Sequence
atgc intronic sequence ATGC exonic sequencegtgtttaactaatttcctttgcacaactattatgtttgccgcttttagtacataccttaattaatggagttattcttctataaattgcaacagTGCTGCGGTATTCCATAATGCAAGCACACGGTTCTGTGATGGGGCTCGCTTTGGTCTAGGTGCTGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g62900.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g62900.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G028535_T02 (Zea mays), 3'ss of exon 17
------------------------------------------gtgtttaactaatttcctttgcacaactattatgtttgccgctt--ttagtacataccttaattaatgga---gttattcttctataaattgcaacagTGCTGCGGTATTCCATAATGCAAGCACACGGTTCTGTGATGGGGCTCGCTTTGGTCTAGGTGCTGAG
| | || | | | || | | | || | | || || | | | || || | ||| || | || ||||||||||| || || || ||||||||||||||| |||| ||||||||| | || ||||| ||||||||||||
gtactgaaaccttctttccaacattcttgtggttgaactttgctatgcaagtgttatttgttactgatttgttcgatcattcaattgcctatgatgtttttagatctgacgacacatcattttttgtttaactgcaacagTGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTTTGGGCTAGGTGCTGAG
upper sequence: LOC_Os01g62900.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA07G16510.1 (Glycine max), 3'ss of exon 14
---gtgtttaactaatttcctt-tgcacaactattatgtttgccgcttttagtacatacct-taattaatggagtt--attcttctataaattgcaa-cagTGCTGCGGTATTCCATAATGCAAGCACACGGTTCTGTGATGGGGCTCGCTTTGGTCTAGGTGCTGAG
| ||| ||| | | | || | | |||| || | || ||| || | | | | | | | ||| || | | | ||| ||||||||| |||||||| |||||||| ||| ||||||||||||| |||||||||| || ||||| |||
tgtttctttgcataactactctatgaaatatgattaagtctaatactag-agttgatgttgatgactgaggaatatgcatttttgcttgattctcaaacagTGCTGCTGTATTCCACAATGCAAGTACAAGGTTCTGTGATGGAACTCGCTTTGGCCTTGGTGCAGAG
upper sequence: LOC_Os01g62900.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA03G12240.1 (Glycine max), 3'ss of exon 17
--gtgtttaactaatttcctttgcacaactattatgtttgccgctt-ttagtacatacc-ttaatt--aatgga-gttattcttctataaattgcaacagTGCTGCGGTATTCCATAATGCAAGCACACGGTTCTGTGATGGGGCTCGCTTTGGTCTAGGTGCTGAG
| || | ||| || || | |||| | | | | || | ||| | || | | ||| | | | | ||| | | ||||||||||| |||||||| |||||||| || ||||| |||||||| || |||||||| || ||||| |||
ttaaatagaattcattctctcacaacttagactatgaataactcatgttgcttcatgtcattgacttgaatatatgcgacttttccttgtgtacaaacagTGCTGCTGTATTCCACAATGCAAGTACGCGGTTTTGTGATGGAGCACGCTTTGGGCTTGGTGCAGAG
upper sequence: LOC_Os01g62900.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA01G24530.1 (Glycine max), 3'ss of exon 18
gtgtttaactaatttcctttgcacaact---attatgtttgccgctt-ttagtacatacc-ttaatt--aatgga-gttattcttctataaattgcaacagTGCTGCGGTATTCCATAATGCAAGCACACGGTTCTGTGATGGGGCTCGCTTTGGTCTAGGTGCTGAG
| ||| | | || || |||| | |||| | | ||| || | ||| | || | | ||| | | | | | | | | ||||||||||| |||||||| |||||||| |||||||| |||||||| || |||||||| || || || |||
-tattttagcatccattctttcataacttagactatgaataactcttgttgcttcatgtcattgactggaatatacgcaactttgccttgtgtacaaacagTGCTGCTGTATTCCACAATGCAAGTACACGGTTTTGTGATGGAGCACGCTTTGGGCTTGGCGCAGAG
upper sequence: LOC_Os01g62900.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA18G40770.1 (Glycine max), 3'ss of exon 19
--gtgtttaactaatttcctttgcacaactatta-tgtttgccgcttttagtacataccttaattaatggagt---tattcttctataaattgcaa-cagTGCTGCGGTATTCCATAATGCAAGCACACGGTTCTGTGATGGGGCTCGCTTTGGTCTAGGTGCTGAG
|| || | | || || |||| || ||| | | | | | | | ||| | | ||| | ||| || | | | ||| ||||||||| |||||||| || ||||| ||| |||| |||||||| ||||||||||| || ||||| |||
tcctgcttcattgtgtttctatgcataaatatgaataaatttagtctagacttgatattgatgtcagaggaatatacatttttgcttgattctcaaacagTGCTGCTGTATTCCACAACGCAAGTACAAGGTTTTGTGATGGAGCTCGCTTTGGCCTTGGTGCAGAG
upper sequence: LOC_Os01g62900.1 (Oryza sativa), 3'ss of exon 17
lower sequence: Vv08s0007g01060.t01 (Vitis vinifera), 3'ss of exon 17
gtgtttaactaatttcctttgcacaact---attatgtttgccgcttt-tagtacataccttaattaa--tggagttattcttc--tataaattgcaacagTGCTGCGGTATTCCATAATGCAAGCACACGGTTCTGTGATGGGGCTCGCTTTGGTCTAGGTGCTGAG
| | ||| || | | | | || | ||| || | | ||||| | |||| | || | | || ||| || |||||||||||| || |||||||||||||| || || || |||||||| || || ||||| || ||||| |||
-tacaaatgcaatggtctgtaaattgtttgagtaatttatgctaaattgttgcacatatttgtgttaaccttgaaatgtggctcattatctatctcaacagTGCTGCAGTTTTCCATAATGCAAGTACCCGATTTTGTGATGGAGCACGTTTTGGACTTGGTGCAGAGMapped 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|428854|gb|D25010.1|D25010EST: GCAAGTTGATAG TGCTGCGGTATTCCATAATGCAAGCACACGGTTCTGTGATGGGGCTCGCTT
genomic: GCAAGTTGATAGgtgtttaact ... attgcaacagTGCTGCGGTATTCCATAATGCAAGCACACGGTTCTGTGATGGGGCTCGCTT
EST:
gi|33683776|gb|CF312015.1|CF312015EST: ATCACTACTGATGGAAAGGCAGCAGAGACTTTTCTACAGCAAGTTGATAG TGCTGCGGTATTCCATAATGCAAGCACACGGTTCTGTGATGGGGCTCGCTT
genomic: ATCACTACTGATGGAAAGGCAGCAGAGACTTTTCTACAGCAAGTTGATAGgtgtttaact ... attgcaacagTGCTGCGGTATTCCATAATGCAAGCACACGGTTCTGTGATGGGGCTCGCTT
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),
37 (downstream exon)
Score:
5TGCACACACAGATTGCATTATCACTACTGATGGAAAGGCAGCAGAGACTTTTCTACAGCAAGTTGATAGgtgtttaact ... attgcaacagTGCTGCGGTATTCCATAATGCAAGCACACGGTTCTGTGATGGGGCTCGCTTTGGTCTAGGTGCTGAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccgcttttagtacataccttaattaatggagttattcttctataaattgcaacagTGCTGCGGTATTCCATAATGCAAGCACACGGTTCTGTGATGGGGCTCGCTTTGGTCTAGGTGCTGAG
aattaat putative branch site (score: 5)
ttattcttctataaat TA-rich tract