGAG

EST: gi|71307467|gb|DR789938.1|DR789938

EST:     AGTCAGGAATGAATCTTTCGGATGAAATTGTAGAGAGTATAATTGACAAG                         ACATTTGAGGAGGCAGACACAAAGCATGATGGAAGAATTGACAAGGAAGAG
genomic: AGTCAGGAATGAATCTTTCGGATGAAATTGTAGAGAGTATAATTGACAAGgtctgttaaa ... tcattacaagACATTTGAGGAGGCAGACACAAAGCATGATGGAAGAATTGACAAGGAAGAG

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: 319

GTTAAGCAGATGGTTGTTGCAACACTTGCCGAGTCAGGAATGAATCTTTCGGATGAAATTGTAGAGAGTATAATTGACAAGgtctgttaaa ... tcattacaagACATTTGAGGAGGCAGACACAAAGCATGATGGAAGAATTGACAAGGAAGAGTGGCGCAATCTAGTCATTCGGCATCCTTCTTTGCTGAAGAACATGACTC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 221

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 262