RetrogeneDB ID: retro_ptro_692

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:47362449..47362933(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM173B
• Ensembl ID: ENSPTRG00000016724
• Aliases: None
• Description: Pan troglodytes protein FAM173B (FAM173B), mRNA. [Source:RefSeq mRNA;Acc:NM_001243095]

Sequence

>retro_ptro_692
GGGGGAGGTACATCCCTAGAAACACCTAAAGAAGAAAGTCAGTCAAGACGTATTCTACCTTCGACTTTTGAAGCCAACCG
TTTGAAGAAAAGCAACTAGGGGTTTTTATTTATTGAGATTGTGGGCGGGACTCTGGTGGCTGTATGCTGTAGCTATGCCA
TTTATAGCACCAGTCCTCTCAAAAGTCTGTTTGCCTTTTGTACCTGCAACTACAAAGCAGATAAAAAATGTGAAAATGTT
GCTATGCAGAGGAGGATCCCTGGTAGACATTGGTAATGGCGATGGACACATTAATAACACAGTAATAACAGCTGCAAAGG
AAAGATTCACAGCAGTTGGTTGTGAATTAAATCCGTGGCTAGTTTGGTATTCCAAGTATCATGGTTGGCAAGAAAGTGTG
CGTGGCTCTGCCAAATTTTATATTTCAGATTTGTGGGCAGTTACTTTTTCATAGTACTCAAACACTGTTATTTTTGGTGT
GCCT

Alignment

ORF - retro_ptro_692 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.73 %
• Parental protein coverage: 68.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GGGIPLETLKEESQSRHVLPANFEVNSLQKSN-WGFLLTGLVGGTLVAVYAVATPFVTPALRKVCLPFVP
          GGG..LET.KEESQSR..LP..FE.N.L.KSN..GF.L..L..G.L...YAVA.PF..P.L.KVCLPFVP
Retrocopy GGGTSLETPKEESQSRRILPSTFEANRLKKSN>RGFYLLRLWAG-LWWLYAVAMPFIAPVLSKVCLPFVP

Parental  ATTKQIENVVKMLRCRRGSLVDIGSGDGRI---VIAAAKKGFTAVGYELNPWLVWYSRYRAWREGVHGSA
          ATTKQI.NV.KML.CR.GSLVDIG.GDG.I...VI.AAK..FTAVG.ELNPWLVWYS.Y..W.E.V.GSA
Retrocopy ATTKQIKNV-KMLLCRGGSLVDIGNGDGHINNTVITAAKERFTAVGCELNPWLVWYSKYHGWQESVRGSA

Parental  KFYISDLWKVTFSQYSNVVIFGVP
          KFYISDLW.VTFS.YSN.VIFGVP
Retrocopy KFYISDLWAVTFS*YSNTVIFGVP

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	9.40 RPM
SRP007412_cerebellum	0.00 RPM	8.68 RPM
SRP007412_heart	0.00 RPM	7.34 RPM
SRP007412_kidney	0.00 RPM	10.46 RPM
SRP007412_liver	0.00 RPM	7.01 RPM
SRP007412_testis	0.00 RPM	5.80 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_692 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_692 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_692 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1105

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000002277	1 retrocopy	retro_dnov_1076,
Homo sapiens	ENSG00000150756	1 retrocopy	retro_hsap_1105,
Macaca mulatta	ENSMMUG00000020111	1 retrocopy	retro_mmul_858,
Nomascus leucogenys	ENSNLEG00000011587	1 retrocopy	retro_nleu_198,
Oryctolagus cuniculus	ENSOCUG00000025588	1 retrocopy	retro_ocun_1244,
Pan troglodytes	ENSPTRG00000016724	1 retrocopy	retro_ptro_692 ,