RetrogeneDB ID: retro_rnor_337

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 10:37356178..37356640(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000005821
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Fam162a
• Ensembl ID: ENSRNOG00000002255
• Aliases: None
• Description: Protein FAM162A [Source:UniProtKB/Swiss-Prot;Acc:Q4QQV3]

Sequence

>retro_rnor_337
ATGTGGAGCCTCCGCGGCCTGCGCCTGGAGGCTGGGCATTATTTTAGGTTATATGAAAGAAATGCTTCCTCAACTCCAAG
GTTAACCAGAAACACCGACTTGAAGATGATCAGTGGATTCTGGACCAAGCCACAGGAAAGTCCCAAAGCTCCAACCCAGT
CTTACAGACACGGGGTGCCGCCGCACAAGCCCACAGACTTAGAGAAGAAGATCCTGCTGTGGTCAGGCCGCTTCAAGAAG
GAGGAAGAGAGCCCAGAGACGATCCGGTTTGAGATGCTTGGTGCTGCAAAGAACAAGTTCTGGGTGAAGGTCAGCTATTT
AATGAGGGCCCCCGACAGTGGCAGTTTATTCTATATGGTTATTGAGGGCAAGAAGGCTGTGAAAAGACGAGTCTTTACAA
GCTTGAACCTAGAAAGGAAAGCCTGTCTGAGAGAGGAGGCAGCTATGAAGGCCAAAACAGAC

Alignment

ORF - retro_rnor_337 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.35 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MWSLRGLRLAAGHCFRLCERNVSSPLRLTRNTDLKRINGFCTKPQESPKAPTQSYRHRVPLHKPTDFEKK
          MWSLRGLRL.AGH.FRL.ERN.SS..RLTRNTDLK.I.GF.TKPQESPKAPTQSYRH.VP.HKPTD.EKK
Retrocopy MWSLRGLRLEAGHYFRLYERNASSTPRLTRNTDLKMISGFWTKPQESPKAPTQSYRHGVPPHKPTDLEKK

Parental  ILLWSGRFKKEEEIPETISFEMLDAAKNKIRVKVSYLMIALTVAGCVYMVIEGKKAAKRHESLTSLNLER
          ILLWSGRFKKEEE.PETI.FEML.AAKNK..VKVSYLM.A.......YMVIEGKKA.KR....TSLNLER
Retrocopy ILLWSGRFKKEEESPETIRFEMLGAAKNKFWVKVSYLMRAPDSGSLFYMVIEGKKAVKR-RVFTSLNLER

Parental  KARLREEAAMKAKAD
          KA.LREEAAMKAK.D
Retrocopy KACLREEAAMKAKTD

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	26.39 RPM
SRP017611_kidney	0.00 RPM	33.84 RPM
SRP017611_liver	0.00 RPM	29.18 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_337 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_337 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_337 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014316	1 retrocopy	retro_amel_1533,
Monodelphis domestica	ENSMODG00000018300	1 retrocopy	retro_mdom_785,
Mustela putorius furo	ENSMPUG00000004773	1 retrocopy	retro_mputfur_1616,
Otolemur garnettii	ENSOGAG00000003194	1 retrocopy	retro_ogar_2064,
Rattus norvegicus	ENSRNOG00000002255	2 retrocopies	retro_rnor_2587, retro_rnor_337 ,
Tursiops truncatus	ENSTTRG00000013401	1 retrocopy	retro_ttru_791,