ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TAAGCATTCAAATGCTTACATGCTTGTGTACATTCGTGAAAGTGACAGAGAAAAAATTATTTGCAATTTAGATGAAAACGACATACCAGAACACCTTAAGgtaatacttcttcccttttcttttcttgggtatcacagaacttgttctgatgtcatgaaaacctttaccag

Basic information

species	Oryza sativa
transcript	LOC_Os01g56490.1
intron #	13
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os01g56490.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA20G11330.1 (Glycine max), 5'ss of exon 5

TAAGCATTCAAATGCTTACATGCTTGTGTACATTCGTGAAAGTGACAGAGAAAAAATTATTTGCAATTTAGATGAAAACGACATACCAGAACACCTTAAGgtaatacttcttcccttttcttttcttgggtatcacagaactt--gttctgatgt-catgaaaacctttaccag--------------------------
 ||| | ||||||||||| ||||||||||| || |||||||||||||  || ||||| || |||||| | ||||| || |||||  ||| |||  | | |||||   |   | | | ||    | | ||    |  |  |     |  | | ||   |  || |  |||   ||                          
CAAGTACTCAAATGCTTATATGCTTGTGTATATACGTGAAAGTGACAAGGACAAAATCATATGCAATGTGGATGAGAAAGACATTGCAGCACATTTAAGGgtaagcatctgttcttatttacatttaggactccgaaagatgcaagcccagttgaatacaaacatgttttttagaatatgggtttggtgctaactcaacc

upper sequence: LOC_Os01g56490.1 (Oryza sativa), 5'ss of exon 13
lower sequence: AT5G06600.3 (Arabidopsis thaliana), 5'ss of exon 13

TAAGCATTCAAATGCTTACATGCTTGTGTACATTCGTGAAAGTGACAGAGAAAAAATTATTTGCAATTTAGATGAAAACGACATACCAGAACACCTTAAGgtaatacttcttcc--cttttcttttcttgggtatcacagaacttgtt----ctgatgtcatgaaaacctttaccag
 ||| | || ||||||||||||||||| || || || |||||||||| ||| ||||| || |||||  | ||||| || |||||| |||||||  | | ||||| |  | |||   | |||  ||  | |  |||    |   | |||    |||||        |   |||  |||
AAAGTACTCGAATGCTTACATGCTTGTATATATCCGAGAAAGTGACAAAGATAAAATAATCTGCAACGTTGATGAGAAAGACATAGCAGAACATTTAAGGgtaaaatattttcgggcattttcttagtagtttatttgcgtcttggttttacctgatcgttcattacattttgacag

upper sequence: LOC_Os01g56490.1 (Oryza sativa), 5'ss of exon 13
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 5'ss of exon 13

TAAGCATTCAAATGCTTACATGCTTGTGTACATTCGTGAAAGTGACAGAGAAAAAATTATTTGCAATTTAGATGAAAACGACATACCAGAACACCTTAAGgtaatacttc----ttcccttttcttttcttgggtatcacagaact---tgttctgatg--tcatgaaaacctttaccag------------
 ||| |||||||||| |||||||| ||||| || |||||||||||||  || ||||| ||||||||| | ||||| || |||||  | ||||| ||   ||||| | |      || | |||  |    ||   |    || |  |   | ||  ||||  | |  | |     | |||             
GAAGTATTCAAATGCATACATGCTGGTGTATATACGTGAAAGTGACAAGGACAAAATAATTTGCAATGTGGATGAGAAGGACATTGCTGAACATCTCCGGgtaagattctgctattacatttagtcaattttatttcttcaaatttctatttttggatgcatgactagagttcattccatggcttgcaccag

upper sequence: LOC_Os01g56490.1 (Oryza sativa), 5'ss of exon 13
lower sequence: Vv13s0073g00610.t01 (Vitis vinifera), 5'ss of exon 13

TAAGCATTCAAATGCTTACATGCTTGTGTACATTCGTGAAAGTGACAGAGAAAAAATTATTTGCAATTTAGATGAAAACGACATACCAGAACACCTTAAGgtaa--tacttcttcccttttcttttcttgggtatcacagaact-tgttctgatgtcatgaaaacctttaccag-------------------
 ||  | |||||||| |||||||||||||| || |||||||||||||  || ||||| ||||| ||| | || || || || ||  | ||||||||||  ||||  |  || ||      |  |   ||| ||    || |  | ||||||      |  |     || | ||                    
AAAATACTCAAATGCATACATGCTTGTGTATATACGTGAAAGTGACAAGGAGAAAATAATTTGTAATGTGGACGAGAAGGATATTGCTGAACACCTTAGAgtaagatgtttatttgtaaatactgagttgagttcttcaaacttctgttctttcaatagaattgtattgagcactttagttattatattccag

upper sequence: LOC_Os01g56490.1 (Oryza sativa), 5'ss of exon 13
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 5'ss of exon 13

TAAGCATTCAAATGCTTACATGCTTGTGTACATTCGTGAAAGTGACAGAGAAAAAATTATTTGCAATTTAGATGAAAACGACATACCAGAACACCTTAAGgtaatacttcttcccttttcttttcttgggtatcacagaacttgt---tctgatgt-catgaaaaccttta-ccag-------------------------
 ||  | |||||||| |||||||||||||| || |||||||||||||  || ||||| ||||| ||| | ||||| || |||||  | |||||||||| ||||| || | |    || | | |  |||     || |||  | ||   |   ||||   || |    |  | ||||                         
GAAATACTCAAATGCATACATGCTTGTGTATATACGTGAAAGTGACAAGGAGAAAATCATTTGTAATGTGGATGAGAAGGACATTGCTGAACACCTTAGGgtaaaacatttggttttatttgtaattgaactacagagatttggtaatttccatgtgtctgcatgtgtggatccagactgacaatcaaaatctaatcccag

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|89163644|gb|CI100534.1|CI100534

EST:     AAAAAATTATTTGCAATTTAGATGAAAACGACATACCAGAACACCTTAAG                         ATTAGGTTGAG
genomic: AAAAAATTATTTGCAATTTAGATGAAAACGACATACCAGAACACCTTAAGgtaatacttc ... cctttaccagATTAGGTTGAG

EST: gi|88223226|gb|CI223075.1|CI223075

EST:     AAAAAATTATTTGCAATTTAGATGAAAACGACATACCAGAACACCTTAAG                         ATTAGGTTGAGAAAAGAAAATGAAG
genomic: AAAAAATTATTTGCAATTTAGATGAAAACGACATACCAGAACACCTTAAGgtaatacttc ... cctttaccagATTAGGTTGAGAAAAGAAAATGAAG

EST: gi|86260523|gb|CI066396.1|CI066396

EST:     AAAAAATTATTTGCAATTTAGATGAAAACGACATACCAGAACACCATAAG                         ATTAAGTTGAGAAAAGAAAATGAAGAAAGAGAGTATAAG
genomic: AAAAAATTATTTGCAATTTAGATGAAAACGACATACCAGAACACCTTAAGgtaatacttc ... cctttaccagATTAGGTTGAGAAAAGAAAATGAAGAAAGAGAGTATAAG

EST: gi|86504086|gb|CI146719.1|CI146719

EST:     AAAAAATTATTTGCAACTTAGATGAAAACGACATACCAGAACACCTTAAG                         ATTAGGTTGAGAAAAGAAAATGAAG
genomic: AAAAAATTATTTGCAATTTAGATGAAAACGACATACCAGAACACCTTAAGgtaatacttc ... cctttaccagATTAGGTTGAGAAAAGAAAATGAAG

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), 63 (downstream exon)
Score: 32

TAAGCATTCAAATGCTTACATGCTTGTGTACATTCGTGAAAGTGACAGAGAAAAAATTATTTGCAATTTAGATGAAAACGACATACCAGAACACCTTAAGgtaatacttc ... cctttaccagATTAGGTTGAGAAAAGAAAATGAAGAAAGAGAGTATAAGAAAAAGGAGAAAGCAGAGGCCCACATGTTCACTGCATTAAAG