ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtacacagactgcagtgatgaatttacaggagcataacattttatgtaagccttgcagaagaaagcaagtaacctcatttaatatcaaattattttgtagGACTTTGGTGATGACAAGCCCTTGTCTTGGAGCCACTTCACTGCTGAGGGAGATGTTGAGTTCAAAGCTTTGCTCTTTGTTCCTCCCAAGGCTCCACATG

Basic information

species	Oryza sativa
transcript	LOC_Os06g50300.1
intron #	9
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G399073_T02 (Zea mays), 3'ss of exon 11

-------------------------gtacaca--gactgcagtgatgaatttacaggagcataacattt-tatgtaagccttgcagaagaaagcaagtaacctcatttaatatcaaattattttgtagGACTTTGGTGATGACAAGCCCTTGTCTTGGAGCCACTTCACTGCTGAGGGAGATGTTGAGTTCAAAGCTTTGCTCTTTGTTCCTCCCAAGGCTCCACATG
                         ||||  |  || |    |  |   |||     |  | | | ||| | |||  | ||||  || ||||   | |    | | || |||  || |||||||  ||||||| ||||||||||||||  ||  ||||||||||||||||||||| |||||||||||||||||||||||||||||  |||| || |||||||| ||||
gtaatactgtagtgatgaattagtagtaccgaatgatttttttattttttttggtcaaagaaagcttttgtttgttggtcttgttgatgaaac--atttgtataacttcataataa-ttatttttcagGACTTCGGTGATGACAAGCCTATGGGTTGGAGCCACTTCACTGCTGAAGGAGATGTTGAGTTCAAAGCTTTGCTCTTCATTCCACCGAAGGCTCCGCATG

upper sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G141931_T01 (Zea mays), 3'ss of exon 9

gtacacagactgcagtgatgaatt---tacaggagcataacattttatgt---------aagccttgcagaagaa--------agcaagtaacctcatttaa--tatcaaattattttgtagGACTTTGGTGATGACAAGCCCTTGTCTTGGAGCCACTTCACTGCTGAGGGAGATGTTGAGTTCAAAGCTTTGCTCTTTGTTCCTCCCAAGGCTCCACATG
    | | |||| ||  ||| |||   ||   |  |  |||||||  | |         |||| ||||      |           || ||     || |||  || ||| |  ||||  ||||||| ||||||||||||||  ||  |||||||||||||||||| || |||||||||||||||||||||||||||||| | || || |||||||||||||
--gtaaatactgtagcaatggattagttagtagtactcaacatttgtttttgccaaagaaagctttgcttgtacaccttgtttgataaatatttgtatataacttaacaattcttttttcagGACTTCGGTGATGACAAGCCTATGGGTTGGAGCCACTTCACTGCCGAAGGAGATGTTGAGTTCAAAGCTTTGCTCTTTATCCCCCCGAAGGCTCCACATG

upper sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA14G40320.2 (Glycine max), 3'ss of exon 9

-----gtacacagactgcagtgatgaat--ttacaggagcataacattttatgtaagccttgcagaagaaagcaagtaacc--tcatttaatatcaaatt---attttgt--agGACTTTGGTGATGACAAGCCCTTGTCTTGGAGCCACTTCACTGCTGAGGGAGATGTTGAGTTCAAAGCTTTGCTCTTTGTTCCTCCCAAGGCTCCACATG
      |   ||   |||  || |   |  ||| |     |    ||||  ||| |   |  |   |   ||   || |    ||||  | |     |||    ||||||  |||| ||  ||||||| || || ||  | ||||| || |||||||||||||| |||||||||||||| ||  | || ||||| || || ||||| || || |
gtaacattgccaatttgccatgcttgttccttatacatcaagggaatttattgtgaaattcacttcactgagtttgttaatattcataaagttgtggatttatgttttgtgcagGATTTCAGTGATGAGAAACCTTTAGCATGGAGTCATTTCACTGCTGAGGGTGATGTTGAGTTCAAGGCAGTCCTGTTTGTACCACCTAAGGCACCTCAAG

upper sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S126_38V6.1 (Physcomitrella patens), 3'ss of exon 9

------------------------------------------------------------------------------------------gtacacagactgcagtgatgaatttacaggagcataa-cattttatgtaagccttgcagaagaaagcaagtaacctcatttaatatcaaattattttgt--agGACTTTGGTGATGACAAGCCCTTGTCTTGGAGCCACTTCACTGCTGAGGGAGATGTTGAGTTCAAAGCTTTGCTCTTTGTTCCTCCCAAGGCTCCACATG
                                                                                          | |    | ||       |  ||    ||| | |||| ||  |  |       ||| ||      |         || |||  | ||   || | |  |  |||| ||  ||   ||||||||  |||| |||||||| |||| ||||||||||||||| |||||||||||  |  | | | | ||||| ||||||||  |||
gtgagggttggacttcaaatcctatgatagacttggctatctgtcaaacgtgtgattaagacaagaggttgccgcatgttgagacttgtggaagttggtctctgaatctatatgactaggggaataatcagctcgtcatgttgttgaagtgacgggttgtcctaatcttttgttgtccttttttctcattcagGATTTCAGTACCGACAAGCCAATGTCGTGGAGCCATTTCAATGCTGAGGGAGATGTGGAGTTCAAAGCAGTCATATATATCCCTCCTAAGGCTCCTTATG

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|88964250|gb|CI045443.1|CI045443

EST:     AGGAGGTTACTGAAGAAGAATACACAAAGTTTTACCACTCACTTGCTAAG                         GACTTTGGTGATGACAAGCCCTTGTCTTGGAGCCACTTCACTGCTGAGGGA
genomic: AGGAGGTTACTGAAGAAGAATACACAAAGTTTTACCACTCACTTGCTAAGgtacacagac ... tattttgtagGACTTTGGTGATGACAAGCCCTTGTCTTGGAGCCACTTCACTGCTGAGGGA

EST: gi|86902578|gb|CI304397.1|CI304397

EST:     CAAAGTTTTACCACTCACTTGCTAAG                         GACTTTGGTGATGACAAGCCCTTGTCTTGGAGCCACTTCACTGCTGAGGGA
genomic: CAAAGTTTTACCACTCACTTGCTAAGgtacacagac ... tattttgtagGACTTTGGTGATGACAAGCCCTTGTCTTGGAGCCACTTCACTGCTGAGGGA

EST: gi|10611619|gb|AU108385.1|AU108385

EST:     AATACACAAAG-TTTACCACTCAC-TGCTAA-                         GACTTTGGTGATGACAAGCCCCTTGTC-TGGAGCCACTTCACTGCTGAGGG
genomic: AATACACAAAGTTTTACCACTCACTTGCTAAGgtacacagac ... tattttgtagGACTTTGGTGATGACAAG-CCCTTGTCTTGGAGCCACTTCACTGCTGAGGG

EST: gi|58689260|gb|CK077947.1|CK077947

EST:     AGGAGGTTACTGAAGAAGAATACACAAAGTTTTACCACTCACTTGCTAAG                         GACTTTGGTGATGACAAGCCCTTGTCTTGGAGCCACTTCACTGCTGAGGGA
genomic: AGGAGGTTACTGAAGAAGAATACACAAAGTTTTACCACTCACTTGCTAAGgtacacagac ... tattttgtagGACTTTGGTGATGACAAGCCCTTGTCTTGGAGCCACTTCACTGCTGAGGGA

EST: gi|15008597|gb|AU222985.1|AU222985

EST:     CAAAGTTTTACCACTCACTTGNTAAG                         GACTTTGGTGATGACAAGCCCTTGTCTTGGAGCCNCTTCACTGCTGAGGGA
genomic: CAAAGTTTTACCACTCACTTGCTAAGgtacacagac ... tattttgtagGACTTTGGTGATGACAAGCCCTTGTCTTGGAGCCACTTCACTGCTGAGGGA

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: 75 (upstream exon), 75 (downstream exon)
Score: 88

TGAGTGGGAGCTTCTGAATGATGTGAAGGCTATATGGCTTCGTAGCCCTAAGGAGGTTACTGAAGAAGAATACACAAAGTTTTACCACTCACTTGCTAAGgtacacagac ... tattttgtagGACTTTGGTGATGACAAGCCCTTGTCTTGGAGCCACTTCACTGCTGAGGGAGATGTTGAGTTCAAAGCTTTGCTCTTTGTTCCTCCCAAGGCTCCACATG

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gtaagccttgcagaagaaagcaagtaacctcatttaatatcaaattattttgtagGACTTTGGTGATGACAAGCCCTTGTCTTGGAGCCACTTCACTGCTGAGGGAGATGTTGAGTTCAAAGCTTTGCTCTTTGTTCCTCCCAAGGCTCCACATG