RetrogeneDB ID: retro_ptro_708

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:89640285..89643119(+)
• Located in intron of: ENSPTRG00000005284

Retrocopy information

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

Parental gene information

• Parental gene symbol: CENPC1
• Ensembl ID: ENSPTRG00000016096
• Aliases: None
• Description: Centromere protein C 1 [Source:UniProtKB/TrEMBL;Acc:K7C596]

Sequence

>retro_ptro_708
ATGGCTGCGTCGGGTCTGGATCATCTCAAAAATGGCTACAGAAGATTTTGTCGACCTTCCAGGGCACGTGACATTAACAC
AGAGCAAGGCCAGAATGTTCTGGAAATCTTACAAGACTGTTTTGAAGAAAAAAGTCTTGCCAATGATTTTAGCACAAATT
CTACAAAATCAGTGCTTAATTCAACACGCAAAATAAAAGACACTTGTGTTCAGTCACCAAGCAAAGAGTGCCAGAAATCA
CATCCAAAGTCAGTTCCACTTTCTTCAAGGAAGAAAGAAGCCTCTCTGCAGTTTGTTGTAGAACCAAGTGAAGCCACCAA
CAGATCAGTTCAGGCCCATGAAGTTCGTCAGAAAATTCTGGCAACTGATGTTAGTTCCAAAAATACACCTGACTCGAAAA
AAATGTCAAGTAGAAACATAAATGATCATCACAGTGAAGCTGATGAAGAATTTTACTTATCTGTTGGCTCACCTTATGTT
CTTTTGGATGCAAAAACATCTGTATCGCAAAATGTTATTCCATCTAGTGCCCAAAAGAGAGAGACTTACACTTTTGAAAA
TTCAGTAAATATGCTGCCTTCAAGTACAGAGGTTTCACTTAAAACCAAAAAAAGGTTAAACTTTGAAGATAAAGTTATTT
TAAAGAAAATAGAAATAGATAATAAAGTATCAGATAAAGAGGATAAAACATCAGAAGGACAAGAAAGAAAACCATCAGGA
TCATCTCAGAATAGAATACGACATTCAGAATATGAAATTTAATGACAAGCTAAAAAAAGTTTTTCAACATTGTTTTTAGA
AACAGTAAAACGAAAAAGTGAATCCAGTCCCATTGTTAGGCATGGAGGAATTGCTCCACCTCATTCGTGTCCTCCCGATG
ATATGAAGTTGATAGAGGATGAATTTATAATTGATGAGTCAGATCAAAGTTTTGCCAGTAGATCTTGGGATTACTATACC
AAGAAAGGCGGGGCCTCTGAAACAACGCACCATATCCCCGGCTGAGAGCACTGCACTCCTTCAAGATAGAAAGTCAAGAG
AAAAGCATCATAATATATTAGCTAAGACTTTGGCAAATGACAAACATTCCCATAAACCTCACCTAGTAGAGACATCTCAG
CCCTCTGATAAAACAGTACTGGATACAAGTTATGCTTTGACAGGTGAAACAGAAAATGACTGTAGATCTACAAAATATGA
AATGTATTCCAAGAATGCAGAAAAATCATCTAGAAGCAAAAGGACTATAAAACAAAAACAGAGAAGAAAATTTATGGCTA
AACCAGCTGAAGAACAGCTCGATGTGGGACAGACTAAAGATGAAAACATACATATGTCACATATTACCCAAGACAAATTT
CAAAGAAATTCAGACAGAAATATGGAAGAGCGTGAAGAGATGGGAAATGATTGTGCTTCCAAAAAACAGATGCCACCTGT
GGGAAGCAAGAAAAGTAGCACTAGAAAAGATAAGGAAGAATCTAAAAAGAAGCGCTTTTCTAGTGAGTCCAAGAACAAAC
TTTTGTCTGAAGAAGTGACTTCAACTGTCACGAGAAGTCGAAGAATTTCCAGGCATCCGTCTAATTGGTGGGTGGTAAAA
TCAGAGGAGAGTCCTGTTTATAGCAATTCTTCAATAAGAAATGAATTACCACTGCATCCCAACAGTAGGCAAAAATCTGC
TAAGAAAACAAATCAGTCATCTAAGAATATTGGGAAAAAAACTATTCCACTTAAAAGGCAGAAGACAGCAACTAAAGACA
GCCAAAGGGTACAGAAGTTTTTAAATGCTAAAGGTTCTGGATGTATCATTGGTCATGATGAAATTTCCAGTTGTTTGCTG
AGTGAGCCATTGGAAAGTGATGAGGCAGACTTGGCTAAGAGGAAAAATCTGGATTGTTCTAGATCTACAGGAAGCTCAAA
GAATGAAGATAATATTATGACTGCACAGAATGTTCCCCTAAAGCCTCAGACCAGTGGATATATATGTAATACACCAACAG
AGTCAAACTTGGATTCTGGAGAGCATAAGACTTCAGTTTTAGAGGAAAGTGGACCTTCCAGGCTCAATAATAATTATTTA
ATGTCTGGAAAGAATAATAATGATGTGGATGATGAGGAAGTTCCTGGAAGTTCAGATGACTCAAAACGATCTAAAGTGAT
ACCAAAGAACAGAATCCATCACAAACTAGTATTGCCCTCCAACACACCAAATGTTCGCAGGACCAAGAGAACACGTTTGA
AACCTTTGGAGTACTGGCGAGGACAGCAAATAGATTATCAAGGAAGGCCATCAGGAAGATTTGTGATTAGTGGAATACTA
TCTCCAGGCAAAATATCGTCTAAAAGGAAGGCAAGAGAAAATATTGGAAAAGTCGACAAAAAAATCTAATAAGAAAAGGA
TCTGTCTTGATAACGATGAAAGAAAGACTAGCTTAATGGTAAATCTAGGTATACCTCTTGGAGATCCTTTGCAGCCAGCA
ATGGTAAAGGACCCAGAAACAAGAGAGATTATTCTCATGGATCTTGTAAGGCCACAAGATACATATCAATTTTTTGTTAA
GCATGGTGAGTTGAAGGTATATAACACATTGGATACACCCTTTTTTTCTACTGGGAAATTGGTATTAAGACCACAAGAAG
AAAAGGGAAAGCAGCATGTTGGCCAGGATATATTGTTTTTTTATGTTAACTTTGGTGACCTTTTGTGTACTTTACACGAA
ATACCTTATATAATAAGTACTGGGGATTCGTTCTATGTTCCTTCAGGTAACTATTATAACATCAAAAATCTCCTGAATGA
GGAAAGTGTTCTTCTTTTTACTCAGATAAAAAGA

Alignment

ORF - retro_ptro_708 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.45 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAASGLDHLKNGYRRRFCRPSRARDINTEQGQNVLEILQDCFEEKSLANDFSTNSTKSVPNSTRKIKDTC
          MAASGLDHLKNGYRR.FCRPSRARDINTEQGQNVLEILQDCFEEKSLANDFSTNSTKSV.NSTRKIKDTC
Retrocopy MAASGLDHLKNGYRR-FCRPSRARDINTEQGQNVLEILQDCFEEKSLANDFSTNSTKSVLNSTRKIKDTC

Parental  IQSPSKECQKSHPKSVPVSSKKKEASLQFVVEPSEATNRSVQAHEVHQKILATDVSSKNTPDSKKMSSRN
          .QSPSKECQKSHPKSVP.SS.KKEASLQFVVEPSEATNRSVQAHEV.QKILATDVSSKNTPDSKKMSSRN
Retrocopy VQSPSKECQKSHPKSVPLSSRKKEASLQFVVEPSEATNRSVQAHEVRQKILATDVSSKNTPDSKKMSSRN

Parental  INDHHSEADEEFYLSVGSPFVLLDAKTSVSQNVIPSSAQKRETYTFENSVNMLPSSTEVSVKTKKRLNFD
          INDHHSEADEEFYLSVGSP.VLLDAKTSVSQNVIPSSAQKRETYTFENSVNMLPSSTEVS.KTKKRLNF.
Retrocopy INDHHSEADEEFYLSVGSPYVLLDAKTSVSQNVIPSSAQKRETYTFENSVNMLPSSTEVSLKTKKRLNFE

Parental  DKVMLKKIEIDNKVSDEEDKTSEGQERKPSGSSQNRIRDSEYEIQRQAKKSFSTLFLETVKRKSESSPIV
          DKV.LKKIEIDNKVSD.EDKTSEGQERKPSGSSQNRIR.SEYEI..QAKKSFSTLFLETVKRKSESSPIV
Retrocopy DKVILKKIEIDNKVSDKEDKTSEGQERKPSGSSQNRIRHSEYEI**QAKKSFSTLFLETVKRKSESSPIV

Parental  RHAATAPPHSCPPDDTKLIEDEFIIDELDQSFASRSW-ITIPRKAGSLKQRTISPAESTALLQGRKSREK
          RH...APPHSCPPDD.KLIEDEFIIDE.DQSFASRSW.ITIPRKAG.LKQRTISPAESTALLQ.RKSREK
Retrocopy RHGGIAPPHSCPPDDMKLIEDEFIIDESDQSFASRSW>ITIPRKAGPLKQRTISPAESTALLQDRKSREK

Parental  HHNILPKTLANDKHSHKPHPVETSQPSDKTVLDTSYALIGETVNNYRSTKYEMYSKNAEKPSRSKRTIKQ
          HHNIL.KTLANDKHSHKPH.VETSQPSDKTVLDTSYAL.GET.N..RSTKYEMYSKNAEK.SRSKRTIKQ
Retrocopy HHNILAKTLANDKHSHKPHLVETSQPSDKTVLDTSYALTGETENDCRSTKYEMYSKNAEKSSRSKRTIKQ

Parental  KQRRKFMAKPAEEQLDVGQSKDENIHTSRITQDEFQRNSDRNMEEREEMGNDCVSKKQMPPVGSKKSSTR
          KQRRKFMAKPAEEQLDVGQ.KDENIH.S.ITQD.FQRNSDRNMEEREEMGNDC.SKKQMPPVGSKKSSTR
Retrocopy KQRRKFMAKPAEEQLDVGQTKDENIHMSHITQDKFQRNSDRNMEEREEMGNDCASKKQMPPVGSKKSSTR

Parental  KDKEESKKKRFSSESKNKLVPEEVTSTVTKSRRISRRPSDWWVVKSEESPVYSNSSVRNELPMHHNSSQK
          KDKEESKKKRFSSESKNKL..EEVTSTVT.SRRISR.PS.WWVVKSEESPVYSNSS.RNELP.H.NS.QK
Retrocopy KDKEESKKKRFSSESKNKLLSEEVTSTVTRSRRISRHPSNWWVVKSEESPVYSNSSIRNELPLHPNSRQK

Parental  STKKTNQSSKNIRKKTIPLKRQKTATKGNQRVQKFLNAEGSGGIVGHDEISRCSLSEPLESDEADLAKKK
          S.KKTNQSSKNI.KKTIPLKRQKTATK..QRVQKFLNA.GSG.I.GHDEIS.C.LSEPLESDEADLAK.K
Retrocopy SAKKTNQSSKNIGKKTIPLKRQKTATKDSQRVQKFLNAKGSGCIIGHDEISSCLLSEPLESDEADLAKRK

Parental  NLDCSRSTRSSKNEDNIMTAQNVPLKPQTSGYTCNIPTESNLDSGEHKTSVLEESGPSRLNNNYLISGK-
          NLDCSRST.SSKNEDNIMTAQNVPLKPQTSGY.CN.PTESNLDSGEHKTSVLEESGPSRLNNNYL.SGK.
Retrocopy NLDCSRSTGSSKNEDNIMTAQNVPLKPQTSGYICNTPTESNLDSGEHKTSVLEESGPSRLNNNYLMSGKN

Parental  -NDVDDEEVHGSSDDSKQSKVIPKNRIHHKLVLPSNTPNVRRTKRTRLKPLEYWRGERIDYQGRPSGGFV
          .NDVDDEEV.GSSDDSK.SKVIPKNRIHHKLVLPSNTPNVRRTKRTRLKPLEYWRG..IDYQGRPSG.FV
Retrocopy NNDVDDEEVPGSSDDSKRSKVIPKNRIHHKLVLPSNTPNVRRTKRTRLKPLEYWRGQQIDYQGRPSGRFV

Parental  ISGVLSPDTISSKRKAKENTGKVN-KKSNKKRICLDNDERKTNLMVNLGIPLGDPLQPTRVKDPETREII
          ISG.LSP..ISSKRKA.EN.GKV..KKSNKKRICLDNDERKT.LMVNLGIPLGDPLQP..VKDPETREII
Retrocopy ISGILSPGKISSKRKARENIGKVD>KKSNKKRICLDNDERKTSLMVNLGIPLGDPLQPAMVKDPETREII

Parental  LMDLVRPQDTYQFFVKHGELKVYKTLDTPFFSTGKLILGPQEEKGKQHVGQDILVFYVNFGDLLCTLHET
          LMDLVRPQDTYQFFVKHGELKVY.TLDTPFFSTGKL.L.PQEEKGKQHVGQDIL.FYVNFGDLLCTLHE.
Retrocopy LMDLVRPQDTYQFFVKHGELKVYNTLDTPFFSTGKLVLRPQEEKGKQHVGQDILFFYVNFGDLLCTLHEI

Parental  PYILSTGDSFYVPSGNYYNIKNLRNEESVLLFTQIKR
          PYI.STGDSFYVPSGNYYNIKNL.NEESVLLFTQIKR
Retrocopy PYIISTGDSFYVPSGNYYNIKNLLNEESVLLFTQIKR

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	0.05 RPM	3.29 RPM
SRP007412_cerebellum	0.00 RPM	7.17 RPM
SRP007412_heart	0.06 RPM	5.45 RPM
SRP007412_kidney	0.03 RPM	7.77 RPM
SRP007412_liver	0.00 RPM	4.12 RPM
SRP007412_testis	0.32 RPM	23.92 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_708 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_708 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_708 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1038
Pongo abelii	retro_pabe_870

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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 ,