RetrogeneDB ID: retro_ptro_1911

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:104072225..104073240(-)
• Located in intron of: ENSPTRG00000015166

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC98
• Ensembl ID: ENSPTRG00000023645
• Aliases: CCDC98, FAM175A
• Description: None

Sequence

>retro_ptro_1911
CATGCTTTTTTTAGCTTTTATAATTCCTCAAGTGAAGTAAATGAGCAAGCACTGAAGAAAATATTCTCCAATGTCAAAAA
GAATGTGATAGGTTGGTACAAATTCTGTCGTCATTCAGATCAGATCATGACGTTTAGAGAGAGGCTGCTTCACAAAAACT
CGCAGGAGCATTTTTCAAACCAAGAACTTATTTTTCTACTATTAACACCAAGTATAATAACAGAAAGCTGCTCTACTCAT
CGACTGAAACATGCCTTGAAACCTCAAAGAGGACTTTTTCACAGGGTACCTTTAGTGGTTGCCAATCTGGATATTTCTGA
ACAACTAGGTTATAAAACTGTATCAGGTTCCTGTACATCCACTGGTTTTAGCCAAGCAGTAAAAACACACAGCTCTAAAT
TTTTTGAAGAAGATGGATCAGTAAAGGAGGTACATAAGATAAATGAAATGTAATGCTTCATTACAAGAGGAATTAAAGAG
TATATGCAAAAAAACATGGAAGACAATGAACAAGCAATAAATAAACTAGTAAAGGATATAAACAGATTAAAACAAGAAAT
TGGAAAAAAGGAGTTGAGCATAGATTCAGGCAGCCTGAGAGAAGAATATCTAAAAAGACCCTCAGGGGAACATTTTTCCT
GGTCAAGCATTATGGACCTTTTATCCAGATTCTGAATTTCTTCATTCGTGTGTTATGTCTTTAAAAAACAGACATGTTTC
TAAAAGCTGTAACAACAACCTCCACCTCGATGTAGTAGCCAAACTGACCTTAATGGTAGAACACACTGACATTCCTGAAG
CTAGTCCAGCTAGTAGACCGCAAATGATTAAGCATAAAGCCTTAGACTTAGATGACAGATTACAATTCAAGAAATCACAG
CAGTTAGAGACATAAGACAAACCATGTAAAACAGATACTGATAGTAGTGACCAAGAAAAAGCATCTACAATGAGCAGCCC
AGAAATAGATGAAGAGATTGAGAAAATGAAGGGATCTAGTGAATATCCATCCAGT

Alignment

ORF - retro_ptro_1911 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.71 %
• Parental protein coverage: 82.89 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YQLFSFYNSSGEVNEQALKKILSNVKKNVVGWYKFRRHSDQIMTFRERLLHKNLQEHFSNQDLVFLLLTP
          ...FSFYNSS.EVNEQALKKI.SNVKKNV.GWYKF.RHSDQIMTFRERLLHKN.QEHFSNQ.L.FLLLTP
Retrocopy HAFFSFYNSSSEVNEQALKKIFSNVKKNVIGWYKFCRHSDQIMTFRERLLHKNSQEHFSNQELIFLLLTP

Parental  SIITESCSTHRLEHSLYKPQKGLFHRVPLVVANLGMSEQLGYKTVSGSCMSTGFSRAVQTHSSKFFEEDG
          SIITESCSTHRL.H.L.KPQ.GLFHRVPLVVANL..SEQLGYKTVSGSC.STGFS.AV.THSSKFFEEDG
Retrocopy SIITESCSTHRLKHAL-KPQRGLFHRVPLVVANLDISEQLGYKTVSGSCTSTGFSQAVKTHSSKFFEEDG

Parental  SLKEVHKINEMYASLQEELKSICKK-VEDSEQAVDKLVKDVNRLKREI-EKRRGAQIQAAREKNIQKDPQ
          S.KEVHKINEM........K....K..ED.EQA..KLVKD.NRLK.EI.EKR..A.IQAA.EKNI.KDPQ
Retrocopy SVKEVHKINEM*CFITRGIKEYMQKNMEDNEQAINKLVKDINRLKQEI>EKRS*A*IQAA*EKNI*KDPQ

Parental  ENIFLCQALRTFFPNSEFLHSCVMSLKNRHVSKSSCNYNHHLDVVDNLTLMVEHTDIPEASPASTPQIIK
          .NIF..QAL.TF.P.SEFLHSCVMSLKNRHVSKS.CN.N.HLDVV..LTLMVEHTDIPEASPAS.PQ.IK
Retrocopy GNIFPGQALWTFYPDSEFLHSCVMSLKNRHVSKS-CNNNLHLDVVAKLTLMVEHTDIPEASPASRPQMIK

Parental  HKALDLDDRWQFKRSRLLDTQDKRSKADTGSSNQDKASKMSSPETDEEIEKMKGFGEYSQS
          HKALDLDDR.QFK.S..L.T.DK..K.DT.SS.Q.KAS.MSSPE.DEEIEKMKG..EY..S
Retrocopy HKALDLDDRLQFKKSQQLET*DKPCKTDTDSSDQEKASTMSSPEIDEEIEKMKGSSEYPSS

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	1.79 RPM
SRP007412_cerebellum	0.00 RPM	3.05 RPM
SRP007412_heart	0.00 RPM	3.15 RPM
SRP007412_kidney	0.00 RPM	4.55 RPM
SRP007412_liver	0.00 RPM	1.64 RPM
SRP007412_testis	0.11 RPM	26.35 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1911 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1911 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1911 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_2208
Macaca mulatta	retro_mmul_1499

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013241	1 retrocopy	retro_chof_2580,
Homo sapiens	ENSG00000163322	1 retrocopy	retro_hsap_4024,
Macaca mulatta	ENSMMUG00000015357	2 retrocopies	retro_mmul_1499, retro_mmul_2320,
Nomascus leucogenys	ENSNLEG00000009133	2 retrocopies	retro_nleu_1198, retro_nleu_661,
Pongo abelii	ENSPPYG00000014898	2 retrocopies	retro_pabe_2208, retro_pabe_3301,
Pan troglodytes	ENSPTRG00000023645	2 retrocopies	retro_ptro_1911 , retro_ptro_2728,