RetrogeneDB ID: retro_pabe_870

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:90375422..90376991(+)
• Located in intron of: ENSPPYG00000004819

Retrocopy information

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

Parental gene information

• Parental gene symbol: CENPC
• Ensembl ID: ENSPPYG00000014736
• Aliases: None
• Description: centromere protein C [Source:HGNC Symbol;Acc:1854]

Sequence

>retro_pabe_870
ACACGTATTCAGTCACCAAGCAAAGAGTGCCAGAAATCACATCCAAAGTCAGTTCCACTTTCTTCAAGGAAGAAAGAAGC
CTCTCTGCAGTTTGTTGTAGAACCAAGTGAAGCCACCAACAGATCAGTTCAGGCCCATGAAGTTCGTCAGAAAATTCTGG
CAACTGATGTTAGTTCCAAAAATACACCTGACTCGAAAAAAATGTCAAGTAGAAACATAAATGATCATCACAGTGAAGCT
GATGAAGAATTTTACTTATCTGTTGGCTCACCTTCTGTTCTTTTGGATGCAAAAACATCTGTATTGCAAAATGTTATTCC
ATCTAGTGCCCAAAAGAAAGAGACTTACACTTTTGAAAATTCAGTAAATATGCTGCCTTCAAGTACAGAGGTTTCACTTA
AAACCAAACAAAGGTTAAACTTTGAAGATAAAGTTATTTTAAAGAAAATAGAAATAGATAATAAAGTATCAGATGAAGAG
GATACAACATCAGAAGGACAAGAAAGAAAACCATCAGGATCATCTCAGAATAGAATACGAAATTCAGAATATGAAATTCA
ATGACAAGCTAAAAAAAGTTTTTCAACATTGTTTTTAGAAACAGCAAAACGAAAAAGTGAATCCAGTCCCATTGTTAGGC
ATGGAGAAATTGCTCCACCTCATTCGTGTCCTCCCGATGATATGAAGTTGACAGAGGATGAATTTATAATTGATGAGTCA
GATCAAAGTTTTGCCAGTAGATCTTGGATTACTATACCAAGAAAGGCAGGGCCTCTGAAACAACGCACCATATCCCCGGC
TGAGAGCACTGCACTCCTTCAAGATAGAAAGTCAAGAGAAAAGCATTATAATATATTAGCTATGACTTTGGCAAATGACA
AACATTCCCATAAACCTCACCTAGTAGAGACATCTCAGCCCTCTGATAAAACAGTACTGGATACAAGTTATGCTTTGACA
GGTGAAACACAAAATGACTGTAGATCTACAAAATATGAAATGTATTCCAAGAATGCAGAAAAATCATCTAGAAGCAAAAG
GACTAAAAAACAAAAACAGAGAAGAAAATTTATGGCTAAACCAGCTGAAGAACAGCTCGATGTGGGACAGTCTAAAGATG
AAAACATACATACGTCACATATTACCCAAGACAAATTTCAAAGAAATTCAGACAGAAATATGGAAGAGTGTGAAGAGATG
GGAAATGATTGTGCTTCCAAAAAACAGATGCCACCTGTGGGAAGCAAGAAAAGTAGCACTAGAAAAGATAAGGAAGAATC
TAAAAAGAAGCGCTTTTCCAGTGAGTCCAAGAACAAACTTGTACCTGAAGAAGTGACTTCAACTGTCACGAGAAGTCGAA
GAATTTCCAGACATCCATCTAATTGGTGGGTGGTAAAATCAGAGGAGAGTCCTGTTGATAGCAATTCTTCAATAAGAAAT
GAATTACCAGTGCATCACAACAGTAGGCAAAAATCTGCTAAGAAAACAAATCAGTCATCTAAGAATATTGGGAAAAAAAC
TATTCCACTTAAAAGGCAGAAGACAGCAACTAAAGACAGCCAAAGAGTA

Alignment

ORF - retro_pabe_870 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.85 %
• Parental protein coverage: 55.89 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TRIQSPSKECQKSHSKSVPVSSRNKEASLQSVVESSEATNRSVQAHEVRQKILATDVSSKNTPDSKKKSS
          TRIQSPSKECQKSH.KSVP.SSR.KEASLQ.VVE.SEATNRSVQAHEVRQKILATDVSSKNTPDSKK.SS
Retrocopy TRIQSPSKECQKSHPKSVPLSSRKKEASLQFVVEPSEATNRSVQAHEVRQKILATDVSSKNTPDSKKMSS

Parental  RNINDHHSEADEEFYLSVGSPSVLLDAKTSVSQNVIPSSAQKRETYTFENSVNMLPSSTEVSVKTKKRLN
          RNINDHHSEADEEFYLSVGSPSVLLDAKTSV.QNVIPSSAQK.ETYTFENSVNMLPSSTEVS.KTK.RLN
Retrocopy RNINDHHSEADEEFYLSVGSPSVLLDAKTSVLQNVIPSSAQKKETYTFENSVNMLPSSTEVSLKTKQRLN

Parental  FDDKVMLKKIEIDNKVSDEEDKTSEGQERKPSGSSQNRIRDSEYEIQRQAKKSFSTLFLETVKRKSESSP
          F.DKV.LKKIEIDNKVSDEED.TSEGQERKPSGSSQN...........QAKKSFSTLFLET.KRKSESSP
Retrocopy FEDKVILKKIEIDNKVSDEEDTTSEGQERKPSGSSQNXXXXXXXXXX*QAKKSFSTLFLETAKRKSESSP

Parental  IVRHVATAPPHSCPPDDTKLIEDEFIIDESDQSFASRSWITIPRKAGPLKQRTVSPAESTALLQGRKSRE
          IVRH...APPHSCPPDD.KL.EDEFIIDESDQSFASRSWITIPRKAGPLKQRT.SPAESTALLQ.RKSRE
Retrocopy IVRHGEIAPPHSCPPDDMKLTEDEFIIDESDQSFASRSWITIPRKAGPLKQRTISPAESTALLQDRKSRE

Parental  KHHNILPKTLANDKHSHKPHPVETSQPSDKTVLDTSHALIGETENNYRSTKYEMYSKNAEKPSRSKRTIK
          KH.NIL..TLANDKHSHKPH.VETSQPSDKTVLDTS.AL.GET.N..RSTKYEMYSKNA...........
Retrocopy KHYNILAMTLANDKHSHKPHLVETSQPSDKTVLDTSYALTGETQNDCRSTKYEMYSKNAXXXXXXXXXXX

Parental  QKQRRKFMAKPAEEQLDVGQSKDENIHTSHITQDEFQRNSDRNMEEREEMGNDCVSKKQMPPVGSKKSST
          ......FMAKPAEEQLDVGQSKDENIHTSHITQD.FQRNSDRNMEE.EEMGNDC.SKKQMPPVGSKKSST
Retrocopy XXXXXXFMAKPAEEQLDVGQSKDENIHTSHITQDKFQRNSDRNMEECEEMGNDCASKKQMPPVGSKKSST

Parental  RKDKEESKKKRFSSESKNKLVPEEVTSTVTRSRRISRRPSDWWVVKSEESPVYSNSSIRNE-PVPHNSRQ
          RKDKEESKKKRFSSESKNKLVPEEVTSTVTRSRRISR.PS.WWVVKSEESPV.SNSSIRNE.PV.HNSRQ
Retrocopy RKDKEESKKKRFSSESKNKLVPEEVTSTVTRSRRISRHPSNWWVVKSEESPVDSNSSIRNELPVHHNSRQ

Parental  KSAKKTKESSKNIRKKTIPLKRQKTANKQRQKL
          KSAKKT..SSKNI.KKTIPLKRQKTA.K..Q..
Retrocopy KSAKKTNQSSKNIGKKTIPLKRQKTATKDSQRV

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	0.11 RPM	6.41 RPM
SRP007412_cerebellum	0.24 RPM	16.78 RPM
SRP007412_heart	0.09 RPM	5.06 RPM
SRP007412_kidney	0.23 RPM	6.63 RPM
SRP007412_liver	0.18 RPM	3.92 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_870 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_870 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_870 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1038
Pan troglodytes	retro_ptro_708

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000145241	1 retrocopy	retro_hsap_1038,
Mus musculus	ENSMUSG00000029253	1 retrocopy	retro_mmus_1910,
Nomascus leucogenys	ENSNLEG00000009058	1 retrocopy	retro_nleu_911,
Pongo abelii	ENSPPYG00000014736	1 retrocopy	retro_pabe_870 ,
Pan troglodytes	ENSPTRG00000016096	1 retrocopy	retro_ptro_708,