RetrogeneDB ID: retro_nleu_1450

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397293.1:21974427..21975253(-)
• Located in intron of: ENSNLEG00000004475

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD4
• Ensembl ID: ENSNLEG00000010139
• Aliases: None
• Description: None

Sequence

>retro_nleu_1450
ATGAAGCGCCAATGGGGCAAGAATCACAAGGCGCATATCATTGCCTTGGTGGGAAGCCTGAAGGCAATGAGAAGGATCTG
GTGAAACTGGCTAAATTCCTCAAGAAGGAGAAAGTAAATGTTGACATGATGAATTTTGGGGAAGAGGAGGTGAACACAGA
AAAGCTGACAGCCTTTGTAAACACGTTGAATGGCAAAGATGGAAGCGGTTCTCATCTGGTGGCAGTGCCTCCTGGGCCCA
GCTTCACTGATGCTCTCATCAGTTCTCCAATTTTGGCTGGGGAAGGAGGTGCCATGCTAGATCTCGGTGCCAGTGACTTT
GAATTTGGAATAGATCCCAGTGGTGATCCTGAGCTGGCCTTGGCCCTCAAGTTTCTATGGGGGAGCAGCAGCAGTGGCAG
AAGGGGGAGCCCAGATGAGCAGCTGCAGCTTCTGCTGCTGAGGTCAGGATTGCTACAACTGGGACTGAAGGCTCAGATGA
GGCCCTGCTGAAGATGACCATTAGCCAACAAGAGTTTGGCCATACCAGACTTCCTGACCTAAGCAGTGTGACTGAGGAAG
AGGAGATTGCTTGTGTCATGCAGGGAGCAGAGTTTGGCCAGGCGGAATCAGCAGACATTGATGCCAGCTCAGCCATGGAC
ACATCTGAGCCAGCCAAGGAGGAGGATGATTACGATGTGATGCAGGATCCCGAGTTCCTTCAGAGTGTCCTAGAGAACCT
CCCAGGTATGGATCCCAACAATGAAGCCATCTGAACTGCTGTGGGCTCCCTGGCCTCCCAGGCCACCAAGGATGGCAAGA
AGGACAAGAAGGAGGAAGACAAGAAG

Alignment

ORF - retro_nleu_1450 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.52 %
• Parental protein coverage: 70.47 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LKHRQGKNHKMRIIAFV-GSPVEDNEKDLVKLAKRLKKEKVNVDIINFGEEEVNTEKLTAFVNTLNGKDG
          .K...GKNHK..IIA.V.G.P.E.NEKDLVKLAK.LKKEKVNVD..NFGEEEVNTEKLTAFVNTLNGKDG
Retrocopy MKRQWGKNHKAHIIALV<GKP-EGNEKDLVKLAKFLKKEKVNVDMMNFGEEEVNTEKLTAFVNTLNGKDG

Parental  TGSHLVTVPPGPSLADALISSPILAGEGGAMLGLGASDFEFGVDPSADPELALALR-VSMEEQRQRQEEE
          .GSHLV.VPPGPS..DALISSPILAGEGGAML.LGASDFEFG.DPS.DPELALAL..VSM.EQ.Q.Q..E
Retrocopy SGSHLVAVPPGPSFTDALISSPILAGEGGAMLDLGASDFEFGIDPSGDPELALALK<VSMGEQQQWQKGE

Parental  ARRAAAASAAEAGIATTGTEGERDSDDALLKMTISQQEFGRTGLPDLSSMTEEEQIAYAMQMSLQGAEFG
          .R.AAAASAAE..IATTGTEG...SD.ALLKMTISQQEFG.T.LPDLSS.TEEE.IA..MQ....GAEFG
Retrocopy PR*AAAASAAEVRIATTGTEG---SDEALLKMTISQQEFGHTRLPDLSSVTEEEEIACVMQ----GAEFG

Parental  QAESADIDASSAMDTSEPAKEEDDYDVMQDPEFLQSVLENLPGVDPNNEAIRNAMGSLASQATKDGKKDK
          QAESADIDASSAMDTSEPAKEEDDYDVMQDPEFLQSVLENLPG.DPNNEAI..A.GSLASQATKDGKKDK
Retrocopy QAESADIDASSAMDTSEPAKEEDDYDVMQDPEFLQSVLENLPGMDPNNEAI*TAVGSLASQATKDGKKDK

Parental  KEEDKK
          KEEDKK
Retrocopy KEEDKK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_1450 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012565	1 retrocopy	retro_cfam_591,
Callithrix jacchus	ENSCJAG00000007357	1 retrocopy	retro_cjac_2808,
Dasypus novemcinctus	ENSDNOG00000007446	1 retrocopy	retro_dnov_1556,
Homo sapiens	ENSG00000159352	1 retrocopy	retro_hsap_2531,
Nomascus leucogenys	ENSNLEG00000010139	1 retrocopy	retro_nleu_1450 ,
Pongo abelii	ENSPPYG00000000871	1 retrocopy	retro_pabe_1862,
Pan troglodytes	ENSPTRG00000013893	1 retrocopy	retro_ptro_1474,
Sus scrofa	ENSSSCG00000006628	1 retrocopy	retro_sscr_981,
Tupaia belangeri	ENSTBEG00000016911	1 retrocopy	retro_tbel_238,
Tursiops truncatus	ENSTTRG00000007019	1 retrocopy	retro_ttru_903,