RetrogeneDB ID: retro_hsap_1038

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 12:89893869..89896716(+)
• Located in intron of: ENSG00000139323

Retrocopy information

• Ensembl ID: ENSG00000226982
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CENPC
• Ensembl ID: ENSG00000145241
• Aliases: CENPC, CENP-C, CENPC1, MIF2, hcp-4
• Description: centromere protein C [Source:HGNC Symbol;Acc:1854]

Sequence

>retro_hsap_1038
ATGGCTGTGTCGGGTCTGGATCATCTCAAAAATGGCTACAGAAGAAGATTTTGTCAACCTTCCAGGGCACGTGACATTAA
CACAGAGCAAGGCCAGAATGTTCTGGAAATCTTACAAGACTGTTTTGAAGAAAAAAGTCTTGCCAATGATTTTAGCACAA
ATTCTACAAAATCAGTGCTTAATTCAACACGCAAAATAAAAGACACTTGTATTCAGTCACCAAGCAAAGAGTGCCAGAAA
TCACATCCAAAGTCAGTTCCACTTTCTTCAAGGAAGAAAGAAGCCTCTCTGCAGTTTGTTGTAGAACCAAGTGAAGCCAC
CAACAGATCAGTTCAGGCCCATGAAGTTCGTCAGAAAATTCTGGCAACTGATGTTAGTTCCAAAAATACACCTGACTTGA
AAAAAATGTGAAGTAGAAACATAAATGATCATCACAGTGAAGCTGATGAAGAATTTTACTTATCTGTTGGCTCACCTTCT
GTTCTTTTGGATGCAAAAACATCTGTATCGCAAAATGTTATTCCATCTAGTGCCCAAAAGAGAGAGACTTACACTTTTGA
AAATTCAGTAAATATGCTGCCTTCAAGTACAGAGGTTTCACTTAAAACCAAAAAAAGATTAAACTTTGAAGATAAAGTTA
TTTTAAAGAAAATAGAAATAGATAGAAATAGATAATAAAGTATCAGATAAAGAGGATAAAACATCAGAAGGACAAGAAAG
AAAACCATCAGGATCATCTCAGAATAGAATACGACATTCAGAATATGAAATTCAATGACAAGCTAAAAAAAGTTTTTCAA
CATTGTTTTTAGAAACAGTAAAACGAAAAAGTGAATCCAGTCCCATTGTTAGGCATGGAGGAATTGTTCCACCTCATTCG
TGTCCTCCCGATGATATGAAGTTGATAGAGGATGAATTTATAATTGATAAGTCAGATCAAAGTTTTGCCAGTAGATCTTG
GGATTACTATACCAAGAAAGGCGGGGCCTCTGAAACAACGCACCATATCCCCGGCTGAGAGCACTGCACTCCTTCAAGAT
AGAAAGTCAAGAGAAAAGCATCATAATATATTAGCTAAGACTTTGGCAAATGACAAACATTCCCATAAACCTCACCTAGT
AGAGACATCTCAGCCCTCTGATAAAACAGTACTGGATACAAGTTATGCTTTGACAGGTGAAACAGAAAATGACTGTAGAT
CTACAAAATATGAAATGTATTCCAAGAATGCAGAAAAATCATCTGGAAGCAAAAGGACTATAAAACAAAAACAGAGAAGA
AAATTTATGGCTAAACCAGCTGAAGAACAGCTCGATGTGGGACAGACTAAAGATGAAAACATACATATGTCACATATTAC
CCAAGACAAATTTCAAAGAAATTCAGACAGAAATATGGAAGAGCGTGAAGAGATGGGAAATGATTGTGCTTCCAAAATAC
AGATGCCACCTGTGGGAAGCAAGAAAAGTAGCACTAGAAAAGATAAGGAAGAATCTAAAAAGAAGCGCTTTTCTAGTGAG
TCCAAGAACAAACTTGTGTCTGAAGAAGTGACTTCAACTGTCACGAGAAGTCGAAGAATTTCCAGGCATCCGTCTAATTG
GTGGGTGGTAAAATCAGAGGAGAGTCCTGTTTATAGCAATTCTTCAATAAGAAATGAATTACCACTGCATCACAACAGTA
GGCAAAAATCTGCTAAGAAAACAAATCAGTCATCTAAGAATATTGGGAAAAAAACTATTCCACTTAAAAGGCAGAAGACA
GCAACTAAAGACAGCCAAAGAGTACAGAAGTTTTTAAATGCTAAAGGTTCTGGAGGTATCATTGGTCATGATGAAATTTC
CAGTTGTTTCCTGAGTGAGCCATTGGAAAGTGATGAGGCAGACTTGGCTAAGAGGAAAAATCTGGATTGTTCTAGATCTA
CAGGAAGCTCAAAGAATGAAGATAATATTATGACTGCACAGAATGTTCCCCTAAAGCCTCAGACCAGTGGATATACATGT
AATACACCAACAGAGTCAAACTTGGATTCTGGAGAGCATAAGACTTCAGTTTTAGAGGAAAGTGGACCTTCCAGGCTCAA
TAATAATTATTTAATGTCTGGAAAGAATAATAATGATGTGGATGATGAGGAAGTTCCTGGAAGTTCAGATGACTCAAAAC
GAACTAAAGTGATACCAAAGAACAGAATCCATCACAAACTAGTATTGCCCTCCAACACACCAAATGTTCGCAGGACCAAG
AGAACACGTTTGAAACCTTTGGAGTACTGGCGAGGACAGCAAATAGATTATCAAGGAAGGCCATCAGGAGGATTCGTGAT
TAGTGGAATACTATCTCCAGGCAAAATATCGTCTAAAAGGAAGGCAAGAGAAAATATTGGAAAAGTTGACAAAAAAATCT
AATAAGAAAAGGATCTGTCTTGATAACGATGAAAGAAAGACTAGCTTAATGGTAAATCTAGGTATACCTCTTGGAGATCC
TTTGCAGCCAGCAATGGTAAAGGACCCAGAAACAAGAGAGATTATTCTCATGGATCTTGTAAGGCCACAAGATACATATC
AATTTTTTGTTAAGCATGGTGAGTTGAAGGTATATAACACATTGGATACACCCTTTTTTTCTACTGGGAAATTGATATTA
AGACCACAAGAAGAAAAGGGAAAGCAGCATGTTGGCCAGGATATATTGTTTTTTTATGTTAACTTTGGTGACCTTTCGTG
TACTTTACACGAAATACCTTATATAATAAGTACTGGGGATTCGTTCTATGTTCCTTCAGGTAACTATTATAACATCAAAA
ATCTCCTGAATGAGGAAAGTGTTCTTCTTTTTACTCAGATAAAAAGA

Alignment

ORF - retro_hsap_1038 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.22 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAASGLDHLKNGYRRRFCRPSRARDINTEQGQNVLEILQDCFEEKSLANDFSTNSTKSVPNSTRKIKDTC
          MA.SGLDHLKNGYRRRFC.PSRARDINTEQGQNVLEILQDCFEEKSLANDFSTNSTKSV.NSTRKIKDTC
Retrocopy MAVSGLDHLKNGYRRRFCQPSRARDINTEQGQNVLEILQDCFEEKSLANDFSTNSTKSVLNSTRKIKDTC

Parental  IQSPSKECQKSHPKSVPVSSKKKEASLQFVVEPSEATNRSVQAHEVHQKILATDVSSKNTPDSKKISSRN
          IQSPSKECQKSHPKSVP.SS.KKEASLQFVVEPSEATNRSVQAHEV.QKILATDVSSKNTPD.KK..SRN
Retrocopy IQSPSKECQKSHPKSVPLSSRKKEASLQFVVEPSEATNRSVQAHEVRQKILATDVSSKNTPDLKKM*SRN

Parental  INDHHSEADEEFYLSVGSPSVLLDAKTSVSQNVIPSSAQKRETYTFENSVNMLPSSTEVSV-KTKKRLNF
          INDHHSEADEEFYLSVGSPSVLLDAKTSVSQNVIPSSAQKRETYTFENSVNMLPSSTEVS..K.KK....
Retrocopy INDHHSEADEEFYLSVGSPSVLLDAKTSVSQNVIPSSAQKRETYTFENSVNMLPSSTEVSL>KPKKD*TL

Parental  DDKVMLKK---IEIDNKVSDEEDKTSEGQERKPSGSSQNRIRDSEYEIQRQAKKSFSTLFLETVKRKSES
          ..K....K...IEIDNKVSD.EDKTSEGQERKPSGSSQNRIR.SEYEIQ.QAKKSFSTLFLETVKRKSES
Retrocopy KIKLF*RK*K*IEIDNKVSDKEDKTSEGQERKPSGSSQNRIRHSEYEIQ*QAKKSFSTLFLETVKRKSES

Parental  SPIVRHAATAPPHSCPPDDTKLIEDEFIIDESDQSFASRSW-ITIPRKAGSLKQRTISPAESTALLQGRK
          SPIVRH....PPHSCPPDD.KLIEDEFIID.SDQSFASRSW.ITIPRKAG.LKQRTISPAESTALLQ.RK
Retrocopy SPIVRHGGIVPPHSCPPDDMKLIEDEFIIDKSDQSFASRSW>ITIPRKAGPLKQRTISPAESTALLQDRK

Parental  SREKHHNILPKTLANDKHSHKPHPVETSQPSDKTVLDTSYALIGETVNNYRSTKYEMYSKNAEKPSRSKR
          SREKHHNIL.KTLANDKHSHKPH.VETSQPSDKTVLDTSYAL.GET.N..RSTKYEMYSKNAEK.S.SKR
Retrocopy SREKHHNILAKTLANDKHSHKPHLVETSQPSDKTVLDTSYALTGETENDCRSTKYEMYSKNAEKSSGSKR

Parental  TIKQKQRRKFMAKPAEEQLDVGQSKDENIHTSHITQDEFQRNSDRNMEEHEEMGNDCVSKKQMPPVGSKK
          TIKQKQRRKFMAKPAEEQLDVGQ.KDENIH.SHITQD.FQRNSDRNMEE.EEMGNDC.SK.QMPPVGSKK
Retrocopy TIKQKQRRKFMAKPAEEQLDVGQTKDENIHMSHITQDKFQRNSDRNMEEREEMGNDCASKIQMPPVGSKK

Parental  SSTRKDKEESKKKRFSSESKNKLVPEEVTSTVTKSRRISRRPSDWWVVKSEESPVYSNSSVRNELPMHHN
          SSTRKDKEESKKKRFSSESKNKLV.EEVTSTVT.SRRISR.PS.WWVVKSEESPVYSNSS.RNELP.HHN
Retrocopy SSTRKDKEESKKKRFSSESKNKLVSEEVTSTVTRSRRISRHPSNWWVVKSEESPVYSNSSIRNELPLHHN

Parental  SSRKSTKKTNQSSKNIRKKTIPLKRQKTATKGNQRVQKFLNAEGSGGIVGHDEISRCSLSEPLESDEADL
          S..KS.KKTNQSSKNI.KKTIPLKRQKTATK..QRVQKFLNA.GSGGI.GHDEIS.C.LSEPLESDEADL
Retrocopy SRQKSAKKTNQSSKNIGKKTIPLKRQKTATKDSQRVQKFLNAKGSGGIIGHDEISSCFLSEPLESDEADL

Parental  AKKKNLDCSRSTRSSKNEDNIMTAQNVPLKPQTSGYTCNIPTESNLDSGEHKTSVLEESGPSRLNNNYLM
          AK.KNLDCSRST.SSKNEDNIMTAQNVPLKPQTSGYTCN.PTESNLDSGEHKTSVLEESGPSRLNNNYLM
Retrocopy AKRKNLDCSRSTGSSKNEDNIMTAQNVPLKPQTSGYTCNTPTESNLDSGEHKTSVLEESGPSRLNNNYLM

Parental  SGKN--DVDDEEVHGSSDDSKQSKVIPKNRIHHKLVLPSNTPNVRRTKRTRLKPLEYWRGERIDYQGRPS
          SGKN..DVDDEEV.GSSDDSK..KVIPKNRIHHKLVLPSNTPNVRRTKRTRLKPLEYWRG..IDYQGRPS
Retrocopy SGKNNNDVDDEEVPGSSDDSKRTKVIPKNRIHHKLVLPSNTPNVRRTKRTRLKPLEYWRGQQIDYQGRPS

Parental  GGFVISGVLSPDTISSKRKAKENIGKVN-KKSNKKRICLDNDERKTNLMVNLGIPLGDPLQPTRVKDPET
          GGFVISG.LSP..ISSKRKA.ENIGKV..KKSNKKRICLDNDERKT.LMVNLGIPLGDPLQP..VKDPET
Retrocopy GGFVISGILSPGKISSKRKARENIGKVD>KKSNKKRICLDNDERKTSLMVNLGIPLGDPLQPAMVKDPET

Parental  REIILMDLVRPQDTYQFFVKHGELKVYKTLDTPFFSTGKLILGPQEEKGKQHVGQDILVFYVNFGDLLCT
          REIILMDLVRPQDTYQFFVKHGELKVY.TLDTPFFSTGKLIL.PQEEKGKQHVGQDIL.FYVNFGDL.CT
Retrocopy REIILMDLVRPQDTYQFFVKHGELKVYNTLDTPFFSTGKLILRPQEEKGKQHVGQDILFFYVNFGDLSCT

Parental  LHETPYILSTGDSFYVPSGNYYNIKNLRNEESVLLFTQIKR
          LHE.PYI.STGDSFYVPSGNYYNIKNL.NEESVLLFTQIKR
Retrocopy LHEIPYIISTGDSFYVPSGNYYNIKNLLNEESVLLFTQIKR

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
bodymap2_adipose	0.00 RPM	13.70 RPM
bodymap2_adrenal	0.04 RPM	30.60 RPM
bodymap2_brain	0.07 RPM	19.06 RPM
bodymap2_breast	0.04 RPM	22.70 RPM
bodymap2_colon	0.00 RPM	14.60 RPM
bodymap2_heart	0.00 RPM	11.46 RPM
bodymap2_kidney	0.08 RPM	17.02 RPM
bodymap2_liver	0.00 RPM	5.43 RPM
bodymap2_lung	0.04 RPM	14.57 RPM
bodymap2_lymph_node	0.00 RPM	15.73 RPM
bodymap2_ovary	0.02 RPM	26.78 RPM
bodymap2_prostate	0.00 RPM	27.54 RPM
bodymap2_skeletal_muscle	0.00 RPM	4.20 RPM
bodymap2_testis	0.00 RPM	30.05 RPM
bodymap2_thyroid	0.04 RPM	43.93 RPM
bodymap2_white_blood_cells	0.12 RPM	27.62 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1038 was not detected

EST

No EST(s) were mapped for retro_hsap_1038 retrocopy.

TSS

No TSS is located nearby retro_hsap_1038 retrocopy 5' end.

Lab

retro_hsap_1038 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1038 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_708
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,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.09 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.10 RPM
CEU_NA12004	0.04 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.04 RPM
CEU_NA12827	0.09 RPM
CEU_NA12872	0.05 RPM
CEU_NA12873	0.03 RPM
FIN_HG00183	0.05 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.03 RPM
FIN_HG00321	0.06 RPM
FIN_HG00328	0.05 RPM
FIN_HG00338	0.02 RPM
FIN_HG00349	0.03 RPM
FIN_HG00375	0.02 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.02 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.02 RPM
GBR_HG00114	0.03 RPM
GBR_HG00119	0.02 RPM
GBR_HG00131	0.06 RPM
GBR_HG00133	0.02 RPM
GBR_HG00134	0.02 RPM
GBR_HG00137	0.05 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.03 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.02 RPM
TSI_NA20518	0.03 RPM
TSI_NA20532	0.10 RPM
TSI_NA20538	0.05 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.10 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.03 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.07 RPM
YRI_NA18916	0.04 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.03 RPM
YRI_NA19118	0.06 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.04 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).