ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GTTGCTGATTTTGGTCTTGCAAGGTTAGCTATGGATGCTTGCACTCATGTAACCACACGAGTGATGGGAACTTTCGGgttagtaaaacagcggcaagttcaagagaacagttaaaacctgcttgtaatctgacacacgcttcttatttag

Basic information

species	Zea mays
transcript	GRMZM5G872442_T03
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G872442_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g02040.1 (Oryza sativa), 5'ss of exon 5

GTTGCTGATTTTGGTCTTGCAAGGTTAGCTATGGATGCTTGCACTCATGTAACCACACGAGTGATGGGAACTTTCGGgttagtaaaaca-----------gcggcaagttcaagagaacagttaaaacctgcttgtaatctgacacacgcttcttatttag
|||||||||||||| ||||||||  |||||||||||||   ||| |||||||| ||||| |||||||||||||| |||| ||||||  |            | |   |  ||||||||||    | |  | | | | |||| |       || ||||  ||
GTTGCTGATTTTGGCCTTGCAAGACTAGCTATGGATGCAGTCACGCATGTAACTACACGGGTGATGGGAACTTTTGGgtaagtaaattactgcctgccttactgagggcacaagagaacatcgtacattttcatatgatctaatgattatttgttatgcag

upper sequence: GRMZM5G872442_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA16G19520.1 (Glycine max), 5'ss of exon 6

GTTGCTGATTTTGGTCTTGCAAGGTTAGCTATGGATGCTTGCACTCATGTAACCACACGAGTGATGGGAACTTTCGGgttagtaaaacagcggcaagttcaagagaacagttaaaacctgcttgta---at--ctgacacacgcttc-ttatttag---------------------------------------------
 |  | |||||||| || || |  |||||  | ||||||   || |||||||||||||| ||| |||||||||||||||  ||||     |  | | |||     |    | |   |||    |||   ||  | ||  || |  || ||  |||                                              
ATCTCGGATTTTGGGCTAGCCAAATTAGCAGTTGATGCTAATACACATGTAACCACACGTGTGGTGGGAACTTTCGGgtgggtaatgt--ctactatttctctttacttttcactccctttgcgtacagattacggattcatgactcatttcttaataatgctcaaacagtaaaaatgattcgttttttccctcttaaaag

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|22520879|gb|BU079690.1|BU079690

EST:     GCTATGGATGCTTGCACTCATGTAACCACACGAGTGATGGGAACTTTCGG                         GTACCTTGCTCCAGAGTACGCGTCAAGCGGCAAGTTGACTGAGAGATCTGA
genomic: GCTATGGATGCTTGCACTCATGTAACCACACGAGTGATGGGAACTTTCGGgttagtaaaa ... tcttatttagGTACCTTGCTCCAGAGTACGCGTCAAGCGGCAAGTTGACTGAGAGATCTGA

EST: gi|26559092|gb|CA831327.1|CA831327

EST:     GCTATGGATGCTTGCACTCATGTAACCACACGAGTGATGGGAACTTTCGG                         GTACCTTGCTCCAGAGTACGCGTCAAGCGGCAAGTTGACTGAGAGATCTGA
genomic: GCTATGGATGCTTGCACTCATGTAACCACACGAGTGATGGGAACTTTCGGgttagtaaaa ... tcttatttagGTACCTTGCTCCAGAGTACGCGTCAAGCGGCAAGTTGACTGAGAGATCTGA

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: 48 (upstream exon), 49 (downstream exon)
Score: 158

GTTGCTGATTTTGGTCTTGCAAGGTTAGCTATGGATGCTTGCACTCATGTAACCACACGAGTGATGGGAACTTTCGGgttagtaaaa ... tcttatttagGTACCTTGCTCCAGAGTACGCGTCAAGCGGCAAGTTGACTGAGAGATCTGATGTATTCTCATTCGGTGTCGTCCTCTTGGAGCTTATTACTGGTAGAAAG

Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 18

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 18