RetrogeneDB ID: retro_ptro_2531

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:57065417..57066251(+)
• 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_2531
ATGGCTCCTAGGAAGGGCAGCAGTTGGGTAGCCAAGACCAACTCCTTAGGGAGGTGGAAGCTCACCTCCTTTCTTAAAGA
CTTCGAAATGGAAATATGAATCAAGCCAACTGAGTCAGTCAGGCAGAACCTCTTCAAAGAGGTGGATAACCTCTACAACA
TCCAGATCCTGTGGCTCCCAAAGGCACTGCGCAAAGATGAATGTCTTAACTACTTCTCCTTTGGAGGAAACAAACAAGGC
TTAGAAGAGGCAGCAACAGCTGACCTGGATATCACCGAAATAAGCAAACGAACTGCAGAAGCTATTCAAACATCCCTGAA
ATCTACTAAAGCATGAAAGGTGATACAAGTAGATGAAATGATAGTGGAAGAGAATGAAGAGGAGGAAAATAAACGCAGGG
ATCTTCAAACTGCAAGAGTCAAAAGGTGAACTCCATCCAAGAAGAGAACTCAGTCTGTACAAGGAAAAGGCAGAAGAGAA
AGGTCAAGCTGTGCTAACACTGTTACCCGAACTGTGGGCTGATTGGACGTGTCCATAGTGAAACCAACTCCAGGCCTGAT
ACCCACGTTTGACTTGAGGGTCTTCATGATCCCTGGCCTGTGCACTCCTGCCACAGGAGAGCAGAATTACAACATCTCAG
GAAATGGCAGCCCTCTTGCCCATAGCAAAGAGATCTTCCTCACTGTGCCAGCGGGTGGCAAAGAGTGCATGTGATTTTTT
GCCAGTGACTTGCAGAGGCTCAGTATTGCCCAGCTAGATCCGTAGGCCTTGGGAAACATTAAGAAGCTCTCCAAACATCT
TGCCCAAATCTGCAGCAGCACACGCACCCATAAA

Alignment

ORF - retro_ptro_2531 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.43 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 6
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAPRKGSSRVAKTNSLRRRKLASFLKDFDREVEIRIKQIESDRQNLLKEVDNLYNIEILRLPKALREMNW
          MAPRKGSS.VAKTNSL.R.KL.SFLKDF..E.EI.IK..ES.RQNL.KEVDNLYNI.IL.LPKALR....
Retrocopy MAPRKGSSWVAKTNSLGRWKLTSFLKDF--EMEI*IKPTESVRQNLFKEVDNLYNIQILWLPKALRKDEC

Parental  LDYFALGGNKQALEEAATADLDITEINKLTAEAIQTPLKSAKTRKVIQVDEMIVEEEEEEENEHKNLQTA
          L.YF..GGNKQ.LEEAATADLDITEI.K.TAEAIQT.LKS.K..KVIQVDEMIVEE.EEEEN....LQTA
Retrocopy LNYFSFGGNKQGLEEAATADLDITEISKRTAEAIQTSLKSTKA*KVIQVDEMIVEENEEEENKRRDLQTA

Parental  RVKRCPPSKKRTQSIQGKGKRKRSSRANTVTPAVGRLEVSMVKPTPGLTPRFDSRVFKTPGLRTPAAGER
          RVKR..PSKKRTQS.QGKG.R.RSS.ANTVT..VG.L.VS.VKPTPGL.P.FD.RVF..PGL.TPA.GE.
Retrocopy RVKR*TPSKKRTQSVQGKGRRERSSCANTVTRTVG*LDVSIVKPTPGLIPTFDLRVFMIPGLCTPATGEQ

Parental  IYNISGNGSPLADSKEIFLTVPVGGGESLRLLASDLQRHSIAQLDPEALGNIKKLSNRLAQICSSIRTHK
          .YNISGNGSPLA.SKEIFLTVP.GG.E.....ASDLQR.SIAQLDP.ALGNIKKLS..LAQICSS.RTHK
Retrocopy NYNISGNGSPLAHSKEIFLTVPAGGKECM*FFASDLQRLSIAQLDP*ALGNIKKLSKHLAQICSSTRTHK

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_2531 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2531 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2531 has 0 orthologous retrocopies within eutheria group .

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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,