ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GCCTGTTACTAATTTCAATGAATTGGCGCTGCACTTCATTGAATGTATGTATGTGCATTTGGAAAATGTCCGGCCAAAGgtgattagagcaaatggcaattttttgtgtcagttatattttgatgttgtatgaaaacacaagcagacaagctgttatttccttttcattttgaag

Basic information

species	Zea mays
transcript	GRMZM2G061485_T01
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G061485_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os06g47830.1 (Oryza sativa), 5'ss of exon 6

GCCTGTTACTAATTTCAATGAATTGGCGCTGCACTTCATTGAATGTATGTATGTGCATTTGGAAAATGTCCGGCCAAAGgtgattagagcaaatggcaattttttgtgtcagttatattttgatgttgtatgaaaacacaagcagaca--agctgttatttccttttcattttgaag
|||| |||  |||||||| ||| ||| ||| || |||||||| |||||| ||||||||||||||| ||| |   | |||||   || ||||| |       | || || || || ||||   |     | ||| ||  | || || ||  |    |   | ||||| ||||||||||
GCCTATTAACAATTTCAACGAAGTGGTGCTACATTTCATTGAGTGTATGCATGTGCATTTGGAAAGTGTTCAATCGAAGgtacataaagcaagtaattcaatattatggcaattctattacta----atttgacaatgctagaagtcattaatgatcgctacctttccattttgaag

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|71329934|gb|DR801689.1|DR801689

EST:     TGCACTTCATTGAATGTATGTATGTGCATTTGGAAAATGTCCGGCCAAAG                         ATGAAGGATCATTTCCCTCGTGCTGTTCAAGCAAATGTGTCTG
genomic: TGCACTTCATTGAATGTATGTATGTGCATTTGGAAAATGTCCGGCCAAAGgtgattagag ... cattttgaagATGAAGGATCAATTCCCTCGTGCTGTTCAAGCAAATGTGTCTG

EST: gi|76280525|gb|DV020093.1|DV020093

EST:     TGCACTTCATTGAATGTATGTATGTGCATTTGGAAAATGTCCGGCCAAAG                         ATGAAGGATCAATTCCCTCGTGCTGTTCAAGCAAATGTGTCTGCTCACGAG
genomic: TGCACTTCATTGAATGTATGTATGTGCATTTGGAAAATGTCCGGCCAAAGgtgattagag ... cattttgaagATGAAGGATCAATTCCCTCGTGCTGTTCAAGCAAATGTGTCTGCTCACGAG

EST: gi|93017035|gb|EB642555.1|EB642555

EST:     TGCACTTCATTGAATGTATGTATGTGCATTTGGAAAATGTCCGGCCAAAG                         ATGAAGGATCAATTCCCTCGTGCTGTTCAAGCAAATGTGTCTGCTCACGAG
genomic: TGCACTTCATTGAATGTATGTATGTGCATTTGGAAAATGTCCGGCCAAAGgtgattagag ... cattttgaagATGAAGGATCAATTCCCTCGTGCTGTTCAAGCAAATGTGTCTGCTCACGAG

EST: gi|71321702|gb|DR797544.1|DR797544

EST:     TGCACTTCATTGAATGTATGTATGTGCATTTGGAAAATGTCCGGCCAAAG                         ATGAAGGATCAATTCCCTCGTGCTGTTCAAGCAAATGTGTCTGCTCACGAG
genomic: TGCACTTCATTGAATGTATGTATGTGCATTTGGAAAATGTCCGGCCAAAGgtgattagag ... cattttgaagATGAAGGATCAATTCCCTCGTGCTGTTCAAGCAAATGTGTCTGCTCACGAG

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: 40 (upstream exon), 39 (downstream exon)
Score: 10

GCCTGTTACTAATTTCAATGAATTGGCGCTGCACTTCATTGAATGTATGTATGTGCATTTGGAAAATGTCCGGCCAAAGgtgattagag ... cattttgaagATGAAGGATCAATTCCCTCGTGCTGTTCAAGCAAATGTGTCTGCTCACGAGATGCAAGCTCAAGTCGCTCACACAGTTCAAACAAATGTGCCTGCTTATA

Block sizes: 40 (upstream exon), 10 (downstream exon)
Score: 2

Block sizes: 40 (upstream exon), 10 (downstream exon)
Score: 1