ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaaactagttatagttagttctgtctttgtcaccaaagaaatttatcaaatatatatgcattggtttaaatataaagaaacatgtgtgcagGTGCTGTGGAAATGCGATGGGTTGACACATACTTCCCATTCACTAACCCGTCCTTTGAACTCGAGATATATTTTCAG

Basic information

species	Oryza sativa
transcript	LOC_Os12g34860.1
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G078756_T01 (Zea mays), 3'ss of exon 4

gtaaactagttatagttagttctgtctttgtcaccaaagaaatttatcaaat--atatatgcattggtttaaatataaagaaacat-gtgtgcagGTGCTGTGGAAATGCGATGGGTTGACACATACTTCCCATTCACTAACCCGTCCTTTGAACTCGAGATATATTTTCAG
|||||  | || ||| | ||||     || |||    ||    | |  ||||  ||   ||  |  | | || |||| | |||  |  | |||||||||||| || ||||||||||||||||||||||||||||| || ||||| |||||||| ||||| ||||||||||||
gtaaatcatttgtagcttgttc----cttatcatttgaggggatgacgaaattgatccttgtttcagataaactatagaaaaatgtcatctgcagGTGCTGTAGAGATGCGATGGGTTGACACATACTTCCCATTTACCAACCCATCCTTTGAGCTCGAAATATATTTTCAG

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AC211349.4_FGT001 (Zea mays), 3'ss of exon 4

gtaaactagttatagttagttctgtctttgtcaccaaagaaatttatcaaatatata--tgcattggtttaaatataaagaaaca-tgtgtgcagGTGCTGTGGAAATGCGATGGGTTGACACATACTTCCCATTCACTAACCCGTCCTTTGAACTCGAGATATATTTTCAG
|||||  | || ||  | |||      |||| |    ||    | || ||||| ||   ||  |  | | || |||| | |||     | |||||||||||| || ||||||||||||||||| ||||||||||| || ||||| |||||||| ||||| ||||| ||||||
gtaaatcacttgtaacttgttt----cttgttatttgaggggatgatgaaatagatccttgtttcagctaaactatagaaaaatggcatctgcagGTGCTGTAGAGATGCGATGGGTTGACACTTACTTCCCATTTACCAACCCATCCTTTGAGCTCGAAATATACTTTCAG

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA02G10060.1 (Glycine max), 3'ss of exon 4

---------gtaaactagttat-agttagttctgt--ctttgtcaccaaagaaatttatcaaatatatatgcattggtttaaatataaagaaacatgtgtgcagGTGCTGTGGAAATGCGATGGGTTGACACATACTTCCCATTCACTAACCCGTCCTTTGAACTCGAGATATATTTTCAG
         |    |||||||| |  | ||  | |  |||||    |||| | | ||  ||||  ||  | | |     ||||| |        |    | ||||||||||||||||||| ||||| || || || |||||||| ||||| || || |||||||| || || |||||  ||
tatacacaaggcgtctagttatgaacttgtgatattcctttgaagtcaaatataatttgcaaagctacgtactta----taaattttcccttttactgtttcagGTGCTGTGGAAATGCGCTGGGTGGATACTTATTTCCCATTTACTAATCCATCATTTGAACTTGAAATTTATTTCAAG

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA18G52890.1 (Glycine max), 3'ss of exon 6

gtaaactagttatagttagttctgtctt--tgtcaccaaagaaatttatcaaatatatatgcattggtttaaatataaagaaa------catgtgtg---cagGTGCTGTGGAAATGCGATGGGTTGACACATACTTCCCATTCACTAACCCGTCCTTTGAACTCGAGATATATTTTCAG-----------------------
   | |    |  |  |   |||  |      | |   ||   ||||      | || ||    |  | |    ||  | |        | | || |   ||||||||||||||||||| ||||| || || || |||||||| ||||| || || |||||||| || ||||||||  ||                       
---agcctcctccatctccctctaaccaaacattatgtaaatgattttctttttttaaatagccttctctgcgcatttatagtttttcccttttgcgtttcagGTGCTGTGGAAATGCGCTGGGTGGATACTTATTTCCCATTTACTAATCCATCGTTTGAACTTGAAATATATTTCAAGGCATGCTATGCATACTTATCTCT

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT3G58140.1 (Arabidopsis thaliana), 3'ss of exon 4

--------------------------------------------------------------------gtaaactagttatagttagttctgtctttgtcaccaaagaaatttatcaaatatatatgcattggtttaaatataaagaaacatgtgtg-----cagGTGCTGTGGAAATGCGATGGGTTGACACATACTTCCCATTCACTAACCCGTCCTTTGAACTCGAGATATATTTTCAG
                                                                       |  |  |||   | | |  |   ||  |     ||||| ||    ||||||| ||| | |  ||| | | | |       | | ||     ||||| | ||||| ||| |||||||||| ||||| |||||||| || || || || ||||| || |||||||||||| ||
gtacattaagatccaataaacaatctatattcttcagcaagtgtaaataacttcaaagatggtttattaagagttgtttaggatgattatttcattaatttaagaagaagttggggaaatatacatgaaataatttga-tctgagcttctttttttggctgccagGTTCGGTGGAGATGAGATGGGTTGATACATATTTCCCATTTACCAATCCATCTTTTGAGCTTGAGATATATTTTAAG

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv19s0027g01220.t01 (Vitis vinifera), 3'ss of exon 4

-------------gtaaactagtt-atagttagttctgtctttgtcaccaaagaaat-ttatcaaatatatatgcattggtttaaatataaagaaacatgtgtgcagGTGCTGTGGAAATGCGATGGGTTGACACATACTTCCCATTCACTAACCCGTCCTTTGAACTCGAGATATATTTTCAG------------
             | || |||    | || ||||| |    |||      |  | ||  | |  |  || | ||   |||  ||||| |   ||||    | |||||||  |||||||||||| ||| |||| ||||| ||||| ||||| ||||| || |||||||| |||||||||||||||            
tcttgaaatttctgaaatctatcagaaaggtagttttcatcttggggtttaccatatactgtatagaatctgtg---tgggctaaatctgttgaaa----tttgcagGTAATGTGGAAATGCGCTGGATTGATACATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGGTATGCTTTTGA

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv19s0027g01150.t01 (Vitis vinifera), 3'ss of exon 5

-------------gtaaactagtt-atagttagttctgtctttgtcaccaaagaaatttatcaaatatatatgcattggtttaaatataaagaaacatgtgtgcagGTGCTGTGGAAATGCGATGGGTTGACACATACTTCCCATTCACTAACCCGTCCTTTGAACTCGAGATATATTTTCAG
             | || |||    | || | ||| |    |||      |  ||||     | | | || ||| | || | |||| ||  ||||    | |||||||  |||||||||||| ||| |||| ||||| ||||| ||||| ||||| || |||||||| ||||| |||||||||
tcttgaaatttctgaaatctatcagaaaggtggttttcatcttggggtttaccaaatactgtataga-atctgcgtgggct-aaatctattgaaa----tttgcagGTAATGTGGAAATGCGCTGGATTGATACATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATGTATTTTCAG

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv11s0103g00120.t01 (Vitis vinifera), 3'ss of exon 4

--gtaaactagttatagttagttct----gtctttgtcaccaaagaaatttatcaaata-tatatgcatt------ggtttaaatataaagaaacatgtgtgcagGTGCTGTGGAAATGCGATGGGTTGACACATACTTCCCATTCACTAACCCGTCCTTTGAACTCGAGATATATTTTCAG
   |||| |   |  | |   |       |   |||||| |   ||  |||| || ||| | |||| | |      ||  ||||| |   ||||    | |||||||| |||||||||||| ||| |||| ||||| ||||| ||||| ||||| || |||||||| |||||||||||||||
ccttaaaatttctgaaatctatcagaaaggaggttgtcatctt-gaggtttaccatatactgtatggaatctccgtgggctaaatctgttgaaa----tttgcagGTGATGTGGAAATGCGCTGGATTGATACATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAG

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|24468878|gb|CA305827.1|CA305827

EST:     AGCTGCAGACCTCAAGAAAACACTGGAAGGCTTGGCAAAACATCTCTTTG                         GTGCTGTGGAAATGCGATGGGTTGACACATACCTTCCCATTCACTAACCCG
genomic: AGCTGCAGACCTCAAGAAAACACTGGAAGGCTTGGCAAAACATCTCTTTGgtaaactagt ... atgtgtgcagGTGCTGTGGAAATGCGATGGGTTGACACATA-CTTCCCATTCACTAACCCG

EST: gi|29629251|gb|CB634262.1|CB634262

EST:     AGCTGCAGACCTCAAGAAAACACTGGAAGGCTTGGCAAAACATCTCTTTG                         GTGCTGTGGAAATGCGATGGGTTGACACATACTTCCCATTCACTAACCCGT
genomic: AGCTGCAGACCTCAAGAAAACACTGGAAGGCTTGGCAAAACATCTCTTTGgtaaactagt ... atgtgtgcagGTGCTGTGGAAATGCGATGGGTTGACACATACTTCCCATTCACTAACCCGT

EST: gi|29662500|gb|CB658775.1|CB658775

EST:     AGCTGCAGACCTCAAGAAAACACTGGAAGGCTTGGCAAAACATCTCTTTG                         GTGCTGTGGAAATGCGATGGGTTGACACATACTTCCCATTCACTAACCCGT
genomic: AGCTGCAGACCTCAAGAAAACACTGGAAGGCTTGGCAAAACATCTCTTTGgtaaactagt ... atgtgtgcagGTGCTGTGGAAATGCGATGGGTTGACACATACTTCCCATTCACTAACCCGT

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: 68 (upstream exon), 65 (downstream exon)
Score: 18

TTCACTCCAGATGAATGGTCAGATTCTGGCATGGATGGGACAGCATATGCAGCTGCAGACCTCAAGAAAACACTGGAAGGCTTGGCAAAACATCTCTTTGgtaaactagt ... atgtgtgcagGTGCTGTGGAAATGCGATGGGTTGACACATACTTCCCATTCACTAACCCGTCCTTTGAACTCGAGATATATTTTCAG

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

agaaatttatcaaatatatatgcattggtttaaatataaagaaacatgtgtgcagGTGCTGTGGAAATGCGATGGGTTGACACATACTTCCCATTCACTAACCCGTCCTTTGAACTCGAGATATATTTTCAG