ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaatcaagtatttatttactaccagtaaactagatcttaaatagatttatgtgaatattttaaatatttgtactaccttttgctttcttccagGTGGACAAGCAAAAACTCTAATGTTCGTTCAAATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGCACTTTAAAGTTTGCTGAAAGGGTGTCTGG

Basic information

species	Zea mays
transcript	GRMZM5G845682_T02
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G845682_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g44560.1 (Oryza sativa), 3'ss of exon 17

gtaatcaagtatttatttactaccagtaaactagatcttaaatagatttatgtgaatattttaaatatttgtactaccttttgctttcttccagGTGGACAAGCAAAAACTCTAATGTTCGTTCAAATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGCACTTTAAAGTTTGCTGAAAGGGTGTCTGG
|||||||| |||||| ||   |  | | |   |  |   |  ||||||||||    | |||  ||   |  |  ||     |  | |||| |||||||||||||||| || |||||||| ||||||||||||||||||||||||||||||||||| |||||||||||| ||||||||||||||||||| |||||
gtaatcaattatttagttgaaa--aatcatgcatgtgg-agttagatttatg---gtttttgtaactataatcttataaaataatctcttgcagGTGGACAAGCAAAGACACTAATGTTTGTTCAAATAAATCCTGATGTTGAGTCATATTCAGAGACTATAAGCACTCTAAAGTTTGCTGAAAGGGTTTCTGG

upper sequence: GRMZM5G845682_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA05G35130.1 (Glycine max), 3'ss of exon 15

gtaatcaagtatttatttactaccagtaaactagatcttaaatagatttatgtgaatattttaa--atatttg--tactaccttttgctttcttcca--gGTGGACAAGCAAAAACTCTAATGTTCGTTCAAATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGCACTTTAAAGTTTGCTGAAAGGGTGTCTGG
||||     |||| ||    |   |    ||  |   | ||     | |||||  || || | |  || ||||  |  |  ||||   ||| || ||  ||||  ||||| || || || ||||| |||||||| ||| | || ||    |||||||| |||||  | |||||||||||||||||||||||||| |||||
gtaaatctttattcatcatttgttatgtcacatgccttgaatcttttctatgtagattttcttatgatctttgactcttgtctttgattttattgcacagGTGACCAAGCGAAGACACTCATGTTTGTTCAAATTAATTCAGACGTAAGTTCATATTCTGAAACACTGAGCACTTTAAAGTTTGCTGAAAGGGTTTCTGG

upper sequence: GRMZM5G845682_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA05G37800.1 (Glycine max), 3'ss of exon 17

--------------------------------gtaatcaagtatttatttactaccagtaa-actagatcttaaatagatttatgtgaatattttaaatatttgtactaccttttgctttcttcca-----gGTGGACAAGCAAAAACTCTAATGTTCGTTCAAATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGCACTTTAAAGTTTGCTGAAAGGGTGTCTGG
                                ||| |    |||||  || |      |   | |     ||||  | |||   || | |   |||   | ||| | || ||||  |  |  |  |     ||||| ||||| ||||| || ||||| || ||  | |||||||||||||  |||||||| |||||| ||||||| || |||||||||||| |||| |||||
gtaattgttgccattattggtatcaatttacagtattgttatatttggtttcatttgtttgcattttgatttaagcatattgcagtca-tggcttactaaattgcaatagctttgtccgttgtatatgatagGTGGTCAAGCGAAAACCCTTATGTTTGTACAGCTTAATCCTGATGTTGCTTCATATTCTGAAACTGTAAGCACCTTGAAGTTTGCTGAACGGGTTTCTGG

upper sequence: GRMZM5G845682_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G01800.1 (Glycine max), 3'ss of exon 18

-----------------------------gtaatcaagtatttatttactaccagtaaactagatctt-----aaatagatttatgtgaatattt--taaat---atttgtactaccttttgctttcttccagGTGGACAAGCAAAAACTCTAATGTTCGTTCAAATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGCACTTTAAAGTTTGCTGAAAGGGTGTCTGG
                               | |   || | |||||  |  || |    |  || ||     ||  | |||   || |    ||  |||||   | | |   |  |  |||   | ||  |||||| ||||| ||||| || ||||| || ||  | |||||||||||||  |||||||| |||||| ||||||| || |||||||||||  |||| || ||
gtaattgttgccattattggtatcaatttacagttttgt-tatatttggtttcatttgtttgcattttgatttaagcatattgcagtcatggcttactaaattgcaatagctttgtcccttgtaattttatagGTGGTCAAGCGAAAACCCTTATGTTTGTACAGCTTAATCCTGATGTTGCTTCATATTCTGAAACTGTAAGCACCTTGAAGTTTGCTGAGCGGGTTTCCGG

upper sequence: GRMZM5G845682_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S34_101V6.1 (Physcomitrella patens), 3'ss of exon 17

--------------------------------------------------------------gtaatcaagtatttatttactaccagtaaactag-atcttaaatagatttatgtga-----atattttaaatatttgtactaccttttgctttcttccagGTGGACAAGCAAAAACTCTAATGTTCGTTCAAATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGCACTTTAAAGTTTGCTGAAAGGGTGTCTGG
                                                              | | | |||  |     || |   |||    |    | |||  |    || ||| |     || || |  |||||||   | | | | | | |  | ||||||| |||||||| ||| | |||||||| || ||||  || ||||| ||||| | |  ||| ||||||||||| || |||||||||||||| |||||   
gtatgggcatatgggaaagttattcagtactctgcatgttgactatagctaccttgttatttgcagtgaagagtaccagtagttttagttccttgttgtgttacttgtcattttgtaataagcatcttgtggatatttgc-ttgcatatggatcttgtgcagGTGGCCAAGCAAAGACTTTGATGTTCGTACACATAAGCCCAGATGTGGAGTCCTTTGGAGAGACTATAAGCACATTGAAGTTTGCTGAAAGAGTGTCAAC

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|6227215|gb|AW155744.1|AW155744

EST:     GTGCCTTATAGAAACAGCAAGCTAACACAAGTTCCTTCAAAGTTCTTTAG                         GTGGACAAGCAAAAACTCTAATGTTTCGTTCAAATAAATCCTGATGTTGAG
genomic: GTGCCTTATAGAAACAGCAAGCTAACACAAGTTC-TTCAAAGTTCTTTAGgtaatcaagt ... tttcttccagGTGGACAAGCAAAAACTCTAATGTT-CGTTCAAATAAATCCTGATGTTGAG

EST: gi|9733627|gb|BE512379.1|BE512379

EST:     CGTGCCTTATAGAAACAGCAAGCTAACACAAGTTCTTCAAAGTTCTTTAG                         GTGGACAAGCAAAAACTCTGATGTTCGTTCAAATAAATCCTGATGTTGAGT
genomic: CGTGCCTTATAGAAACAGCAAGCTAACACAAGTTCTTCAAAGTTCTTTAGgtaatcaagt ... tttcttccagGTGGACAAGCAAAAACTCTAATGTTCGTTCAAATAAATCCTGATGTTGAGT

EST: gi|211520868|gb|FL034525.1|FL034525

EST:     CGTGCCTTATAGAAACAGCAAGCTAACACAAGTTCTTCAAAGTTCTTTAG                         GTGGACAAGCAAAAACTCTAATGTTCGTTCAAATAAATCCTGATGTTGAGT
genomic: CGTGCCTTATAGAAACAGCAAGCTAACACAAGTTCTTCAAAGTTCTTTAGgtaatcaagt ... tttcttccagGTGGACAAGCAAAAACTCTAATGTTCGTTCAAATAAATCCTGATGTTGAGT

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), 49 (downstream exon)
Score: 175

CTTTCTGCGTTAGGCGATGTGATTTTTGCTCTGTCACAGAAAAGTATCCACGTGCCTTATAGAAACAGCAAGCTAACACAAGTTCTTCAAAGTTCTTTAGgtaatcaagt ... tttcttccagGTGGACAAGCAAAAACTCTAATGTTCGTTCAAATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGCACTTTAAAGTTTGCTGAAAGGGTGTCTGG

Block sizes: 47 (upstream exon), 44 (downstream exon)
Score: 14

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 17

Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 23

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

aaatagatttatgtgaatattttaaatatttgtactaccttttgctttcttccagGTGGACAAGCAAAAACTCTAATGTTCGTTCAAATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGCACTTTAAAGTTTGCTGAAAGGGTGTCTGG