RetrogeneDB ID: retro_rnor_2587

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 8:92958354..92958733(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_rnor_2587
AGAAACACTGACTTGAAGAGGATCAATGGATTCTGCACCAAGCCACAGGAAAGTCCCAAAGCTCCAAACCCAGTCTTAGA
GACACAGGATGCCGCTGCACAAGTCCACAGACTTCAAGAGGAAGATTCTGCTATGGTCAGGCCACTTCAAGAAGGAGGAA
GAGATACCAGAGACAATCTCATTTGAGATGCTTGACGCTGCAAAGAACAAGATCCGGGTGAAGGTCAGCTATTTAATGAT
TGCCCTGACAGTGGCAGGATGCGTCTATATGGTTATTGAGGGCAAGAAGGCTGCGAAAAGACATGAGTCTTTAACAAGCT
TGAACCTAGAAAGGAAAGCCCGTCTGAGAGTGGAGGCAGCTATGAAGGCCAAAACGGAC

Alignment

ORF - retro_rnor_2587 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.91 %
• Parental protein coverage: 81.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RNTDLKRINGFCTKPQESPKAP-TQSYRHRVPLHKPTDFEKKILLWSGRFKKEEEIPETISFEMLDAAKN
          RNTDLKRINGFCTKPQESPKAP.TQS.RHR.PLHK.TDF..KILLWSG.FKKEEEIPETISFEMLDAAKN
Retrocopy RNTDLKRINGFCTKPQESPKAP>TQS*RHRMPLHKSTDFKRKILLWSGHFKKEEEIPETISFEMLDAAKN

Parental  KIRVKVSYLMIALTVAGCVYMVIEGKKAAKRHESLTSLNLERKARLREEAAMKAKAD
          KIRVKVSYLMIALTVAGCVYMVIEGKKAAKRHESLTSLNLERKARLR.EAAMKAK.D
Retrocopy KIRVKVSYLMIALTVAGCVYMVIEGKKAAKRHESLTSLNLERKARLRVEAAMKAKTD

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_2587 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2587 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2587 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,