ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GGTTGCGCCGAAGTCCACCCTTGGCAACTGGATGAAGGAAATCCAACGTTTTTGCCCTATCCTACGTGCTGTGAAGTTCTTGGGCAATCCAGAAGAGCGGgttggtctcaagtctattctttaatcccttatggaatttttactgccatgttactgaatactgatctcttattcttctgtgccag

Basic information

species	Zea mays
transcript	AC235535.1_FGT001
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: AC235535.1_FGT001 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 5'ss of exon 6

GGTTGCGCCGAAGTCCACCCTTGGCAACTGGATGAAGGAAATCCAACGTTTTTGCCCTATCCTACGTGCTGTGAAGTTCTTGGGCAATCCAGAAGAGCGGgttggt---ctcaag-tctattctttaatcccttatg-gaatttttactgccatgttactgaatactgatctcttattcttctgtgccag
 ||||| || ||||| || |||||||||||||| |||||||| ||||| ||||||||||| |||||||||||||| ||||| || |||||||||||| ||||| ||   || |   ||   |||  || |  |  |  |||    | |||   |  ||||||| | |    |   |||||  |  | |||
TGTTGCACCAAAGTCTACTCTTGGCAACTGGATAAAGGAAATTCAACGGTTTTGCCCTATTCTACGTGCTGTGAAATTCTTAGGGAATCCAGAAGAGAGGgttagtttacttagcctccgctctccaaccattcttatgaacaacttctgatgttgtactgaacatt----ttgcattctgtttggtcag

upper sequence: AC235535.1_FGT001 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 5'ss of exon 6

GGTTGCGCCGAAGTCCACCCTTGGCAACTGGATGAAGGAAATCCAACGTTTTTGCCCTATCCTACGTGCTGTGAAGTTCTTGGGCAATCCAGAAGAGCGGgttggtctcaagtctattctttaatcccttatggaatttttactgccatgttactgaatactgatctcttattcttctgtgccag
 ||||| || |||||||| ||||| ||||||||||||||||| ||||| ||||| ||| | || |||||| | |||||||| || || || |||||  ||||    | || ||    ||| | || | |  || | || ||  ||  || || || |   |  || | | || |||    | |||
TGTTGCACCAAAGTCCACTCTTGGGAACTGGATGAAGGAAATACAACGGTTTTGTCCTGTTCTGCGTGCTATCAAGTTCTTAGGAAACCCCGAAGAAAGGgtaatccccatgttatctctgtcattcat-gtgaacttcttg-tggtatattgctaa---catatttgtcatacttg---gtcag

upper sequence: AC235535.1_FGT001 (Zea mays), 5'ss of exon 6
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 5'ss of exon 6

GGTTGCGCCGAAGTCCACCCTTGGCAACTGGATGAAGGAAATCCAACGTTTTTGCCCTATCCTACGTGCTGTGAAGTTCTTGGGCAATCCAGAAGAGCGGgttggtc--tcaagtc-tattctttaatcccttatggaatttttactgccatgttactgaatactgatctcttattcttctgtgccag
 ||||| || || || || ||||||||||||||||| ||||| | ||||||||| ||  | || ||||||||||||||  | || ||||| || ||  ||||  |||  ||| | | |  | |   |    || |    || ||       |   |||| |   || |  |   ||| ||| |||   
TGTTGCCCCAAAATCGACTCTTGGCAACTGGATGAATGAAATTCGACGTTTTTGTCCAGTTCTGCGTGCTGTGAAGTTTCTTGGAAATCCTGATGAAAGGgtgtgtcattcaggccctgctttcagagtaattctttttttatttacagttttccactgcactttgctaacac-ttcgtctctgcag-

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|22491353|gb|BU051276.1|BU051276

EST:     TTTGCCCTATCCTACGTGCTGTGAAGTTCTTGGGCAATCCAGAAGAGCGG                         AACCATATAAGGGACGATTTGCTACAGCCT
genomic: TTTGCCCTATCCTACGTGCTGTGAAGTTCTTGGGCAATCCAGAAGAGCGGgttggtctca ... tctgtgccagAACCATATAAGGGACGATTTGCTACAGCCT

EST: gi|20300252|gb|BQ163195.1|BQ163195

EST:     TTTGCCCTATCCTACGTGCTGTGAAGTTCTTGGGCAATCCAGAAGAGCGG                         AACCATATAAGGGACGATTTGCTACAGCCTGGAAAATTTGATGTGTGCGTG
genomic: TTTGCCCTATCCTACGTGCTGTGAAGTTCTTGGGCAATCCAGAAGAGCGGgttggtctca ... tctgtgccagAACCATATAAGGGACGATTTGCTACAGCCTGGAAAATTTGATGTGTGCGTG

EST: gi|19350725|gb|BM895257.1|BM895257

EST:     TTTGCCCTATCCTACGTGCTGTGAAGTTCTTGGGCAATCCAGAAGAGCGG                         AACCATATAAGGGACGATTTGCTACAGCCTTGAAAATTTGATGTGTGCGTG
genomic: TTTGCCCTATCCTACGTGCTGTGAAGTTCTTGGGCAATCCAGAAGAGCGGgttggtctca ... tctgtgccagAACCATATAAGGGACGATTTGCTACAGCCTGGAAAATTTGATGTGTGCGTG

EST: gi|20300542|gb|BQ163485.1|BQ163485

EST:     TTTGCCCTATCCTACGTGCTGTGAAGTTCTTGGGCAATCCAGAAGAGCGG                         AACCATATAAGGGACGATTTGCTACAGCCTGGAAAATTTGATGTGTGCGTG
genomic: TTTGCCCTATCCTACGTGCTGTGAAGTTCTTGGGCAATCCAGAAGAGCGGgttggtctca ... tctgtgccagAACCATATAAGGGACGATTTGCTACAGCCTGGAAAATTTGATGTGTGCGTG

EST: gi|87153564|gb|DY398353.1|DY398353

EST:     TTTGCCCTATCCTACGTGCTGTGAAGTTCTTGGGCAATCCAGAAGAGCGG                         AACCATATAAGGGACGATTTGCTACAGCCTGGAAAATTTGATGTGTGCGTG
genomic: TTTGCCCTATCCTACGTGCTGTGAAGTTCTTGGGCAATCCAGAAGAGCGGgttggtctca ... tctgtgccagAACCATATAAGGGACGATTTGCTACAGCCTGGAAAATTTGATGTGTGCGTG

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: 250

GGTTGCGCCGAAGTCCACCCTTGGCAACTGGATGAAGGAAATCCAACGTTTTTGCCCTATCCTACGTGCTGTGAAGTTCTTGGGCAATCCAGAAGAGCGGgttggtctca ... tctgtgccagAACCATATAAGGGACGATTTGCTACAGCCTGGAAAATTTGATGTGTGCGTGACTAGTTTTGAAATGGCAATCAAAGAAAAATCTGCGTTGAGGCGCTTCA

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 109

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 93