RetrogeneDB ID: retro_rnor_2730

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 9:49466040..49466499(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000016444
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Arpc5l
• Ensembl ID: ENSRNOG00000014317
• Aliases: None
• Description: actin-related protein 2/3 complex subunit 5-like protein [Source:RefSeq peptide;Acc:NP_001032856]

Sequence

>retro_rnor_2730
ATGGCCCGGAACACACTGTCCTCACGCTTCCGCCGAGTGGATATCGACGAATTTGACGAGAACAAATTCGTAGACGAGCA
CGAAGAGGCGGCGGCGGCGTCGGGCGAGCCAGGCCCCGACCCCTGCGAGGTAGACGGGCTCCTGCGGCAAGGGGACATGC
TTCGGGCATTCCATGCAGCCTTGCGGAACTCTCCAATCAACACCAAGAATCAAGCTGTGAAGGAACGAGCCCAGGGTATA
GTCCTGAAAGTACTCACAAACTTCAAGAGCAGCGAGATTGAGCAGGCTGTGCAGTCACTGGACAGGAATGGCATTGACTT
GCTAATGAAGTACATTTATAAAGGGTTTGAGAAGCCCACAGAAAATAGCAGTGCAGTGTTACTCCAGTGGCATGAAAAGG
CTTTAGCTGTTGGAGGACTAGGCTCCATTATAAGAGTTCTTACAGCAAGAAAGACTGTT

Alignment

ORF - retro_rnor_2730 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.35 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MARNTLSSRFRRVDIDEFDENKFVDEHEEAAAASGEPGPDPCEVDGLLRQWDMLRAFHAALRNSPINTKN
          MARNTLSSRFRRVDIDEFDENKFVDEHEEAAAASGEPGPDPCEVDGLLRQ.DMLRAFHAALRNSPINTKN
Retrocopy MARNTLSSRFRRVDIDEFDENKFVDEHEEAAAASGEPGPDPCEVDGLLRQGDMLRAFHAALRNSPINTKN

Parental  QAVKERAQGIVLKVLTNFKSSEIEQAVQSLDRNGIDLLMKYIYKGFEKPTENSSAVLLQWHEKALAVGGL
          QAVKERAQGIVLKVLTNFKSSEIEQAVQSLDRNGIDLLMKYIYKGFEKPTENSSAVLLQWHEKALAVGGL
Retrocopy QAVKERAQGIVLKVLTNFKSSEIEQAVQSLDRNGIDLLMKYIYKGFEKPTENSSAVLLQWHEKALAVGGL

Parental  GSIIRVLTARKTV
          GSIIRVLTARKTV
Retrocopy GSIIRVLTARKTV

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	3.74 RPM	16.61 RPM
SRP017611_kidney	3.00 RPM	17.93 RPM
SRP017611_liver	2.56 RPM	7.93 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2730 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2730 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2730 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016540	1 retrocopy	retro_amel_1798,
Callithrix jacchus	ENSCJAG00000006730	4 retrocopies	retro_cjac_1282, retro_cjac_1725, retro_cjac_2744, retro_cjac_3941,
Felis catus	ENSFCAG00000028753	1 retrocopy	retro_fcat_1316,
Macaca mulatta	ENSMMUG00000020628	2 retrocopies	retro_mmul_1650, retro_mmul_623,
Mustela putorius furo	ENSMPUG00000013924	1 retrocopy	retro_mputfur_1532,
Oryctolagus cuniculus	ENSOCUG00000002997	1 retrocopy	retro_ocun_518,
Procavia capensis	ENSPCAG00000013936	1 retrocopy	retro_pcap_274,
Pan troglodytes	ENSPTRG00000021362	1 retrocopy	retro_ptro_2185,
Rattus norvegicus	ENSRNOG00000014317	1 retrocopy	retro_rnor_2730 ,
Rattus norvegicus	ENSRNOG00000028062	1 retrocopy	retro_rnor_1873,
Ictidomys tridecemlineatus	ENSSTOG00000007907	2 retrocopies	retro_itri_275, retro_itri_767,
Tupaia belangeri	ENSTBEG00000008398	1 retrocopy	retro_tbel_442,