RetrogeneDB ID: retro_ptro_2746

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:45840856..45841574(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDCA8
• Ensembl ID: ENSPTRG00000000552
• Aliases: CDCA8, borealin
• Description: Pan troglodytes cell division cycle associated 8 (CDCA8), mRNA. [Source:RefSeq mRNA;Acc:NM_001246430]

Sequence

>retro_ptro_2746
CAATTTAAGCTAACTCAGTGAGACAGGAAGAACTCCTCACAGAGAGCGAGAACCTGCACAACCATGGCGTCCTCAGCTCC
CCACAGTGCTGCAGGAGATGCCCTGGCTCAACTACTTTGTCCTTGGAAGAAACAAACAGTGCCTGGACCAAGAGGTGGTG
GCAGCTGACCTGGATGGCACAGAAATACACACACTCACAGCCAGAGCTTTGCAGACAGCCCTGAAACCTGCCACAGCACA
GAAAGCAATACAAGTGGATGAAACCACGGTGGAAGAAGAGAAAATATACAGAAGAATCTTCAAACTGCAAGAGTCGAAAG
GGATCCTCCATGGAAGAAGAGAACCCAGTTTATACTAGGAAAAGGAAAGGCAAGATGTCAAAGCCGTTGTGGCACTGTGG
CCCCAGTGGAGGCTGGCTGGAGCTGCCTATGGTGAAGTCAACACTGGGCCTGACACCCAGGCTTGGCATGAGGGTTCTTC
AAGCCCCCTGGCCTGTGCACCAGCAGCCACAGCATGGATTCCTGCGATCTCAGTTCATGGCAGCCCTCTCTCCAGCAGCA
GAGAGCTCTCCCTGGCTGAGGCCCATCAGAGCAAGGCTGCTGTGATGGGCCAGTGACTTGCCAGGGGCCATACTGCAAAA
CTAGATCCAGGGGCCTTGGAAAGCACAAAGAAGCTCTCCAGTGGTCTTGCCCAAATCTGCAGCAGCCTACAGACCCAC

Alignment

ORF - retro_ptro_2746 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.79 %
• Parental protein coverage: 87.5 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  RIKQIESDRQN-LLKEVDNLYNIEIL-RLPKALREMNWLDYFALGGNKQALE-EAATADLDITEINKLTA
          ..K....DR.N.LL.E..NL.N...L..LP..L.EM.WL.YF.LG.NKQ.L..E...ADLD.TEI..LTA
Retrocopy QFKLTQ*DRKN<LLTESENLHNHGVL<QLPTVLQEMPWLNYFVLGRNKQCLDQEVVAADLDGTEIHTLTA

Parental  EAIQTPLKSAKTRKVIQVDEMIVEEEEEE-ENEHKNLQTARVKRCPPSKKRTQSIQGKGKRKRSSRANTV
          .A.QT.LK.A...K.IQVDE..V...EEE.EN..KNLQTARV.R.PP.KKRTQ.I.GKGK....SR..TV
Retrocopy RALQTALKPATAQKAIQVDETTV---EEE<ENIQKNLQTARVERDPPWKKRTQFILGKGKARCQSRCGTV

Parental  TPAV-GRLEVSMVKPTPGLTPRFDSRVFK-TPGLRTPAAGERIYNISGNGSPLADSKEIFLTVPVGGGES
          .P...G.LE..MVK.T.GLTPR...RV....P....PAA...I..IS..GSPL..S.E..L.........
Retrocopy APVE<GWLELPMVKSTLGLTPRLGMRVLQ<SPLACAPAATAWIPAISVHGSPLSSSRE--LSLAEAHQSK

Parental  LRLLASDLQRHSIAQLDPEALGNIKKLSNRLAQICSSIRTH
          .......L.R...A.LDP.AL...KKLS..LAQICSS..TH
Retrocopy AAVMGQ*LARGHTAKLDPGALESTKKLSSGLAQICSSLQTH

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	1.16 RPM
SRP007412_cerebellum	0.00 RPM	1.43 RPM
SRP007412_heart	0.00 RPM	0.44 RPM
SRP007412_kidney	0.00 RPM	1.15 RPM
SRP007412_liver	0.00 RPM	3.27 RPM
SRP007412_testis	0.00 RPM	62.28 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2746 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2746 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2746 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4052
Macaca mulatta	retro_mmul_2339

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000028556	2 retrocopies	retro_acar_139, retro_acar_200,
Choloepus hoffmanni	ENSCHOG00000004959	1 retrocopy	retro_chof_679,
Callithrix jacchus	ENSCJAG00000002008	1 retrocopy	retro_cjac_380,
Homo sapiens	ENSG00000134690	1 retrocopy	retro_hsap_4052,
Gorilla gorilla	ENSGGOG00000007719	2 retrocopies	retro_ggor_2594, retro_ggor_2721,
Microcebus murinus	ENSMICG00000011926	1 retrocopy	retro_mmur_1589,
Macaca mulatta	ENSMMUG00000014340	2 retrocopies	retro_mmul_1611, retro_mmul_2339,
Nomascus leucogenys	ENSNLEG00000011630	2 retrocopies	retro_nleu_2803, retro_nleu_3006,
Pongo abelii	ENSPPYG00000001526	2 retrocopies	retro_pabe_3224, retro_pabe_3234,
Pan troglodytes	ENSPTRG00000000552	3 retrocopies	retro_ptro_2531, retro_ptro_2533, retro_ptro_2746 ,