RetrogeneDB ID: retro_rnor_2037

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:8365259..8365601(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Zcchc10
• Ensembl ID: ENSRNOG00000006943
• Aliases: None
• Description: Zinc finger CCHC domain-containing protein 10 [Source:UniProtKB/Swiss-Prot;Acc:Q5EB97]

Sequence

>retro_rnor_2037
ATGGCTACTCCCATGCATCGGCTTATAGCTCAGTGGCAAGCTGAAGCCAATAAGCAACACGTAAGATGTCAGAAATGCTT
GGAATTTGGACATTGGACTTATGAATGCAAAGGGAAAGAAAGTACCTACACAGGTCTTCGAGAACAGCAGAGCTGAAGAA
AGCTTTAAAAGAAAAAGAAAATAGATTATTGCAGCAAAGCGATGGAGAGAAAGACCACGAAGAGAAGGCCTAAGAGTGTC
ACGAGTTCCAGTACCTCTAGCAGTGACAGTTCAGCCAGTGAGTCTTAATCAGAGAGCGAGACATCTGCCTCATCCTCTTC
AGAGGACAGTGACTCAGATGGA

Alignment

ORF - retro_rnor_2037 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.5 %
• Parental protein coverage: 68.21 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MATPMHRLIARRQAEANKQHVRCQKCLEFGHWTYECKGK-RKYLHRPSRTAELKKALKEKENRLLQQSMG
          MATPMHRLIA..QAEANKQHVRCQKCLEFGHWTYECKGK.RKYLHR.SRTAELKKALKEKENRLLQQS.G
Retrocopy MATPMHRLIAQWQAEANKQHVRCQKCLEFGHWTYECKGK<RKYLHRSSRTAELKKALKEKENRLLQQSDG

Parental  ETN-TERKTKKKRRPKSVTSTSSSDSSASESSSESETSASSSSEDSDADG
          E...T.R..K.........S.SS....ASES.SESETSASSSSEDSD.DG
Retrocopy EKD>TKRRPKSVTSSSTSSSDSS----ASES*SESETSASSSSEDSDSDG

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	4.24 RPM
SRP017611_kidney	0.00 RPM	5.09 RPM
SRP017611_liver	0.00 RPM	0.74 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2037 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2037 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2037 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000031203	1 retrocopy	retro_cfam_643,
Choloepus hoffmanni	ENSCHOG00000001420	9 retrocopies	retro_chof_1243, retro_chof_1263, retro_chof_1773, retro_chof_2048, retro_chof_2132, retro_chof_2183, retro_chof_501, retro_chof_790, retro_chof_923,
Dasypus novemcinctus	ENSDNOG00000017302	1 retrocopy	retro_dnov_257,
Myotis lucifugus	ENSMLUG00000011366	4 retrocopies	retro_mluc_172, retro_mluc_2240, retro_mluc_2241, retro_mluc_2574,
Monodelphis domestica	ENSMODG00000013827	1 retrocopy	retro_mdom_1405,
Mus musculus	ENSMUSG00000018239	1 retrocopy	retro_mmus_269,
Otolemur garnettii	ENSOGAG00000032171	1 retrocopy	retro_ogar_3011,
Pongo abelii	ENSPPYG00000015776	1 retrocopy	retro_pabe_2395,
Rattus norvegicus	ENSRNOG00000006943	3 retrocopies	retro_rnor_2037 , retro_rnor_2528, retro_rnor_801,
Sorex araneus	ENSSARG00000007221	1 retrocopy	retro_sara_639,