RetrogeneDB ID: retro_cfam_549

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 13:38242443..38244281(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: THRAP3
• Ensembl ID: ENSCAFG00000003389
• Aliases: None
• Description: thyroid hormone receptor associated protein 3 [Source:HGNC Symbol;Acc:22964]

Sequence

>retro_cfam_549
ACAAAGAGGTACCTAGAAGAATAGAACACAGAGAATGGAAAAGATAAGGTGAAGAAACAAATCAATACTGATAAAGAGAA
AAATGAAAGAGAAAGGGAGCTTCTCTGACACAGGCTTGGGTGGTTCAAAAATGAAATCTGATCCATTTGCTCCCAAAACT
GATACAGAGAAGTCTTTTCGGGGTAGCCAGTCTCTCAGAAGGTATAAGCTTCGAGATGACTTTGAGAAGATGGCCGACTT
CATAAGGATGACATGGATGATCAAGATAAGGACAAAGCTAAGGGAAGGAAGGAATTGGAGTTTGATGATGAACCCAAATT
TATGTCGAAAGTCATAGCAGGTGCAAACAAAAACCAGGAAGAGAAGTCAGGCAAATGGGAAGGCCTGGTGTATGCATGCA
CCTCTAGGGAAGGAAAAGCAGAGGAAAACAGAGCAGCTGGAGGAGGAATCTTTCTCTGAAAGATCAAAAAAGGAGGATCA
GGGAGGGCCCAAGAGAACTGAAAGTGGGTACAGAGGATTCATGCCTGAAAAGAATTTCTGAGTGACCACTTACAAAGCAG
TCCAGGAGAAAAGCTCGTCACCTCCCCCAAGAAAGACCTCTGAGAGCCGAGAGAAGTTAGGAGCCAAGGGAGACTTTTGC
ATGGGGAAGTCTTCATTTTCCATTACTCGAGAGGCCCAGGTCAATGTCCGGATGGACTCTTTTGATGAGGACCTTGCAAG
ACCAAGTGGCTTATTGGCTCAGGAACACAAGCTTTGTTGGGATCTAGTCCATAGCAACAAAAAGGAACAGGAATTGTGTT
CCATTTTCCAGCACATACAGTCAGCTCAGTCTCAGCGGAGCCCCTCTGAACTGTTTGACCAGCATATAGTGACCATTGTT
CACCACATAAAAGAGCATCACTTTGGGTCCTCAGGAATGACATTGCATGAGCGTTTTACTAAATACCCGAAGAGAGGAAC
TGAGCAGCAGGCAGCTAAAAACAAGAAAAGCCCAGAAGTACACAGGAGGATAGACATTTCTCCCAGTACGTGCAGCAAAC
ATGGTTTGGCTCATGATGAAATGAAAAGTCCATGGAAACCTGGCTACAAGGCTGAGGGAAAATACCAAGATGATCCTCTT
GACCTCTGCCTTGATATTGAACGTCATAAAAAATATAAGGAGAGAGATCTTAAACGAGGTAAATCAAGAGAGTCAGTGGA
TTCCCGAGACTCAAGCCACTCAAGGGAAAGATTAGCTGAGAAAACAGGGAAAACTCATAAAGGATCAAAGAAGCAGAAGA
AGCATCAGAGGGCACGAGGCCAGTCCAGGTCCTCCTCTTCCTCCCGGTCATCCCACTCCTACAAAGCAGAAGGGTACACT
GAAGAAACAGAGGAGAGGGAAGAGAGCAGCACGGGCTTTGACAAGTCAAGACTAGGGACCAAGGACTTCGTGGGTCCAAA
TGAAAGAGGCGGCAGGGCTAACGGGACCTTTCAATTTCGAGCCCAGAGGGAGAGGCTGGGGCAGAGGCACCTACTCTGGT
AACAACAACAACTACAACAGCAACAACGATTTTCAAAAGAGAAACCTGGAGGAGGAGTGGGACCCTGAGTAAACGCCCAA
GAGCAAGAAGTATTATCTGCATGATGACCCTGAAGGTGAAGGCAGTGAGAAGTGGGTGAGTGGCGGTCGGAGCCGAGGAG
CCTTCCGCCGCGGTTGAGGCCGGTTCATGTTCTGGAAATCCAGCCCCAGCCCCAAATGGGTCCATGACAAGTTTAGTGGG
GAGGAAGGGGAGATTGAAGACGACGAGAGTGGGACAGAGAACCGAAAAGAGAAGGACAACTTACAGCCCACAACTGAG

Alignment

ORF - retro_cfam_549 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.46 %
• Parental protein coverage: 63.99 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TKRYLEEQKTENGKDKEQKQTNTDKEK-MKEKGSFSDTGLGDTKMKSDPFAPKTDTEKSFRGSQSPKRYK
          TKRYLEE..TENGKDK..KQ.NTDKEK.MKEKGSFSDTGLG..KMKSDPFAPKTDTEKSFRGSQS..RYK
Retrocopy TKRYLEE*NTENGKDKVKKQINTDKEK>MKEKGSFSDTGLGGSKMKSDPFAPKTDTEKSFRGSQSLRRYK

Parental  LRDDFEKKMADF-HKDDMDDQDKDKAKGRKESEFDDEPKFMSKVIAGANKNQEEEKSGKWEGLVYAPPGK
          LRDDFEK.MADF.HKDDMDDQDKDKAKGRKE.EFDDEPKFMSKVIAGANKNQ.EEKSGKWEGLVYA....
Retrocopy LRDDFEK-MADF<HKDDMDDQDKDKAKGRKELEFDDEPKFMSKVIAGANKNQ-EEKSGKWEGLVYACTSR

Parental  E-KQRKTEE-LEEESFSERSKKEDRGGPKRTESGHRGFVPEKNFRVTAYKAVQEKSSSPPLRKTSESREK
          E.......E.LEEESFSERSKKED.GGPKRTESG.RGF.PEKNF.VT.YKAVQEKSSSPP.RKTSESREK
Retrocopy E>EKQRKTEQLEEESFSERSKKEDQGGPKRTESGYRGFMPEKNF*VTTYKAVQEKSSSPPPRKTSESREK

Parental  LGAKGDFSTGKSSFSITREAQVNVRMDSFDEDLARPSGLLAQERKLCRDLVHSNKKEQEFRSIFQHIQSA
          LGAKGDF..GKSSFSITREAQVNVRMDSFDEDLARPSGLLAQE.KLC.DLVHSNKKEQE..SIFQHIQSA
Retrocopy LGAKGDFCMGKSSFSITREAQVNVRMDSFDEDLARPSGLLAQEHKLCWDLVHSNKKEQELCSIFQHIQSA

Parental  QSQRSPSELFAQHIVTIVHHVKEHHFGSSGMTLHERFTKYLKRGTEQEAAKNKKSPEIHRRIDISPSTFR
          QSQRSPSELF.QHIVTIVHH.KEHHFGSSGMTLHERFTKY.KRGTEQ.AAKNKKSPE.HRRIDISPST..
Retrocopy QSQRSPSELFDQHIVTIVHHIKEHHFGSSGMTLHERFTKYPKRGTEQQAAKNKKSPEVHRRIDISPSTCS

Parental  KHGLAHDEMKSPREPGYKAEGKYKDDPVDLRLDIERRKKHKERDLKRGKSRESVDSRDSSHSRERSAEKT
          KHGLAHDEMKSP..PGYKAEGKY.DDP.DL.LDIER.KK.KERDLKRGKSRESVDSRDSSHSRER.AEKT
Retrocopy KHGLAHDEMKSPWKPGYKAEGKYQDDPLDLCLDIERHKKYKERDLKRGKSRESVDSRDSSHSRERLAEKT

Parental  EKTHKGSKKQKKHRRARDRSRSSSSSSQSSHSYKAEEYTEETEEREESSTGFDKSRLGTKDFVGPNERGG
          .KTHKGSKKQKKH.RAR..SR.SSSSS.SSHSYKAE.YTEETEEREESSTGFDKSRLGTKDFVGPNERGG
Retrocopy GKTHKGSKKQKKHQRARGQSR-SSSSSRSSHSYKAEGYTEETEEREESSTGFDKSRLGTKDFVGPNERGG

Parental  RARGTFQFRA-RGRGWGRGTYSGNNNNNSNNDFQKRNREEE-WDPEYTPKSKKYYLHDDREGEGSEKWVS
          RA.GTFQFRA.RGRGWGRGTYSG................EE.WDPE.TPKSKKYYLHDD.EGEGSEKWVS
Retrocopy RANGTFQFRA>RGRGWGRGTYSGXXXXXXXXXDFQKRNLEEEWDPE*TPKSKKYYLHDDPEGEGSEKWVS

Parental  RGRGRGAFPRGRGRFMFRKSSTSPKWAHDKFSGEEGEIEDDESGTENREEKDNLQPATE
          .GR.RGAF.RG.GRFMF.KSS.SPKW.HDKFSGEEGEIEDDESGTENR.EKDNLQP.TE
Retrocopy GGRSRGAFRRG*GRFMFWKSSPSPKWVHDKFSGEEGEIEDDESGTENRKEKDNLQPTTE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP012049_cerebellum	0.25 RPM	189.71 RPM
SRP017611_brain	0.71 RPM	117.98 RPM
SRP017611_kidney	0.00 RPM	83.87 RPM
SRP017611_liver	0.00 RPM	78.10 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_549 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_549 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_549 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003389	1 retrocopy	retro_cfam_549 ,
Microcebus murinus	ENSMICG00000007920	1 retrocopy	retro_mmur_671,
Mus musculus	ENSMUSG00000043962	1 retrocopy	retro_mmus_2939,
Pongo abelii	ENSPPYG00000001544	1 retrocopy	retro_pabe_2336,
Pan troglodytes	ENSPTRG00000000535	1 retrocopy	retro_ptro_1771,
Rattus norvegicus	ENSRNOG00000009977	1 retrocopy	retro_rnor_674,