ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gtaagtccttttgttcacttaatgtttactttttctttatgcatgcaatctttaattctttgttggaaccctttatatatttatctgtacaaataaattctcgtacacatttttttcagACAAAGGATGAGAAATACTTCATACACAACCATTTGTCATTTACGGTGAAGTATCACAAGGACGATAATTTGGAACATTCTAGAATAGTGGGATTTGAGG

Basic information

species	Zea mays
transcript	GRMZM2G006117_T01
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G006117_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os09g38530.1 (Oryza sativa), 3'ss of exon 4

gtaagtccttttgttcacttaatgtttactttttctttatgcatgcaatctttaattctttgttggaaccctttatatatttatctgtacaaataaattctcgtacacat---ttttttcagACAAAGGATGAGAAATACTTCATACACAACCATTTGTCATTTACGGTGAAGTATCACAAGGACGATAATTTGGAACATTCTAGAATAGTGGGATTTGAGG
                   |||  | | |  |   || |||| |||     || |   | | ||       || ||||||   |||| |  || ||| | |  || | |    | ||  ||||  ||||| ||||| |||||||| ||||||||||||||||||   |||||||| |||||||||||| |||  |||| |||||||||||||||||||||||
------------------gtaagttgtgcactcaattgatgcttgc-----ttgaccttctattta-----ttcatatatgc-tctggattaacaaactgtgatatataaatgtattcacagAGCAAGGAAGAGAAGTACTTCATTCACAACCATTTGTCATTTTTAGTGAAGTACCACAAGGACGATGATTCAGAACTTTCTAGAATAGTGGGATTTGAGG

upper sequence: GRMZM2G006117_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA04G06420.1 (Glycine max), 3'ss of exon 4

gtaagtccttttgttcacttaatgtttactttttctttatgcatgcaatctttaattctttgttggaaccctttatatatttatctgtacaaataaattctcgtacacattttttt--------cagACAAAGGATGAGAAATACTTCATACACAACCATTTGTCATTTACGGTGAAGTATCACAAGGACGATAATTTGGAACATTCTAGAATAGTGGGATTTGAGG
                                           |    ||||||    |||  | | ||  |    ||  ||||   | |   | | |  |  |||  ||||| |         ||||  ||||| ||||||||||| || |||||||||||| ||||||| || ||||| || || |||         |||  | ||||||| ||||| |||||||
------------------------------------------gtatggtcttta----ttttatagcactatggccattgttatgaatgccggttagtatttttacttattttgtctgaattcgcagAGCAAGGAGGAGAAATACTTTATTCACAACCATTTGGCATTTACTGTTAAGTACCATAAAGACATGCTAACTGAATCTGCTAGAATTGTGGGCTTTGAGG

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|32929714|gb|CF034526.1|CF034526

EST:     TTGCTTATCAAGGTGGATATCATGTTGGTGCCAAAGGCCTGTATTCTGGA                         ACAAAGGATGAGAAATACTTCATACACAACCATTTGTCATTTACGGTGAAG
genomic: TTGCTTATCAAGGTGGATATCATGTTGGTGCCAAAGGCCTGTATTCTGGAgtaagtcctt ... tttttttcagACAAAGGATGAGAAATACTTCATACACAACCATTTGTCATTTACGGTGAAG

EST: gi|149106813|gb|EE188710.2|EE188710

EST:     TTGCTTATCAAGGTGGATATCATGTTGGTGCCAAAGGCCTGTATTCTGGA                         ACAAAGGATGAGAAATACTTCATACACAACCATTTGTCATTTACGGTGAAG
genomic: TTGCTTATCAAGGTGGATATCATGTTGGTGCCAAAGGCCTGTATTCTGGAgtaagtcctt ... tttttttcagACAAAGGATGAGAAATACTTCATACACAACCATTTGTCATTTACGGTGAAG

EST: gi|76018555|gb|DT945725.1|DT945725

EST:     TTGCTTATCAAGGTGGATATCATGTTGGTGCCAAAGGCCTGTATTCTGGA                         ACAAAGGATGAGAAATACTTCATACACAACCATTTGTCATTTACGGTGAAG
genomic: TTGCTTATCAAGGTGGATATCATGTTGGTGCCAAAGGCCTGTATTCTGGAgtaagtcctt ... tttttttcagACAAAGGATGAGAAATACTTCATACACAACCATTTGTCATTTACGGTGAAG

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: 44 (upstream exon), 47 (downstream exon)
Score: 70

TGACAACCTCCCGCTAGTTGTTCCTGTTACAAGGCAAGATAAGAACAGTATTGCTTATCAAGGTGGATATCATGTTGGTGCCAAAGGCCTGTATTCTGGAgtaagtcctt ... tttttttcagACAAAGGATGAGAAATACTTCATACACAACCATTTGTCATTTACGGTGAAGTATCACAAGGACGATAATTTGGAACATTCTAGAATAGTGGGATTTGAGG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 341

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 373

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 490

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ggaaccctttatatatttatctgtacaaataaattctcgtacacatttttttcagACAAAGGATGAGAAATACTTCATACACAACCATTTGTCATTTACGGTGAAGTATCACAAGGACGATAATTTGGAACATTCTAGAATAGTGGGATTTGAGG