RetrogeneDB ID: retro_rnor_674

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 10:22482835..22484634(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Thrap3
• Ensembl ID: ENSRNOG00000009977
• Aliases: None
• Description: Thyroid hormone receptor-associated protein 3 [Source:UniProtKB/Swiss-Prot;Acc:Q5M7V8]

Sequence

>retro_rnor_674
AAAACAAACAAATCCCAGTCTGGCCCTTGCTCTTCTCCCTCATGAGCTGCATCCAGATCTTGGTCTCATTCATTTTCAAA
GTCTCGGTCTGGAAGCCGGTCTGTCTCTCATTCAAGGAAGTGCAGGCTGAGTTCTAGGTCCCGTTCCAGGTCATATTCTC
CAGCTCATAACAGAGAAAAGAGTTACTGCAGAGTATATCAGAATCGAGATTTCTGAGGTCACAACAGAAGCTATAGGAGG
CCCTACTACTTCTATGGGCGAAAGCGAGGTTTTTATCCCTTGGGACAGTATAGCCGAGGTGGCATGGAAACTACCGTTTC
AAATGGCAGAAATACCAGCAAGCATACAGTTCTCTTCAGGGCGGTTCTCGATCCCAGTCCCTCAAGAGAAGGTCCCCTTC
ACCACGGTCCAGGAGTCATTCTAGGATCTCTGATAAGTCATCCTCTGACAGGTCAAGACGGTCCTTGTCCTTCCAGTCGT
CCTCCAACCACAGCAGGGTTGAGTCGTCTAAGCAAAAGTGTAGAAAAGAGAAGAAGTCCTCTTCCAAGGATAGACGGCCA
TCTCAGGGAGCTGGTGATAACCAGGGAGATGAGGCTAACGAGCTGACATTCTCTCGAGGCACCTCTCAAGATATAAAAGA
GTCTGAGAGCTCAAAGTCATGGCCAGACGCTACCACCTGTGGCACTGGTTCTGCTGCACCAGCCACGGTTTCTGATCCCC
AGGCGAGAAGTCCAGCTCTCAAAACCCCCGTCCAGTCTGTGGTGGTTAGGCAAAGGTCACCAAGGCCTAGCCCTGTGCCA
AAACCTAGTCTTCCATTTTCTAATACATGCCAGATGGGGTCATCTACGTCGGGTGGTGCTAGATATCAGTCTGGAACATA
CCAAGGTCAGTTTGACCATGGGTTTTTTAATTCAGCCCAAAAGCGCCCTGTGGGTAAGAGTCCACCAGCCATTGGCTCTG
TATAGGGTTCATCTCAGAAAGAGGAGAGCGCTGCGTTGGGAAGAGCAGCCTACACAAACAGATATCTGGAAGAGCAGAAG
AGGGAGAGTGGGAAGGATAAGGAGCAGAAACAAATACCGATAAAGAGAAGCTGACAAAGAAAGGGGACTTCTCTGACGCT
GATATCAAAATGAAATCTGACTCATTTGCTCTCAAGACGGACACTGAGAAGCCCTTCGCAGGCAACCAGTCACCCAACAG
GTATAAGCTCCGGGATGACTTTGAGAAAAAGATGGCCGACTTCCACAAGGAGAAGATGGATGAGCAAGATAAAGATAAAA
ATAGAAGGAAGGAACCTGAGTTTGATGAAGAGCCCACATTTATGTCTAAAGTCGGAGCCGGTGCGAGCAAAAACCAGGAG
GACGAGAAGTCAGGCAAGTGGGAGAGCCTGCATGGAAGGAAGGAAAAACTGAGGGAAGCAGAGGAGCCTTTCACAGAGAG
ATTCCGAAAGGAGGAGCATGAAGGGTCCACGAGGAGCGAAAGTGGGCACAGGGGCTTTGTGTCCCAAAAGAATTTCTGAG
TGATTGCAAACAGTGTGGTCCAGGAGAAAAGTTCACCGTCTCCACCAAGGAAGACCTCTGAGAGACATGACAAGCTGGGA
ACCAAATGGGGAGTTTTCCTAAGGGAATTCTTCGTTTTCCACTACTCAGGAGGCCCAGGTCAATGTCTGGATGGACTCCT
TCCATGAGGACCTTGCACGACCCAGTGGCTTATTGGCTCAGGAGCAAAAGCTTTGTCCAGATCTAGTCCATAAGAACAAA
AAGGAGCAGGAATTCCGTTCGGTTTTCCAGCACAGTCAG

Alignment

ORF - retro_rnor_674 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.02 %
• Parental protein coverage: 64.14 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KTNKSKSGSRSSRSRSASRSRSRSFSKSRSRSRSVSRSRKRRLSSRSRSRSYSPAHNRERNHPRVYQNRD
          KTNKS.SG..SS.S..ASRS.S.SFSKSRS.SRSVS.SRK.RLSSRSRSRSYSPAHNRE....RVYQNRD
Retrocopy KTNKSQSGPCSSPS*AASRSWSHSFSKSRSGSRSVSHSRKCRLSSRSRSRSYSPAHNREKSYCRVYQNRD

Parental  FRGHNRGYRRPYYFRGRNRGFYPWGQYNRGG-YGNYRSNWQNYRQAYSPRRGRSRSRSPKRRSPSPRSRS
          F.GHNR.YRRPYYF.GR.RGFYP.GQY.RGG..GNYR..WQ.Y.QAYS...G.SRS.S.KRRSPSPRSRS
Retrocopy F*GHNRSYRRPYYFYGRKRGFYPLGQYSRGG<HGNYRFKWQKYQQAYSSLQGGSRSQSLKRRSPSPRSRS

Parental  HSRNSDKSSSDRSRRSSSSRSSSNHSRVESSKRKSTKEKKSSSKDSRPSQAAGDNQGDEAKEQTFSGGTS
          HSR.SDKSSSDRSRRS.S..SSSNHSRVESSK.K..KEKKSSSKD.RPSQ.AGDNQGDEA.E.TFS.GTS
Retrocopy HSRISDKSSSDRSRRSLSFQSSSNHSRVESSKQKCRKEKKSSSKDRRPSQGAGDNQGDEANELTFSRGTS

Parental  QDIKGSESSKPWPDATTYGTGSASRASVSDLSPRERSPALKSPLQSVVVRRRSPRPSPVPKPSPPLSNAS
          QDIK.SESSK.WPDATT.GTGSA..A.VSD..P..RSPALK.P.QSVVVR.RSPRPSPVPKPS.P.SN..
Retrocopy QDIKESESSKSWPDATTCGTGSAAPATVSD--PQARSPALKTPVQSVVVRQRSPRPSPVPKPSLPFSNTC

Parental  QMGSSMSGGAGYQSGAHQGPFDHGSGSLSPSKKSPVGKSPPATGSAYGSSQKEESAASGGAAYTKRYLEE
          QMGSS.SGGA.YQSG..QG.FDH..G......K.PVGKSPPA.GS..GSSQKEESAA.G.AAYT.RYLEE
Retrocopy QMGSSTSGGARYQSGTYQGQFDH--GFFNSAQKRPVGKSPPAIGSV*GSSQKEESAALGRAAYTNRYLEE

Parental  QKTENGKDKEQKQTNTDKEKLKEKG-GFSDADVKMKSDPFAPKTDTEKPFRGSQSPKRYKLRDDFEKKMA
          QK.E.GKDKEQKQ....K.....KG..FSDAD.KMKSD.FA.KTDTEKPF.G.QSP.RYKLRDDFEKKMA
Retrocopy QKRESGKDKEQKQIPI-KRS*QRKG<DFSDADIKMKSDSFALKTDTEKPFAGNQSPNRYKLRDDFEKKMA

Parental  DFHKEEMDEQDKDKCKGRKEPEFDDEPKFISKVIAGASKNQEEEKSGKWESLHAGKEKQRKAEELEEEPF
          DFHKE.MDEQDKDK...RKEPEFD.EP.F.SKV.AGASKNQE.EKSGKWESLH..KEK.R.AEE....PF
Retrocopy DFHKEKMDEQDKDKNR-RKEPEFDEEPTFMSKVGAGASKNQEDEKSGKWESLHGRKEKLREAEE----PF

Parental  TERSRKEERGGSKRSESGHRGFVPEKNFRVTAYKAVQEKSSSPPPRKTSESRDKLGNK-GDFSSGKSSFS
          TER.RKEE..GS.RSESGHRGFV..KNF.V.A...VQEKSS..PPRKTSE..DKLG.K.G.FS.G.SSFS
Retrocopy TERFRKEEHEGSTRSESGHRGFVSQKNF*VIANSVVQEKSSPSPPRKTSERHDKLGTK>GEFS*GNSSFS

Parental  ITREAQVNVRMDSFDEDLARPSGLLAQERKLCRDLVHSNKKEQEFRSIFQHIQ
          .T.EAQVNV.MDSF.EDLARPSGLLAQE.KLC.DLVH.NKKEQEFRS.FQH.Q
Retrocopy TTQEAQVNVWMDSFHEDLARPSGLLAQEQKLCPDLVHKNKKEQEFRSVFQHSQ

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
SRP017611_brain	0.00 RPM	107.34 RPM
SRP017611_kidney	0.00 RPM	118.49 RPM
SRP017611_liver	0.00 RPM	77.46 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_674 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_674 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_674 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 ,