RetrogeneDB ID: retro_rnor_2906

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:33745443..33745921(-)
• Located in intron of: ENSRNOG00000004257

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ccdc43
• Ensembl ID: ENSRNOG00000002748
• Aliases: Ccdc43, RGD1311929
• Description: Coiled-coil domain-containing protein 43 [Source:UniProtKB/Swiss-Prot;Acc:Q5BK07]

Sequence

>retro_rnor_2906
GGTATCCTCTCTACTTTCCTGAAAGAAGATTCCCTCCTTGATATCTATAAGGAAATTGTGGAATGATGGTCAGAAACACA
AAATGTCACCATTAAAGTGGAAAAAAAAAAAGATGAAGTATAGGCCATCGTCACTTTGATTGAGAAGCAGGCACAGATCA
CGGTGAAGCCCAGGTGGTTTCAGAAGACAGGCACCGGGACGCTGCTCTGCTGGCTCAGTATGCTGATGTGACAGATGAAG
AGGATGAAGGAGATGAGAAAAATGATTCAGGTCCTTCAACAACGAACATTCTTCCGACAGATGTATTTTCTGAAACACCA
ATGTGGAAGATGTTCTCAATGCTGAGAGAATGGATCAAGACTCACTTTGGGATGAGTCCAAAAGGAAGAAAGAGCAGGAA
AACTTGCAGAGGGAAAAGGACAAATGAGCCAGTCAGAAGGGCAAGGAGAAGGAAAAGAAAAGGACATAGAGAAGGGAA

Alignment

ORF - retro_rnor_2906 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.17 %
• Parental protein coverage: 72.07 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GILSAFLEEDSLLDICKEIVERWSETRDVTTKVKKE-DEVQAITTLIEKQAQIVVKPR-VVSEEEKQRKA
          GILS.FL.EDSLLDI.KEIVE.WSET..VT.KV....DEV.AI.TLIEKQAQI.VKPR.VVSE....R.A
Retrocopy GILSTFLKEDSLLDIYKEIVE*WSETQNVTIKVXXXXDEV*AIVTLIEKQAQITVKPR<VVSED-RHRDA

Parental  ALLAQYADVTDEETEADEKADPGASTANI-GSDKSLFRNTNVEDVLNARKLERDSLRDESQRKKEQDKLQ
          ALLAQYADVTDEE.E.DEK.D.G.ST.NI..SD...F.NTNVEDVLNA.....DSL.DES.RKKEQ..LQ
Retrocopy ALLAQYADVTDEEDEGDEKNDSGPSTTNI<SSDRCIF*NTNVEDVLNAERMDQDSLWDESKRKKEQENLQ

Parental  REKDKLAKQERKEKEKKRTQRGE
          REKDK.A.Q..KEKEKKRT.R.E
Retrocopy REKDK*ASQKGKEKEKKRT*RRE

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	11.79 RPM
SRP017611_kidney	0.14 RPM	15.14 RPM
SRP017611_liver	0.07 RPM	8.07 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2906 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2906 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2906 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018379	1 retrocopy	retro_amel_1479,
Canis familiaris	ENSCAFG00000014115	1 retrocopy	retro_cfam_456,
Monodelphis domestica	ENSMODG00000011411	1 retrocopy	retro_mdom_1378,
Mustela putorius furo	ENSMPUG00000009224	1 retrocopy	retro_mputfur_1511,
Oryctolagus cuniculus	ENSOCUG00000017526	1 retrocopy	retro_ocun_1500,
Ochotona princeps	ENSOPRG00000006793	2 retrocopies	retro_opri_263, retro_opri_699,
Rattus norvegicus	ENSRNOG00000002748	1 retrocopy	retro_rnor_2906 ,
Sus scrofa	ENSSSCG00000017352	2 retrocopies	retro_sscr_173, retro_sscr_944,