RetrogeneDB ID: retro_rnor_978

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 13:94092042..94092330(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000043025
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Znrd1
• Ensembl ID: ENSRNOG00000000779
• Aliases: Znrd1, HTEX-6, Tctex6
• Description: DNA-directed RNA polymerase I subunit RPA12 [Source:UniProtKB/Swiss-Prot;Acc:Q6MFY5]

Sequence

>retro_rnor_978
ATAGAGTTGGCCCGACCCTGCTCCAACTTTGGATCAGACTTGGATTCCTGCCCAGATTGTGGCTCAGTCCTGCTGCTACC
TGGAGCTTATGACACTGTCATCTGCCCTCGCTGTGGCTTCTCCATCAATGTGAGAGATTTTGAAGGGAAGGTTGTGAAGA
CCTCAGTTGTGTTCAACAAACTGGGGGCTGCCATACCTATGTCTGTGGACAAGGGACCTGAATCCCAGGGACCAGGAGTT
GACGGGCATGACCAGAGGTCACATGGGAATGGCCTACCACACCAGACA

Alignment

ORF - retro_rnor_978 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75. %
• Parental protein coverage: 78.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MELARPCSNFQSDLDFCPDCGSVLPLPGVQDTVICPRCGFSIDVRDFGGKVVKTSVVFNKLGTVIPMSVD
          .ELARPCSNF.SDLD.CPDCGSVL.LPG..DTVICPRCGFSI.VRDF.GKVVKTSVVFNKLG..IPMSVD
Retrocopy IELARPCSNFGSDLDSCPDCGSVLLLPGAYDTVICPRCGFSINVRDFEGKVVKTSVVFNKLGAAIPMSVD

Parental  EGPESQGPVVDRRCSRCGHEGMAYYT
          .GPESQGP.VD....R....G....T
Retrocopy KGPESQGPGVDGHDQRSHGNGLPHQT

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	5.25 RPM
SRP017611_kidney	0.00 RPM	5.44 RPM
SRP017611_liver	0.07 RPM	4.71 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_978 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_978 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_978 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007328	2 retrocopies	retro_chof_1997, retro_chof_2061,
Dasypus novemcinctus	ENSDNOG00000015720	9 retrocopies	retro_dnov_1020, retro_dnov_1103, retro_dnov_1472, retro_dnov_1726, retro_dnov_1798, retro_dnov_1881, retro_dnov_2400, retro_dnov_2420, retro_dnov_933,
Myotis lucifugus	ENSMLUG00000007272	1 retrocopy	retro_mluc_126,
Monodelphis domestica	ENSMODG00000016023	1 retrocopy	retro_mdom_1799,
Mustela putorius furo	ENSMPUG00000007474	1 retrocopy	retro_mputfur_968,
Rattus norvegicus	ENSRNOG00000000779	1 retrocopy	retro_rnor_978 ,
Sorex araneus	ENSSARG00000009716	2 retrocopies	retro_sara_431, retro_sara_745,
Sarcophilus harrisii	ENSSHAG00000001554	1 retrocopy	retro_shar_796,