ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtacagttatctgagtcaagcttgaacatgcctaataatttatttagccagaaagcctaactctgtttctaattataaacagGACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAGGTCTGAATT

Basic information

species	Zea mays
transcript	GRMZM2G164265_T03
intron #	13
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G164265_T03 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 13

-----gtacagttatctgagtcaagcttgaacatgccta-ataatttatttagccagaaagcctaactctgtttctaattataaacagGACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAGGTCTGAATT
     ||||| |    ||||    | |      | | |  || |||| ||| ||    |  |||||||||||||| ||||||| | |||||||||||||||| ||||||||||| | || ||||||||||||||| ||||||||| | || || ||||| || ||||| ||||||||||         
gtaaagtacaatctgttgaggtgtgataattagtacttggattatttgttt-gctgagagtcctaactctgtttc-aattatacatagGACTGGATAATGGATCAGTGGGAGAAGAATTTCTACATAACAGCAATAGCTGGATCAGCTAACGGAAGTTCTTTAGTTGTGATGTCCAAAG---------

upper sequence: GRMZM2G164265_T03 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 13

-----------------------gtacagtt-atctga-gtcaagcttgaacatgcctaataatttatttagccagaaagcctaactctg--tttcta--attataaac----agGACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAGGTCTGAATT
                        || | || ||||   || ||      || |      ||| |||  ||    ||   | |    |||   | ||   ||| | | |    |||||||||| ||||||||||||||||||| |||||| || |   |||| |||||  ||   ||||| ||||| |||||||||||||||||||         
gtgggttttttcttccttgatttatataattcatcttttgttaaataaatacgtatgagttaaattaaataatt-gatgtcttggtgctgggctgctggcattttgatctctcagGACTGGATTATGGAGCAGTGGGAGAAAAATTACTATATCAGTTCAATAGCTGGCGCAGTTAATGGAAGTTCCTTGGTTGTCATGTCCAAAG---------

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|32913238|gb|CF018050.1|CF018050

EST:     CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAG                         GACTGGATAATGGAGCAGTGGGAGAAAAGT
genomic: CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAGgtacagttat ... ttataaacagGACTGGATAATGGAGCAGTGGGAGAAAAGT

EST: gi|67043197|gb|CO469452.1|CO469452

EST:     CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAG                         -ACTGGATA-TGGAGCAGTGGGAGAAAAGT-ACTA
genomic: CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAGgtacagttat ... ttataaacagGACTGGATAATGGAGCAGTGGGAGAAAAGTTACTA

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), 47 (downstream exon)
Score: 256

TTGTGTGGCTTCCTCGGCAAACCTTTGGGCACTCATCATGGACGCTGGAACTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAGgtacagttat ... ttataaacagGACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAGGTCTGAATT

Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 189

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 169

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 200

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

atgcctaataatttatttagccagaaagcctaactctgtttctaattataaacagGACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAGGTCTGAATT