ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtatagtctgtcgtcttgtcacaaaatttgaacattgtgtgcatcggatccatgtcagttgacataatgttctctcattaatagGTTGGCATCAAGGACCATGAGTCGGTAGTGGTGAGGATAACAGGCTGCCCTAATGGATGCGCTAGACCATATATGGCAGAGGTTGGCTTTGTTGGTGATG

Basic information

species	Oryza sativa
transcript	LOC_Os05g42350.1
intron #	5
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os05g42350.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G090338_T01 (Zea mays), 3'ss of exon 5

gtata-gtctgtcgtcttgtcacaaaatt----tgaacat-----tgtgtgcatc-ggatccatgtcagttgacataatgttctctcattaatagGTTGGCATCAAGGACCATGAGTCGGTAGTGGTGAGGATAACAGGCTGCCCTAATGGATGCGCTAGACCATATATGGCAGAGGTTGGCTTTGTTGGTGATG
||||  ||||| | | |||| | ||| ||    || | ||     ||  |  ||  ||| || ||||| || |  | |   | |||  |||||||||||| ||||||||    ||||| || || ||||||||||| || |||||||||||||||||||||||||||||||||||| |||| |||||||||||||
gtatttgtctgacatattgtgagaaatttgttttgtagatgcagatgcatatatttggagccctgtcatttcatgttactgtatctgcttaatagGTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCTAATGGATGCGCTAGACCATATATGGCAGAGCTTGGTTTTGTTGGTGATG

upper sequence: LOC_Os05g42350.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA12G02200.1 (Glycine max), 3'ss of exon 5

gtatagtctgtcgtct-tgtcacaaaatttgaacattgtgtgcatcgg-atccatgtcagttgacataatgttctctcattaatagGTTGGCATCAAGGACCATGAGTCGGTAGTGGTGAGGATAACAGGCTGCCCTAATGGATGCGCTAGACCATATATGGCAGAGGTTGGCTTTGTTGGTGATG
|||| |     | | | | |  ||  |||   |  |  ||   |||   |  || |  | || | |   |  | |||       |||||||| | ||| |   |||||| || || || |||||||| |||||||||||||| || ||||||||||| ||||| ||| ||||  | ||||||||||
gtattgctgcacatatatatggcagtatt--gatttgatggagatcactaatcaggatacttaaaacttttctgtctgcaattcagGTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCTAATGGTTGTGCTAGACCATACATGGCTGAGCTTGGACTAGTTGGTGATG

upper sequence: LOC_Os05g42350.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA11G09890.1 (Glycine max), 3'ss of exon 5

gtatagtctgtcgtcttgtcacaaaatttgaacattgtgtgcatcgg-atccatgtcagttgacataatgttctctcattaat--agGTTGGCATCAAGGACCATGAGTCGGTAGTGGTGAGGATAACAGGCTGCCCTAATGGATGCGCTAGACCATATATGGCAGAGGTTGGCTTTGTTGGTGATG
|||| | |||      | |     | | |  |  |  ||   |||   |  || |  |  ||| | | | |||| ||   |||  |||||||| | ||| |   |||||| || || || |||||||| |||||||||||||| || ||||||||||| ||||| ||  ||||  | ||||||||||
gtattg-ctgcgtatatatatggcagtattgatttgatggagatcactaatcaggatacgtga-aaacttttctgtctgcaattcagGTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCTAATGGTTGTGCTAGACCATACATGGCTGAACTTGGACTAGTTGGTGATG

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|86829536|gb|CI286733.1|CI286733

EST:     AACGAGGGATTCTGCCGATTCTTAAACGAATTAGAGCAGTTTTTGATAAG                         GTTGGCATCAAGGACCATGAGTCGGTAGTGGTGAGGATAACAGGCTGCCCT
genomic: AACGAGGGATTCTGCCGATTCTTAAACGAATTAGAGCAGTTTTTGATAAGgtatagtctg ... tcattaatagGTTGGCATCAAGGACCATGAGTCGGTAGTGGTGAGGATAACAGGCTGCCCT

EST: gi|29621655|gb|CB626666.1|CB626666

EST:     AACGAGGGATTCTGCCGATTCTTAAACGAATTAGAGCAGTTTTTGATAAG                         GTTGGCATCAAGGACCATGAGTCGGTAGTGGTGAGGATAACAGGCTGCCCT
genomic: AACGAGGGATTCTGCCGATTCTTAAACGAATTAGAGCAGTTTTTGATAAGgtatagtctg ... tcattaatagGTTGGCATCAAGGACCATGAGTCGGTAGTGGTGAGGATAACAGGCTGCCCT

EST: gi|5002798|gb|AU067907.1|AU067907

EST:     GAGGGATTCTGCCGATTCTTAAACGAATTAGAGCAGTTTTTGATAAG                         GTTGGCATCAAGGACCATGAGTCGGTAGTGGTGAGGATAACAGGCTGCCCT
genomic: GAGGGATTCTGCCGATTCTTAAACGAATTAGAGCAGTTTTTGATAAGgtatagtctg ... tcattaatagGTTGGCATCAAGGACCATGAGTCGGTAGTGGTGAGGATAACAGGCTGCCCT

EST: gi|66947260|gb|AU312104.1|AU312104

EST:     AACGANGGATTCTGCCGATTCTNNAACGAATTAGAGCAGTTTTTGATAAG                         GTTGGCATCAAGGAC
genomic: AACGAGGGATTCTGCCGATTCTTAAACGAATTAGAGCAGTTTTTGATAAGgtatagtctg ... tcattaatagGTTGGCATCAAGGAC

EST: gi|29625861|gb|CB630872.1|CB630872

EST:     AACGAGGGATTCTGCCGATTCTTAAACGAATTAGAGCAGTTTTTGATAAG                         GTTGGCATCAAGGACCATGAGTCGGTAGTGGTGAGGATAACAGGCTGCCCT
genomic: AACGAGGGATTCTGCCGATTCTTAAACGAATTAGAGCAGTTTTTGATAAGgtatagtctg ... tcattaatagGTTGGCATCAAGGACCATGAGTCGGTAGTGGTGAGGATAACAGGCTGCCCT

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 1 RNA-Seqlibrary.

Block sizes: 69 (upstream exon), 72 (downstream exon)
Score: 58

CATGGCATGTCCTGCCTTACCACTGTGCCCTCTAGCACAAACAGAAGCTGAACGAGGGATTCTGCCGATTCTTAAACGAATTAGAGCAGTTTTTGATAAGgtatagtctg ... tcattaatagGTTGGCATCAAGGACCATGAGTCGGTAGTGGTGAGGATAACAGGCTGCCCTAATGGATGCGCTAGACCATATATGGCAGAGGTTGGCTTTGTTGGTGATG

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gaacattgtgtgcatcggatccatgtcagttgacataatgttctctcattaatagGTTGGCATCAAGGACCATGAGTCGGTAGTGGTGAGGATAACAGGCTGCCCTAATGGATGCGCTAGACCATATATGGCAGAGGTTGGCTTTGTTGGTGATG