ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGTTCTGGTCGTCGGAGTCCCTGTACTACAACCCCGCCTGGCACGCGATCGTCTCTTCTTGGGAAACCGTCGTCTACAGCCCCGTTCTTGATCTTGACAGgtcaggagttctccctcccttcccaactctacgctgcccatgcatggcatctctctatctactgtctgctgctatactactgtgatgttactacccttatatgcacag

Basic information

species	Zea mays
transcript	GRMZM2G030138_T01
intron #	16
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G030138_T01 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os07g08400.1 (Oryza sativa), 5'ss of exon 16

TGTTCTGGTCGTCGGAGTCCCTGTACTACAACCCCGCCTGGCACGCGATCGTCTCTTCTTGGGAAACCGTCGTCTACAGCCCCGTTCTTGATCTTGACAGgtcaggagttctccctcccttcccaactctacgctgcccatgcatggcatctctctatctactgtctgctgctatactactgtgatgttactacccttatatgcacag
| ||||||||||| || |   |||||||||| |||  |||||||  |||||||||||| ||||||||| | || || | ||| ||||||||| ||||||||  ||    | ||    |  |   || |  ||       ||| |     | | |     | ||  ||| | | || ||  | |  ||                     
TATTCTGGTCGTCAGAATTGTTGTACTACAATCCCATCTGGCACATGATCGTCTCTTCATGGGAAACCATTGTGTATAACCCAGTTCTTGATATTGACAGgcaag----tttcttctctctgtgaagtgcacaacatgaatgtaatctctattttgccttccttactgttacgatgcttgtcttgtgcag------------------

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|76924743|gb|DV170112.1|DV170112

EST:     GTCTTTTCTGGGGAAACCGTCGTCTACAGCCCCGTTCTTGATCTTGACAG                         ATGGGCGTTCCCGATCTGCGCTGTCCTGTTGTTTTTGGCGTTTTATTGGCG
genomic: GTCTCTTCTTGGGAAACCGTCGTCTACAGCCCCGTTCTTGATCTTGACAGgtcaggagtt ... atatgcacagATGGGCGTTCCCGATCTGCGCTGTCCTGTTGTTTTTGGCGTTTTATTGGCG

EST: gi|89763544|gb|DY690689.1|DY690689

EST:     GTCTCTTCTTGGGAAACCGTCGTCTACAGCCCCGTTCTTGATCTTGACAG                         ATGGGCGTTCCCGATCTGCGCTGTCCTGTTGTTTTTGGCGTTTTATTGGCG
genomic: GTCTCTTCTTGGGAAACCGTCGTCTACAGCCCCGTTCTTGATCTTGACAGgtcaggagtt ... atatgcacagATGGGCGTTCCCGATCTGCGCTGTCCTGTTGTTTTTGGCGTTTTATTGGCG

EST: gi|9733314|gb|BE512066.1|BE512066

EST:     GTCTCTTCTTGGGAAACCGTCGTCTACAGCCCCGTTCTTGATCTTGACAG                         ATGGGCGTTCCCGATCTGCGCTGTCCTGTTGTTTTTGGCGTTTTATTGGCG
genomic: GTCTCTTCTTGGGAAACCGTCGTCTACAGCCCCGTTCTTGATCTTGACAGgtcaggagtt ... atatgcacagATGGGCGTTCCCGATCTGCGCTGTCCTGTTGTTTTTGGCGTTTTATTGGCG

EST: gi|71449827|gb|DR830877.1|DR830877

EST:     GTCNNNNNNNGGGAAACCGTCGTCTACAGCCCCGTTCTTGATCTTGACAG                         ATGGGCGTTCCCGATCTGCGCTGTCCTGTTGTTTTTGGCGTTTTATTGGCG
genomic: GTCTCTTCTTGGGAAACCGTCGTCTACAGCCCCGTTCTTGATCTTGACAGgtcaggagtt ... atatgcacagATGGGCGTTCCCGATCTGCGCTGTCCTGTTGTTTTTGGCGTTTTATTGGCG

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), 47 (downstream exon)
Score: 3

TGTTCTGGTCGTCGGAGTCCCTGTACTACAACCCCGCCTGGCACGCGATCGTCTCTTCTTGGGAAACCGTCGTCTACAGCCCCGTTCTTGATCTTGACAGgtcaggagtt ... atatgcacagATGGGCGTTCCCGATCTGCGCTGTCCTGTTGTTTTTGGCGTTTTATTGGCGTTGCCTCGGTGGAAGGAGGGGAATTGCCCGGTCACTGCTACCTCTGTAC

Block sizes: 13 (upstream exon), 37 (downstream exon)
Score: 1

Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 7