ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TCATCAACTAACAGGCCTAAACTTGAGTTATACTCCCACACTGGATTATTCTGATCTAGCTAAAATGGTCAGCCGCTGTGTGAAACTCCAGCGTCTCTGGgtgagttcccttctctttgtgttggcttgatatttctgtacgttgagagaaccacataatgaatttgatcctccacag

Basic information

species	Zea mays
transcript	GRMZM5G848945_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G848945_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os04g32460.2 (Oryza sativa), 5'ss of exon 2

TCATCAACTAACAGGCCTAAACTTGAGTTATACTCCCACACTGGATTATTCTGATCTAGCTAAAATGGTCAGCCGCTGTGTGAAACTCCAGCGTCTCTGGgtgagttccctt------------ctctttgtgttggc--ttgatatttctgtacgttgagag----aaccacataatgaatttgatcctccacag-----
|  |||||| |||||  | |||||||| ||| | |||||||| |||  |||||| ||  | |||||| | |||||||||||||| ||||| || || |||||||||||||||             | ||  |||| |   ||| | ||  ||  | |||  |     || ||  ||| |   |||| |||  | |      
TGCTCAACTGACAGGATTGAACTTGAGCTATGCCCCCACACTTGATGCTTCTGACCTTACAAAAATGATTAGCCGCTGTGTGAAGCTCCAACGCCTTTGGgtgagttcccttgttggtttgtacttattcttgtttgttgttgttgttgttgccctttggtaatatcaagcaagtaacggtattgagcctttatattgcag

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|211065841|gb|FL286063.1|FL286063

EST:     CTAGCTAAAATGGTCAGCCGCTGTGTGAAACTCCAGCGTCTCTGG                         GTACTGGATTGCATTTCAGATAAGGGTTTGCAAGTGGTGGCCTCCAGTTGC
genomic: CTAGCTAAAATGGTCAGCCGCTGTGTGAAACTCCAGCGTCTCTGGgtgagttccc ... tcctccacagGTACTGGATTGCATTTCAGATAAGGGTTTGCAAGTGGTGGCCTCCAGTTGC

EST: gi|91875772|gb|EB405729.1|EB405729

EST:     CTGATCTAGCTAAAATGGTCAGCCGCTGTGTGAAACTCCAGCGTCTCTGG                         GTACTGGATTGCATTTCAGATAAGGGTTTGCAAGTGGTGGCCTCCAGTTGC
genomic: CTGATCTAGCTAAAATGGTCAGCCGCTGTGTGAAACTCCAGCGTCTCTGGgtgagttccc ... tcctccacagGTACTGGATTGCATTTCAGATAAGGGTTTGCAAGTGGTGGCCTCCAGTTGC

EST: gi|60344695|gb|DN211668.1|DN211668

EST:     CTGATCTAGCTAAAATGGTCAGCCGCTGTGTGAAACTCCAGCGTCTCTGG                         GTACTGGATTGCATTTCAGATAAGGGTTTGCAAGTGGTGGCCTCCAGTTGC
genomic: CTGATCTAGCTAAAATGGTCAGCCGCTGTGTGAAACTCCAGCGTCTCTGGgtgagttccc ... tcctccacagGTACTGGATTGCATTTCAGATAAGGGTTTGCAAGTGGTGGCCTCCAGTTGC

EST: gi|60398893|gb|DN231709.1|DN231709

EST:     CTGATCTAGCTAAAATGGTCAGCCGCTGTGTGAAACTCCAGCGTCTCTGG                         GTACTGGATTGCATTTCAGATAAGGGTTTGCAAGTGGTGGCCTCCAGTTGC
genomic: CTGATCTAGCTAAAATGGTCAGCCGCTGTGTGAAACTCCAGCGTCTCTGGgtgagttccc ... tcctccacagGTACTGGATTGCATTTCAGATAAGGGTTTGCAAGTGGTGGCCTCCAGTTGC

EST: gi|78092941|gb|DV521315.1|DV521315

EST:     CTGATCTAGCTAAAATGGTCAGCCGCTGTGTGAAACTCCAGCGTCTCTGG                         GTACTGGATTGCATTTCAGATAAGGGTTTGCAAGTGGTGGCCTCCAGTTGC
genomic: CTGATCTAGCTAAAATGGTCAGCCGCTGTGTGAAACTCCAGCGTCTCTGGgtgagttccc ... tcctccacagGTACTGGATTGCATTTCAGATAAGGGTTTGCAAGTGGTGGCCTCCAGTTGC

EST: gi|60350818|gb|DN217791.1|DN217791

EST:     CTGATCTAGCTAAAATGGTCAGCCGCTGTGTGAAACTCCAGCGTCTCTGG                         GTACTGGATTGCATTTCAGATAAGGGTTTGCAAGTGGTGGCCTCCAGTTGC
genomic: CTGATCTAGCTAAAATGGTCAGCCGCTGTGTGAAACTCCAGCGTCTCTGGgtgagttccc ... tcctccacagGTACTGGATTGCATTTCAGATAAGGGTTTGCAAGTGGTGGCCTCCAGTTGC

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), 47 (downstream exon)
Score: 296

TCATCAACTAACAGGCCTAAACTTGAGTTATACTCCCACACTGGATTATTCTGATCTAGCTAAAATGGTCAGCCGCTGTGTGAAACTCCAGCGTCTCTGGgtgagttccc ... tcctccacagGTACTGGATTGCATTTCAGATAAGGGTTTGCAAGTGGTGGCCTCCAGTTGCAAGGACCTACAAGAACTCAGGGTGTTTCCATCAGAATTTTATGTTCCTG

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 186

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 201