RetrogeneDB ID: | retro_btau_456 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 12:1901044..1902451(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | USP10 | ||
| Ensembl ID: | ENSBTAG00000009446 | ||
| Aliases: | None | ||
| Description: | Ubiquitin carboxyl-terminal hydrolase 10 [Source:UniProtKB/Swiss-Prot;Acc:A5PJS6] |
Retrocopy-Parental alignment summary:
>retro_btau_456
CCAGGACTGCAGAGCAGCTTGAGGGCTGCCCCAGGGCTGAATCCCAGCAGGGACACCCTGTTGAGGACAGCTGTGGCTCA
GCCTTCCATGGGGACTGAGACTACTGAGAGCCTTGGAGTCGCTAAGGGACAAATACTTGAATCCTTGGTTGAGGGCACAG
CTGCCAGTGGGGTGGAGTTGCACACCATGGAGAGCTCGAACTCGGCCCCAGCAAGGCCTAGAGCACCCCACCTCCTGTGG
ATGCCCCAGCCTCTGCAGTGGGCACGGTGCCCACCAGTCAGCCCACCAAGTCATGGACCAGTCTTTTTCATGATTCTAAC
TCTATTCTTCCTCCTTGCCTGTGGTTTCTGTGGAAACTAAGAATTCCCCTTCCACCACATCTCCCTTCATCTCTGAAAAG
CAGGCAGAAGTCAAGGAAGGGCTGGTTCCAGTTTCAGAGGATCCCGAAGCCATAAAGATTGCAGAGTTCCTGGAGAACAC
CACCCTGATTCATAAACCAGTGTCGTTGCAACCCTGTGGGCTGATCTACACAGGAAATTGGTGCTACATCAAAGCCACAC
TGCAGGCGTTGGTAGCTTGCCCACCAGTATATCACCTGATGAAGTTCATTCCCCTGTATTTAAAAGTGCAAAGCCCTTGT
ACATCCACACCCATGACAGACAGCTTTGTTTAGCTAATGAATGAGTTTACTAATATGCCAGTACCTCCAAAACCCAGACA
AGGTCTTAGGGATAAAATCATGAGGGATATCTGCCCCAGAGCTGCCTTTGAACCCACTTATATTTGTAGACTCCTGACGG
TGATCAAGTGGAGCCTGTCTGAAAAGGATGGGCAAGAAGATGCTGAGGAGTACTCAGGTTTCATTCTAAATGGACTCCAT
GAGGAAATGCAGAGCCAAAAGAAACTTCTATCACCAAATAATGAAAACCTTACTGTTTCCAGTGGACCCAAAAGCCACTC
AGTGAACAAAGAGGAGCAGGAAGAACCAGAAGAAGGAAGTGAGGACAAGTGGGAGTAAGCAGGCCCCGGAAACAAGACCA
CAGTCACTCATCAGGTGGCCTTTGTTCAGACCCCCATCGCTGGCATTTTTTGGTGGACACATCAGGTCTGTGGTTTACCA
GCAGAGTTCAAGAGTCTGCCACTGGGCAGCTGTTCTTCAATCTGCATCTGGAAATCCAGTCCAACAAGATATGCACTGTC
CAGAACGCACTGGGGAGCCTGGTGGCCAGAGAGTCTGTCCAGGGTGACACCACCAAAACTGAACAAGAGGTGGAGATCAG
CTGGAGAATGACTCTGGAAAAGCTCCGTCTTATGCTCCTGCTGCACCTCCAGCGGTTCGTGTACAAGACTGGGGGCTGTC
AGAAGCTCATCAGAAATGCTGAATATCCTGCGGACTTGGAAATGAGT
ORF - retro_btau_456 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 77.05 % |
| Parental protein coverage: | 58.75 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | PGADSEASCLPA-EAGRDTLLRTAVAQPSVGTDTTENLGVTNGQILESLGEGTAANGVELHTVESSDSDP |
| PG..S.....P.....RDTLLRTAVAQPS.GT.TTE.LGV..GQILESL.EGTAA.GVELHT.ESS.S.P | |
| Retrocopy | PGLQSSLRAAPGLNPSRDTLLRTAVAQPSMGTETTESLGVAKGQILESLVEGTAASGVELHTMESSNSAP |
| Parental | A-KAESAPPPADAPASAAGTVPASQPAKSWASLFHDSKPS-SSSLPVVSVETKYSPPATSPLVSEKQAEV |
| A.KA.S.PPP.DAPASA.GTVP.SQP.KSW.SLFHDS....SSSLPVVSVETK.SP..TSP..SEKQAEV | |
| Retrocopy | A<KA*STPPPVDAPASAVGTVPTSQPTKSWTSLFHDSNSI<SSSLPVVSVETKNSPSTTSPFISEKQAEV |
| Parental | KEGLVPVSEDPVAIKIAELLENVTLIHKPVSLQPRGLINKGNWCYINATLQALVACPPMYHLMKLIPLYS |
| KEGLVPVSEDP.AIKIAE.LEN.TLIHKPVSLQP.GLI..GNWCYI.ATLQALVACPP.YHLMK.IPLY. | |
| Retrocopy | KEGLVPVSEDPEAIKIAEFLENTTLIHKPVSLQPCGLIYTGNWCYIKATLQALVACPPVYHLMKFIPLYL |
| Parental | KVQRPCTSTPMIDSFVRLMNEFTNMPVPPKPRQALGDKIVRDIRPGAAFEPTYIYRLLTVIKSSLSEKGR |
| KVQ.PCTSTPM.DSFV.LMNEFTNMPVPPKPRQ.L.DKI.RDI.P.AAFEPTYI.RLLTVIK.SLSEK.. | |
| Retrocopy | KVQSPCTSTPMTDSFV*LMNEFTNMPVPPKPRQGLRDKIMRDICPRAAFEPTYICRLLTVIKWSLSEKDG |
| Parental | QEDAEEYLGFILNGLHEEMLNLKKLLSPNNDKLTISNGPKSHSVNEDEQEEPGEGSEDEWEQVGPRNKTS |
| QEDAEEY.GFILNGLHEEM...KKLLSPNN..LT.S.GPKSHSVN..EQEEP.EGSED.WE..GP.NKT. | |
| Retrocopy | QEDAEEYSGFILNGLHEEMQSQKKLLSPNNENLTVSSGPKSHSVNKEEQEEPEEGSEDKWE*AGPGNKTT |
| Parental | VTRQADFVQTPITGIF-GGHIRSVVYQQSS-KESATLQPFFTLQLDIQSDKIRTVQDALESLVARESVQG |
| VT.Q..FVQTPI.GIF.GGHIRSVVY.Q.S..ESAT.Q.FF.L.L.IQS.KI.TVQ.AL.SLVARESVQG | |
| Retrocopy | VTHQVAFVQTPIAGIF>GGHIRSVVY-QQS>QESATGQLFFNLHLEIQSNKICTVQNALGSLVARESVQG |
| Parental | YTTKTRQEVEISRRVTLEKLPPVLVLHLKRFVYEKTGGCQKLIKNIEYPVDLEIS |
| .TTKT.QEVEIS.R.TLEKL...L.LHL.RFVY.KTGGCQKLI.N.EYP.DLE.S | |
| Retrocopy | DTTKTEQEVEISWRMTLEKLRLMLLLHLQRFVY-KTGGCQKLIRNAEYPADLEMS |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| ERP005899_liver | 0 .00 RPM | 35 .98 RPM |
| ERP005899_muscle | 0 .00 RPM | 79 .76 RPM |
| SRP017611_brain | 0 .00 RPM | 44 .54 RPM |
| SRP017611_kidney | 0 .00 RPM | 60 .93 RPM |
| SRP017611_liver | 0 .00 RPM | 38 .58 RPM |
| SRP030211_testis | 0 .00 RPM | 19 .04 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_456 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_456 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_456 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000009446 | 1 retrocopy |
retro_btau_456 ,
|
| Pan troglodytes | ENSPTRG00000008421 | 1 retrocopy |