RetrogeneDB ID: retro_rnor_1873

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:25518600..25518887(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Arpc5
• Ensembl ID: ENSRNOG00000028062
• Aliases: None
• Description: Actin-related protein 2/3 complex subunit 5 [Source:UniProtKB/Swiss-Prot;Acc:Q4KLF8]

Sequence

>retro_rnor_1873
GTGACAACTGCTCTCCAGGATGCTTGCTCCCCTCCCCGATCAGCACAAAGAGTCAGGCAGTGAAGGACCAGGCAGGCAGC
ATTGTCTTGAAGGTACTCATCTCTTTTAAAGCTAATGATATTGAAAGAGCTGTTCAGGCTCTGGACAGAAATGGTATGGT
CCTCCTAATCAATATAAAGGCTTTGAGAGCCCCATCTGACAATAGCAGCACTATCTTACTACAGGGTCATGAAAAGACAC
TTGTTCGAGGAGTAGTGTCCATCATTCATGTTTTGACTGTAAGAAAA

Alignment

ORF - retro_rnor_1873 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66. %
• Parental protein coverage: 65.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTAALQAALKNP-PINTKSQAVKDRAGSIVLKVLISFKANDIEKAVQSLDKNGVDLLMKYIYKGFESPSD
          .T.ALQ.A...P.PI.TKSQAVKD.AGSIVLKVLISFKANDIE.AVQ.LD.NG..LL.....K....PSD
Retrocopy VTTALQDACSPP<PISTKSQAVKDQAGSIVLKVLISFKANDIERAVQALDRNGMVLLIN--IKALRAPSD

Parental  NSSAMLLQWHEKALAAGGVGSIVRVLTARK
          NSS..LLQ.HEK.L...GV.SI..VLT.RK
Retrocopy NSSTILLQGHEKTLVR-GVVSIIHVLTVRK

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	58.02 RPM
SRP017611_kidney	0.00 RPM	69.78 RPM
SRP017611_liver	0.00 RPM	34.02 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1873 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1873 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1873 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000560	2 retrocopies	retro_chof_1502, retro_chof_783,
Dasypus novemcinctus	ENSDNOG00000010375	3 retrocopies	retro_dnov_1277, retro_dnov_199, retro_dnov_2495,
Echinops telfairi	ENSETEG00000014969	1 retrocopy	retro_etel_1922,
Monodelphis domestica	ENSMODG00000007194	1 retrocopy	retro_mdom_968,
Mus musculus	ENSMUSG00000008475	1 retrocopy	retro_mmus_281,
Rattus norvegicus	ENSRNOG00000014317	1 retrocopy	retro_rnor_2730,
Rattus norvegicus	ENSRNOG00000028062	1 retrocopy	retro_rnor_1873 ,