ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtatggctattacctggtttcatgtttaggttcagttcattatgaatttgcacgtttgcttaatcaacaacttctgtctgaattgttattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTTGGAGTTGACAGGTGGTGCTTCCATGACAGGGATATTGCCCCTGATGGCAAAACACTCACG

Basic information

species	Oryza sativa
transcript	LOC_Os07g47290.1
intron #	5
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G313536_T01 (Zea mays), 3'ss of exon 4

gtatggctattacctggtttcatgtttaggttcagttc-----------attatgaatttgcacgtttgcttaatcaac-aacttctgtctgaattgttattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTTGGAGTTGACAGGTGGTGCTTCCATGACAGGGATATTGCCCCTGATGGCAAAACACTCACG
|||||   ||  |||    |    ||  | || ||| |            |||||  || |   ||||| |  |  ||| ||||||||| | || ||  ||| |||||||||||||||||||||||||||||||| | |||||  |||  ||||||||||||||||||||||||||||| ||||| || |||||    
gtatgatgatcgcctaacctacctttgtgctttagtcctagccttctgggttatgttttggtctgtttgttggaagaactaacttctgtttcaactgacatttcagTGAGAGCTCACTTTGAGTTCATGGAGAAGTTGGGAGTCAACAAATGGTGCTTCCATGACAGGGATATTGCCCCGGATGGGAAGACACTTGAA

upper sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G005493_T01 (Zea mays), 3'ss of exon 5

gtatggctattacctggtttcatgtttaggttcagttca----ttatgaatttgcacgtttgcttaatcaacaacttctgtctgaattgttattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTTGGAGTTGACAGGTGGTGCTTCCATGACAGGGATATTGCCCCTGATGGCAAAACACTCACG
|||||   || ||||    | |   |  | |  |||||     || ||  ||   | ||||| |  |  |  ||||||||| | |||   ||||||||||||||||||||||||||||||||||||||| || |||||||  |||||||||||||| |||||||||||||||||||| ||||| |||   
gtatgaggatcacctaacctaactctatgttgtagttccagccttctgggtt---atgtttgttgga--actaacttctgtttcaatcactattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTGGGGGTTGACAAATGGTGCTTCCATGATAGGGATATTGCCCCTGATGGGAAAACTCTCGAA

upper sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G335948_T01 (Zea mays), 3'ss of exon 3

gtatggctattacctggt-----ttcatg-tttaggttcagttc-----attatgaatttgcacgtttgcttaatcaac-aacttctgtctgaattgttattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTTGGAGTTGACAGGTGGTGCTTCCATGACAGGGATATTGCCCCTGATGGCAAAACACTCACG
|||||   ||  |||        ||  || |||||   |||         |||||  || |   ||||| |  |  ||| ||||||||| | || ||  |||||||||||||||||||||||||||||||||||| | |||||  |||  |||||||||||||| |||||||||||||| ||||| || |||||    
gtatgatgatcgcctaacctacctttgtgctttagtcccagccttctgggttatgttttggtctgtttgttggaagaactaacttctgtttcaactgacattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGTTGGGAGTCAACAAATGGTGCTTCCATGATAGGGATATTGCCCCGGATGGGAAGACACTTGAA

upper sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G081682_T02 (Zea mays), 3'ss of exon 5

gtatggctattacctggt-----ttcatgtt-taggttcagttc-----attatgaatttgcacgtttgcttaatcaac-aacttctgtctgaattgttattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTTGGAGTTGACAGGTGGTGCTTCCATGACAGGGATATTGCCCCTGATGGCAAAACACTCACG
|||||   ||| |||        ||  || | |||   |||         |||||  || |   ||||| |  |  ||| ||||||||| | || ||  |||||||||||||||||||||||||||||||||||| | ||||||||||  ||||||||||||||||||||||||||||| ||||| || || ||    
gtatgatgattgcctaacctacctttgtgctgtagtcccagccttctgggttatgttttggtctgtttgttggaagaactaacttctgtttcaactggcattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGTTGGGAGTTGACAAATGGTGCTTCCATGACAGGGATATTGCCCCGGATGGGAAGACTCTTGAA

upper sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AC190975.3_FGT004 (Zea mays), 3'ss of exon 2

gtatggctattacctggtttcatgtttaggttcagttcattatgaatttgcacgtttgcttaatcaacaacttctgtctgaattgttattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTTGGAGTTGACAGGTGGTGCTTCCATGACAGGGATATTGCCCCTGATGGCAAAACACTCACG
|||||   ||  |||    |    ||  | |  ||| |      |   | |  | ||   |  |        ||||| | |||||  |||||||||||||||||||||||||||||||||||| | ||||| ||||  ||||||||||||||||||||||||||||| ||||| || |||||    
gtatgatgatcgcctaacctacctttgtgttgtagtccc-----agccttctgggttatgttttgg------tctgtttcaattggcattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGTTGGGAGTCGACAAATGGTGCTTCCATGACAGGGATATTGCCCCGGATGGGAAGACACTTGAA

upper sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA17G07380.1 (Glycine max), 3'ss of exon 5

gtatggctattacctggtttcatgtttaggttcagttcattatgaatttgcacgtttgcttaatcaacaacttctgtctgaattgttattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTTGGAGTTGACAGGTGGTGCTTCCATGACAGGGATATTGCCCCTGATGGCAAAACACTCACG
|||||   |||      | ||  ||| |  | |    ||||  ||  ||    |||||  | |  ||  |    | ||| ||||   ||  ||||||||||| |||||||||||||    || || || ||||||   ||||| ||||| ||||||||||| ||||||||||| ||||| ||   |
gtatgttaattcttgactctccagttgatatacttcacattcagatatt---tgtttgtgtcacaaaataaaattctcttaatt---atcacagTGAGAGCTAACTTTGAGTTCATAAGCAAACTCGGTGTTGACTTTTGGTGTTTCCACGACAGGGATATAGCCCCTGATGGAAAAACTCTTGAG

upper sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT5G57655.1 (Arabidopsis thaliana), 3'ss of exon 4

gtatggctattacctggtttcatgtttaggttcagttcattatgaatttgcacgtttgcttaatcaacaacttctgtctgaattgttattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTTGGAGTTGACAGGTGGTGCTTCCATGACAGGGATATTGCCCCTGATGGCAAAACACTCACG
||| | | |     || ||| ||||| || |||  ||| ||||  | || |  ||    | | | |   | |  ||| | |        ||||||||||||| ||||||||||| || |||| |||||||||||  ||||||| || |||||||| || || || ||||||||||  |||||   |
gtaagtccagattgtgtttttatgtt-agtttctcttcgttatcgagttac-tgtgatttgagttactgattgttgtttaa--------tgcagTGAGAGCTAACTTTGAGTTCTTGAAGAAACTTGGAGTTGATTGGTGGTGTTTTCATGACAGAGACATAGCACCTGATGGCACTACACTTGAG

upper sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv11s0052g01710.t01 (Vitis vinifera), 3'ss of exon 6

gtatggctattacctggtttcatgtttaggttcagttcattatgaatttgcacgt------ttgcttaatcaacaacttctgtctg--aattgttattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTTGGAGTTGACAGGTGGTGCTTCCATGACAGGGATATTGCCCCTGATGGCAAAACACTCACG
         | |  ||  |  || ||    |||  || ||||    || | |  |      |  | | | | |    ||   |||   || |   | |  |||||||||  ||||||||||||| || ||||||||||| ||    ||||||||||||||||||||||| ||||||||||| ||||| ||   |
--------gtaagttgaatctatattgttcttccatttattaattgttggaaaatagtgtataacatgaccgatctttttcctctattaaatacaact-tagTGAGAGCCAACTTTGAGTTCATTGAAAAGCTTGGAGTCGATCTATGGTGCTTCCATGACAGGGATATAGCCCCTGATGGTAAAACCCTGGAG

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|29625366|gb|CB630377.1|CB630377

EST:     TTGGCCTTGGGAGGATGGCACAAATTCGTTGGACATGGCTAAGAGAAGAA                         TGAGAGCTCACTTTGAGTTCATGGAGAAGCTTGGAGTTGACAGGTGGTGCT
genomic: TTGGCCTTGGGAGGATGGCACAAATTCGTTGGACATGGCTAAGAGAAGAAgtatggctat ... gttattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTTGGAGTTGACAGGTGGTGCT

EST: gi|29637953|gb|CB642962.1|CB642962

EST:     TTGGCCTTGGGAGGATGGCACAAATTCGTTGGACATGGCTAAGAGAAGAA                         TGAGAGCTCACTTTGAGTTCATGGAGAAGCTTGGAGTTGACAGGTGGTGCT
genomic: TTGGCCTTGGGAGGATGGCACAAATTCGTTGGACATGGCTAAGAGAAGAAgtatggctat ... gttattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTTGGAGTTGACAGGTGGTGCT

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: 41 (upstream exon), 71 (downstream exon)
Score: 67

CATACGTTCCGTGGTACTGGAGGAGATCCTTTTGGTGCCCCTACAAAGTCTTGGCCTTGGGAGGATGGCACAAATTCGTTGGACATGGCTAAGAGAAGAAgtatggctat ... gttattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTTGGAGTTGACAGGTGGTGCTTCCATGACAGGGATATTGCCCCTGATGGCAAAACACTCACG

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttatgaatttgcacgtttgcttaatcaacaacttctgtctgaattgttattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTTGGAGTTGACAGGTGGTGCTTCCATGACAGGGATATTGCCCCTGATGGCAAAACACTCACG