RetrogeneDB ID: retro_rnor_2823

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:77076990..77077991(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cct3
• Ensembl ID: ENSRNOG00000019090
• Aliases: None
• Description: T-complex protein 1 subunit gamma [Source:UniProtKB/Swiss-Prot;Acc:Q6P502]

Sequence

>retro_rnor_2823
ATGGTGGACCACCATCCAGTGAATGTGCTCAGTCAGAATACAAAGTATGAATCTGTAAGGGAAGTTCAACCTGGAAATAT
CAATTCTGTGAAGACAATTGGGGACATCATCTGGACCTGTTTTTGATCTAAATCTATGAAGAAGATGCTTTTGGACCCAA
TGGGAGGCATCATGATAACCAATGATGGCAATGCCATTCTTTGAGAGATTCAAGTCCAGCATCCTGCAGCGAAATCCATT
ATTGAAATCAGTGGGACCCAGGATGAAGTGGCTAGAGATGGGACCATATCAGTAATTATTCTTGTGGGAGAAATGCTGTC
TGTGGCTGAGCAGTTCCTAGAACAGCAGACGCACTCAACAGTGGTGAGCAGTGCTTACCACATGGCACTGGATGATATGC
TCAGTACTCTGAAGCAAATCAATAGTCCTGTTGATGTCAATGACCGTGATATGATGTTAAACATCATAAATAGCTCTATT
ATTACAAAAGTCATCAGACTATGGTCCTCTTTAGCATACAACATTGCCCTGGATGCTGTCAAGTTTGAAGAGAACAGCTG
AAAGGAAACTGACATCAAGAAATATGCAAGGATGGAAAAGATACCTGGGCAGCATCACTGAAGCCTCTCATGTCTTACAT
GGAGTCATGATTAACAAGGATGTAACCCATCCATGAATGCGTCGCTCTAACAAGAATCATTGGATTGTGCTACTGGATTC
TTCTCTGGAATACAAAACAAGAGAAAGCCAGAGTTTCATTGAGATTACATGAGAGGAGGATTTCACCCGAATCCTGCAAA
TGGGAGAAGAGTACCCTTAGCAGTTGTGTGAGGATATTATCTAGCTGAAACCTGACATGGTCATCACAGAAGAGTGCTTC
ACAAATTTGCCTCAGCACTACCTCATATGGGACAATGTCACAGCTATTTTTAGAGTTTGGAAAATAGACAATAAATCACA
TTGCTAGAGCCTGTGGGGCACGGATAATCAGCAGATCTGAG

Alignment

ORF - retro_rnor_2823 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.15 %
• Parental protein coverage: 61.65 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MMGHRPVLVLSQNTKRESGRKVQSGNINAAKTIADIIRTCLGPKSMMKMLLDPMGGIVMTNDGNAILREI
          M..H.PV.VLSQNTK.ES.R.VQ.GNIN..KTI.DII.TC...KSM.KMLLDPMGGI..TNDGNAIL.EI
Retrocopy MVDHHPVNVLSQNTKYESVREVQPGNINSVKTIGDIIWTCF*SKSMKKMLLDPMGGIMITNDGNAIL*EI

Parental  QVQHPAAKSMIEISRTQDEEVGDGTTSVIILAGEMLSVAEHFLEQQMHPTVVISAYRMALDDMVSTLKKI
          QVQHPAAKS.IEIS.TQDE...DGT.SVIIL.GEMLSVAE.FLEQQ.H.TVV.SAY.MALDDM.STLK.I
Retrocopy QVQHPAAKSIIEISGTQDEVARDGTISVIILVGEMLSVAEQFLEQQTHSTVVSSAYHMALDDMLSTLKQI

Parental  STPVDVNNRDMMLNIINSSITTKVISRWSSLACNIALDAVKTVQFEENGRKEIDIKKYARVEKIP-GGII
          ..PVDVN.RDMMLNIINSSI.TKVI..WSSLA.NIALDAVK...FEEN..KE.DIKKYAR.EKIP.G.I.
Retrocopy NSPVDVNDRDMMLNIINSSIITKVIRLWSSLAYNIALDAVK---FEENS*KETDIKKYARMEKIP>GSIT

Parental  EDSCVLRGVMINKDVTHPRMRRYIKNPRIVLLDSSLEYKKGESQTDIEITREEDFTRILQMEEEYIQQLC
          E.S.VL.GVMINKDVTHP.MRR..KN..IVLLDSSLEYK..ESQ..IEIT.EEDFTRILQM.EEY..QLC
Retrocopy EASHVLHGVMINKDVTHP*MRRSNKNHWIVLLDSSLEYKTRESQSFIEIT*EEDFTRILQMGEEYP*QLC

Parental  EDIIQLKPDVVITEKGISDLAQHYLMRANVTAIRRVRKTDN-NRIARACGARIVSRPE
          EDII.LKPD.VITE.....L.QHYL...NVTAI.RV.K.DN.N.IARACGARI.SR.E
Retrocopy EDII*LKPDMVITEECFTNLPQHYLIWDNVTAIFRVWKIDN>NHIARACGARIISRSE

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	0.50 RPM	95.33 RPM
SRP017611_kidney	0.00 RPM	126.24 RPM
SRP017611_liver	0.07 RPM	62.60 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2823 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2823 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2823 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005776	1 retrocopy	retro_cjac_1243,
Cavia porcellus	ENSCPOG00000009131	1 retrocopy	retro_cpor_813,
Mus musculus	ENSMUSG00000001416	2 retrocopies	retro_mmus_2352, retro_mmus_824,
Otolemur garnettii	ENSOGAG00000008967	1 retrocopy	retro_ogar_2017,
Rattus norvegicus	ENSRNOG00000019090	2 retrocopies	retro_rnor_1450, retro_rnor_2823 ,
Ictidomys tridecemlineatus	ENSSTOG00000001798	1 retrocopy	retro_itri_788,