RetrogeneDB ID: retro_rnor_1450

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 19:32152791..32153622(-)
• 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_1450
ATGGTGGGCCACTGTCCAGTGCTCCTGCTCAGTCAGAATACACAGCGTGTGTCTGGAAGAAAAGTTCAATCTGGAAATAT
CAATACTGCAAAGACAATTGCAGATATCATCTGGACCTGTTTGGAACCTAAATCTATAATGAAGATGCTTTTGGACCCAG
CACGAGGCATTGTGATGACCAATGATGGTAATGCCATTCTTTGAGAGATTCAAGTCCAGCGTCCCGCAGCAAAATCCATG
ATTGAAATTAGCAGGACCTGGGATAAAGAGGTTGGAGATGGGACCACGTCAGTAATTATTCTTGCTGGAGAAATGCTGTC
TGTGGCTGAGCATTTCCTAGAGCAGCAGATGCACCCAACAGTGGTGATCAGTGCTTACCACATGGCACTGGATGATATGA
TCAACACTCTGAAGAAAATCAGTATCCCTGTTGATGTCAATAACCGTGATATGATGTTGAACATCATCAATAGCTCTATT
ACTACAAAAGTTATCAGTCGGTGGTCCTCTTTGGCATGCAACATTGCACTGGATGCTGTTAAGACTGTTCAGTTCGAAGA
GAATGGCAGAAAGGAAATTGCCATGAAGAAGTATGCAAGGGTGGAAAAGATACCCCGGGGTATCTTTGAAGACTCGTGTG
TCTTACGTAGAGTTATGATTAACAAGGATGTGACCCATCCAAGAATGCACCGCTATATTAAGAATCCTCGAATTGTTCTA
CTGGTTTCTTTTCTGGAGTACAAGAAAGGAGAAAGCCAGACTGACATTGAGATTACATGAGAGGAAGATTTCACCCGAAT
CCTGCAAATGGAAGAAGAGTACATCCAGCAG

Alignment

ORF - retro_rnor_1450 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.89 %
• Parental protein coverage: 50.83 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MMGHRPVLVLSQNTKRESGRKVQSGNINAAKTIADIIRTCLGPKSMMKMLLDPMGGIVMTNDGNAILREI
          M.GH.PVL.LSQNT.R.SGRKVQSGNIN.AKTIADII.TCL.PKS.MKMLLDP..GIVMTNDGNAIL.EI
Retrocopy MVGHCPVLLLSQNTQRVSGRKVQSGNINTAKTIADIIWTCLEPKSIMKMLLDPARGIVMTNDGNAIL*EI

Parental  QVQHPAAKSMIEISRTQDEEVGDGTTSVIILAGEMLSVAEHFLEQQMHPTVVISAYRMALDDMVSTLKKI
          QVQ.PAAKSMIEISRT.D.EVGDGTTSVIILAGEMLSVAEHFLEQQMHPTVVISAY.MALDDM..TLKKI
Retrocopy QVQRPAAKSMIEISRTWDKEVGDGTTSVIILAGEMLSVAEHFLEQQMHPTVVISAYHMALDDMINTLKKI

Parental  STPVDVNNRDMMLNIINSSITTKVISRWSSLACNIALDAVKTVQFEENGRKEIDIKKYARVEKIPGGIIE
          S.PVDVNNRDMMLNIINSSITTKVISRWSSLACNIALDAVKTVQFEENGRKEI..KKYARVEKIP.GI.E
Retrocopy SIPVDVNNRDMMLNIINSSITTKVISRWSSLACNIALDAVKTVQFEENGRKEIAMKKYARVEKIPRGIFE

Parental  DSCVLRGVMINKDVTHPRMRRYIKNPRIVLLDSSLEYKKGESQTDIEITREEDFTRILQMEEEYIQQ
          DSCVLR.VMINKDVTHPRM.RYIKNPRIVLL.S.LEYKKGESQTDIEIT.EEDFTRILQMEEEYIQQ
Retrocopy DSCVLRRVMINKDVTHPRMHRYIKNPRIVLLVSFLEYKKGESQTDIEIT*EEDFTRILQMEEEYIQQ

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

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1450 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1450 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1450 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,