ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaagtattcttcttatctatgctgctgtaacttgtgatcacacaatactcatctgaaaactttgcagATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAAAGCTGTTATGAAAAACTCTGGAACTGCAATGCTTGGTGTTGGTGTTTCTTCCAGCAAAAATC

Basic information

species	Oryza sativa
transcript	LOC_Os04g56970.1
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os04g56970.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G119773_T01 (Zea mays), 3'ss of exon 4

----gtaagtattcttcttatctatgctg------ctgtaacttgtgatcacacaatactcatctgaaaactttgcagATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAAAGCTGTTATGAAAAACTCTGGAACTGCAATGCTTGGTGTTGGTGTTTCTTCCAGCAAAAATC
    ||   |  ||  |||  ||   ||       ||| || |||| ||||   |   || ||  |  ||| ||||||||||| ||||||||||||||||||||||||||||| |||||||| |||||||||||||||||||| ||||| ||||||||||||||||||||||||||||
gtgggtggtttctcccctttcctgctctaacttatctgcaaattgttatcatgta--ccttatgagtgaacattgcagATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAAAACTCTGGAACTGCCATGCTCGGTGTTGGTGTTTCTTCCAGCAAAAATC

upper sequence: LOC_Os04g56970.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA08G43500.1 (Glycine max), 3'ss of exon 5

-------------------------------gtaagtattcttcttatctatgctgctgt-aacttgtgatcacacaatactcatctgaaaacttt-gcagATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAAAGCTGTTATGAAAAACTCTGGAACTGCAATGCTTGGTGTTGGTGTTTCTTCCAGCAAAAATC
                                 || || |       |  ||  || ||| | ||| |||  | |  ||   |   || |   |||  |||||||| || ||||| ||||| |||||||||||||| |||||||| |||||| ||||||||||||| ||||||||||| |||||||| ||||| ||||| |
tatttgagtgttgctcctccaccataattggacaattaatgaaaa-gtacattttgatgtcagcttttgaggatattatttgctgttgcatctttttacagATACCCGGGCTTGTAAATGTGGATTTTGCTGATGTAAAAGCTGTGATGAAAGACTCTGGAACTGCTATGCTTGGTGTGGGTGTTTCCTCCAGTAAAAACC

upper sequence: LOC_Os04g56970.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA18G10030.1 (Glycine max), 3'ss of exon 5

--------------------------------------gtaagtattcttcttatctatgctgctgtaacttgtgatcacacaatactcatctgaaaactttgcagATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAAAGCTGTTATGAAAAACTCTGGAACTGCAATGCTTGGTGTTGGTGTTTCTTCCAGCAAAAATC
                                      ||||      || | || |  |||  |  |   ||| ||       |||   |||      ||| ||||||||||| ||||| ||||| |||||||||||||| |||||||| |||||| ||||||||||||||||||||||||| |||||||| ||||| ||||| |
tttcagtgttgctcctccatcataattggacaattaatgtaaagtacattttgatgtcagcttat-caggatgttattcagtgttacgtgtct-----ttttacagATACCTGGGCTTGTAAATGTGGATTTTGCTGATGTAAAAGCTGTGATGAAAGACTCTGGAACTGCAATGCTTGGTGTGGGTGTTTCCTCCAGTAAAAACC

upper sequence: LOC_Os04g56970.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA02G46530.1 (Glycine max), 3'ss of exon 4

---------------------------gtaagtattcttcttatctatgctgctgtaacttgtgatc----acacaatactcatctgaaaact-ttgcagATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAAAGCTGTTATGAAAAACTCTGGAACTGCAATGCTTGGTGTTGGTGTTTCTTCCAGCAAAAATC
                            |  | |||| | | |    |    |  |   || |  |     |||  |||  |   ||     | |||||| ||||||||||||||||||| |||||||| ||||| |||||||| |||||| ||||||| |||||||||||||| || |||||||| ||| | ||||| |
tcacttcttcataattgggcattttggctttgcattcatgtcaagggtatgtccatgctttttttttctcgacattataaactgttgtgccttcttgcagGTACCTGGACTTGTCAATGTGGATTTTGCAGATGTAAAAGCTGTGATGAAAGACTCTGGGACTGCAATGCTTGGAGTAGGTGTTTCCTCCGGTAAAAACC

upper sequence: LOC_Os04g56970.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA14G02110.1 (Glycine max), 3'ss of exon 4

----------------------------gtaagtattcttcttatctatgctgctgtaacttgtgatcacacaatactcatctgaaaa----ctttgcagATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAAAGCTGTTATGAAAAACTCTGGAACTGCAATGCTTGGTGTTGGTGTTTCTTCCAGCAAAAATC
                             |  | |||  | | |    |    |  |   || |  || ||  | | | | |||          |||||| ||||||||||||||||||| |||||||||||||| |||||||| |||||| ||||||| ||||||||||||||||| |||||||| ||| | ||||| |
acttctccttcataattgggcattgtggctttgcatttatgtcaagggtatgtccatggatttttttctcaacacagtaaactggtgtgccttcttgcagGTACCTGGACTTGTCAATGTAGATTTTGCTGATGTAAAAGCTGTGATGAAAGACTCTGGGACTGCAATGCTTGGTGTAGGTGTTTCATCCGGTAAAAACC

upper sequence: LOC_Os04g56970.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G55280.1 (Arabidopsis thaliana), 3'ss of exon 4

---------------------------------------gtaagtattcttcttatctatgctgctgtaacttgtgatcacacaatactcatctgaaaactttgcagATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAAAGCTGTTATGAAAAACTCTGGAACTGCAATGCTTGGTGTTGGTGTTTCTTCCAGCAAAAATC
                                         | | || ||| ||   |      |   |  || |||  | ||| ||   || |      ||| |||||||||||||| |||||||| |||||||| |||||||| || || |||||| | ||||||||||||||||| || || |||||||||||||||||||| |
gtgagtctatgtattgtataaagcacataacaagttggttgatgaatgcttattgattg-atccccaaagattctgaggaaacagtatatattttgttctttttcagATACCTGGACTAGTCAATGTAGATTTTGCAGATGTGAAGGCAGTCATGAAAGATTCTGGAACTGCAATGCTCGGGGTAGGTGTTTCTTCCAGCAAAAACC

upper sequence: LOC_Os04g56970.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv19s0090g01320.t01 (Vitis vinifera), 3'ss of exon 4

--------------------------------gtaagtattctt-cttatctatgctgctgtaact-tgtgatcacacaatactcatctgaaaactttgcagATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAAAGCTGTTATGAAAAACTCTGGAACTGCAATGCTTGGTGTTGGTGTTTCTTCCAGCAAAAATC
                                   | || |     |||||| ||||| ||   || | | ||   | ||||  | | |      |||||||||||| || || || |||||||||||||| ||||| || || || |||||  |||||||||||||||||||||| || || ||||||||||||||||| |
actgatttattatgatattttcctgattaatttccaatactgaagtttatctttgctgttgatcctatataatt-taaaatag-cgtgtccttgttttgcagATACCCGGGCTGGTAAATGTTGATTTTGCAGATGTAAAGGCAGTCATGAAGGACTCTGGAACTGCAATGCTTGGAGTGGGGGTTTCTTCCAGCAAAAACC

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|2311708|gb|C27863.1|C27863

EST:     GGAATATCAGATATTATTACA                         ATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAAAGCTGTTATGAAA
genomic: GGAATATCAGATATTATTACAgtaagtattc ... aactttgcagATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAAAGCTGTTATGAAA

EST: gi|29655620|gb|CB651895.1|CB651895

EST:     CAGATGATGTTCTTCGTCAAGGTGTCCAAGGAATATCACATATTATTACA                         ATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAAAGCTGTTATGACA
genomic: CAGATGATGTTCTTCGTCAAGGTGTCCAAGGAATATCAGATATTATTACAgtaagtattc ... aactttgcagATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAAAGCTGTTATGAAA

EST: gi|29655650|gb|CB651925.1|CB651925

EST:     CAGATGATGTTCTTCGTCAAGGTGTCCAAGGAATATCAGATATTATTACA                         ATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAAAGCTGTTATGAAA
genomic: CAGATGATGTTCTTCGTCAAGGTGTCCAAGGAATATCAGATATTATTACAgtaagtattc ... aactttgcagATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAAAGCTGTTATGAAA

EST: gi|29655649|gb|CB651924.1|CB651924

EST:     CAGATGATGTTCTTCGTCAAGGTGTCCAAGGAATATCAGATATTATTACA                         ATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAGAGCTGTTATGAAA
genomic: CAGATGATGTTCTTCGTCAAGGTGTCCAAGGAATATCAGATATTATTACAgtaagtattc ... aactttgcagATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAAAGCTGTTATGAAA

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: 54 (upstream exon), 69 (downstream exon)
Score: 11

ATTAGATGTTGTTGATGAAAACACGCCCTTGCAAGATGCGTTTCTTCTTGCAGATGATGTTCTTCGTCAAGGTGTCCAAGGAATATCAGATATTATTACAgtaagtattc ... aactttgcagATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAAAGCTGTTATGAAAAACTCTGGAACTGCAATGCTTGGTGTTGGTGTTTCTTCCAGCAAAAATC

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttatctatgctgctgtaacttgtgatcacacaatactcatctgaaaactttgcagATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAAAGCTGTTATGAAAAACTCTGGAACTGCAATGCTTGGTGTTGGTGTTTCTTCCAGCAAAAATC