RetrogeneDB ID: retro_hsap_3121

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 4:166469410..166472200(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000248327
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NOL8
• Ensembl ID: ENSG00000198000
• Aliases: NOL8, C9orf34, NOP132, bA62C3.3, bA62C3.4
• Description: nucleolar protein 8 [Source:HGNC Symbol;Acc:23387]

Sequence

>retro_hsap_3121
AGAGAAATGAAGCCCCTTTATGTGGATGGTCTTAGCCAGGAAATTTCTGAAACAGTCCTCCAAAATCAGTTCAGCAGATT
TGCAGAAGTTTCAGATGTGGAGATCATCACACGGAAAGATGACCATGGAAACCCACAGAAAGTCTTTGCATATATCAGCA
TCAGTGTAGCAGAAGCAGACCTGAAAAAATGTATATCCGTTTTAAATAAAACAAAATGGAAAGGTAGAACATTACAAATT
CAACTAGCAAAAGAAAGCTTTTTGCACAGATTGGCCCAAGAGAAAGAAGAAGCAAAAGCTAAGAAAGGAAAATCAACAAC
AGGTAACATCAACTTGTTAGAAAAGATAGGAGGAGTGGAATTCCATATGAAAGCTGCGCCAGGGACAGAAGCGCCAGGGT
ATAAGAATTGGGTTGTGAGCAAATTTGGAAGAGTGTTACTTGTTCTTCACCTTAAAATTTATCATAAATGTAAAATTATA
AAATATGATCCCTCAAAATACTGCCACAACCTAAAGAAGATAGGGGAGGATTTCACAAACACCATTCCTATATCCAGCCT
GACTTGGGAACTGGAAGGAGGGAATGACCCTATGAGTAAGAAATGGTGAGGAGACTTCTCTGACTTTCATGGCCCTCCCA
AGAAGATGATAAAAGTGCAGAGGGATGAGAGTTCCACTGGGTCTCTGGCCATGAGTCCAAGGCCCAGGTGGGTAATAGAG
AGACCACCCTTAACACAGCAACAAGCTGCACAGAAAAAGAACTTCTAATTCCACTACTCCTAAATCATCTCCTGTACCTG
TTTCTGATACTCAGAAACTTTAAAATCTACCTTTTAGGACTTCTGGATTGGAAACTGCCAAGAAGAGAAGTGGCATTTCT
GATGATTATATTGATTCTAAAGATGAATTAAGAATGATGGTTGCAAAAGAGGAAAACTTACAGAGAACTATACAATCCTC
AATAAATGAACCTGAAACTGATCCCTTTGAAGTTGTAAGGGATAACTTCAAATCAGGAGTTCACAAATTGCATTCTTCAA
CAGGTTTAGGTATCAAAAATAGTGCCTCTTGCCATGACAGTGATGATGATATTACGAGAAATGATTGTGAGTATGACTCA
GGAGATACAGAAGAAATCATTGCGATGAAAAAAAATGTTGCTAAGGTCAAAAACAGTACAGAATTTTCACAAATGGAAAA
ATCTACAGACAAGAAAACTTCCTTCAAAAATAGAGAAAACTGTGAGCTTCTGATCACTGTATTAAAGTACAAGAAAGAAA
AAGCAATGTAGAGTCAGCCCTCGGTCATGGATTAAAGGCTCTTAATTGCAAATCTCCCTCTCACTCCAATAGCAATGAAG
ATGCTGATTCTGCATCAGAATTAGCTGACTCTGAAGGAGACAAGGAGTATAATGCCATGACGAAAAACCGCCTTCGTGTG
AATCTCACTTTAGCTGATTTGGAACAATTGGCTGGCAGTGAACAGAAGGTTTCCAATGAAGATACTGAGAGTGACGGGCC
AGAAACCACCACACAATGCAAGTTTGACAGAGGCTCCAACAGCCCCAAGACTCCCACTGGCCTCCACAGACGCAGACACT
GTATTTGTCCTGACGACACTGTGGCTTTCCTGTTAGAAGGAGAGGAGAGCACCTGTGGCAAACAGAAACCAAAGGAAAAC
AACTGAAAGCCAGAATTCCAGGTTTTCAAGGGAGTAGGCTGTTTATATGAAAAAGGAGTCAATAAAAAAATCCTTGAAAG
ACAATGTTGCCTCTAACAATATTAATAAAGATCAGAATTCCATGAAACATGTGGATCCCAGGATCATATCCATGGAAGAT
GGGTCCCCATATGTTAATGGCTCATCGGGTGAACTGACTCTGTGCCAACATGCAAAGAAGGCGAATGGCCCAACTATATT
CAGCCTCAAAAAAGATAGAACACTTCTGAGAGCCAGGATTGCAAGGCAATGTCCACTAGCAGTTCTGAAAAGAGAAGTAA
GAATTCTATTTCTAGTTTATTGCCATTAAAAGGTAAGAAGTCCTTAAGTCTTAGTGCAAAGACTCACAACATAGGCTTTG
ACAAAGACAGCTGCCATAGTACCACAAGACAGAAGCTTCAGAGGAAGAGAGGTCTGACTCAAGCAGCCTCACATCTCTTG
AGAAATCACCAAAGTTCTCATCCAAGGACACTCAGGAAATCAAAACTGATTTCTCACTTTCTATTAGTAATTCGTCAGAT
CTGAGTGCTAAGGATAAGCATGCTGAAGACGATGAGAAGCATTTGGTAGCCTTGGAAGTGAGGCAAAAAGCAAAAGAAGT
GCAGAAGAAGCTGGTGGATAATGCTCTGGCAAGTTTGGATGGTCATCCAGAGGATAAACTAACGTACATCATCTTCGGTT
CTGACAGTGAATGTGAAACAGAGGAGATATCGACTCAGGAGCAGAGACATCCAGGAGAGGAATGGGTGAAATAGTCTATG
GGTAAAACATTGGGGAAGCTGCCTGATAGCAGTGATGATGAGGAATCTGATTCTGAAGATGACAGTAACAGGTTCAAAAT
TAAACCTCAGTTTGAGGGCAGAGCTGGACAGAAGCTCATGGATTTACAGTCGCACTTTGGCACTGATGACAGATTCTGCA
TGAATTCTCGATTTCTAGAAAGTGACAGTGAAGACGAACAGGAAGAGGTAAATGAAAAGAAACCCGCTAGGAAGAAGAGC
TTGCTGAAGAAAAAAAGAAAGCCTGGATGTTGTACAAAGTGTTTTGAAAATCAACTTAAGCAATTCTACA

Alignment

ORF - retro_hsap_3121 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.66 %
• Parental protein coverage: 95.57 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  RETKRLYVGGLSQDISEADLQNQFSRFGEVSDVEIITRKDDQGNPQKVFAYINISVAEADLKKCMSVLNK
          RE.K.LYV.GLSQ.ISE..LQNQFSRF.EVSDVEIITRKDD.GNPQKVFAYI.ISVAEADLKKC.SVLNK
Retrocopy REMKPLYVDGLSQEISETVLQNQFSRFAEVSDVEIITRKDDHGNPQKVFAYISISVAEADLKKCISVLNK

Parental  TKWKGGTLQIQLAKESFLHRLAQEREAAKAKKEESTTGNANLLEKTGGVDFHMKAVPGTEVPGHKNWVVS
          TKWKG.TLQIQLAKESFLHRLAQE.E.AKAKK..STTGN.NLLEK.GGV.FHMKA.PGTE.PG.KNWVVS
Retrocopy TKWKGRTLQIQLAKESFLHRLAQEKEEAKAKKGKSTTGNINLLEKIGGVEFHMKAAPGTEAPGYKNWVVS

Parental  KFGRVLPVLHLKNQHKRKIIKYDPSKYCHNLKKIGEDFSNTIPISSLTWELEGGNDPMSKKRRGEFSDFH
          KFGRVL.VLHLK..HK.KIIKYDPSKYCHNLKKIGEDF.NTIPISSLTWELEGGNDPMSKK..G.FSDFH
Retrocopy KFGRVLLVLHLKIYHKCKIIKYDPSKYCHNLKKIGEDFTNTIPISSLTWELEGGNDPMSKKW*GDFSDFH

Parental  GPPKKIIKVQKDESSTGSLAMSTRPRRVIERPPLTQQQAAQ-KRTCDSITPSKSSPVPVSDTQKLKNLPF
          GPPKK.IKVQ.DESSTGSLAMS.RPR.VIERPPLTQQQAAQ.KRT..S.TP.KSSPVPVSDTQKL.NLPF
Retrocopy GPPKKMIKVQRDESSTGSLAMSPRPRWVIERPPLTQQQAAQ>KRTSNSTTP-KSSPVPVSDTQKL*NLPF

Parental  KTSGLETAKKRNSISDDDTDSEDELRMMIAKEENLQRTTQPSINESESDPFEVVRDDFKSGVHKLHSLIG
          .TSGLETAKKR..ISDD..DS.DELRMM.AKEENLQRT.Q.SINE.E.DPFEVVRD.FKSGVHKLHS..G
Retrocopy RTSGLETAKKRSGISDDYIDSKDELRMMVAKEENLQRTIQSSINEPETDPFEVVRDNFKSGVHKLHSSTG

Parental  LGIKNRVSCHDSDDDIMRNDREYDSGDTDEIIAMKKNVAKVKNSTEFSQMEKST-KKTSFKNRENCEL-S
          LGIKN..SCHDSDDDI.RND.EYDSGDT.EIIAM...VAKVKNSTEFSQMEKST.KKTSFKNRENCEL.S
Retrocopy LGIKNSASCHDSDDDITRNDCEYDSGDTEEIIAMXXXVAKVKNSTEFSQMEKSTDKKTSFKNRENCEL<S

Parental  DHCIKLQKRKSNVESALSHGLKSLNRKSPSHSSSSEDADSASELADSEGGEEYNAMMKNCLRVNLTLADL
          DHCIK.Q.RKSNVESAL.HGLK.LN.KSPSHS.S.EDADSASELADSEG..EYNAM.KN.LRVNLTLADL
Retrocopy DHCIKVQERKSNVESALGHGLKALNCKSPSHSNSNEDADSASELADSEGDKEYNAMTKNRLRVNLTLADL

Parental  EQLAGSDLKVPNEDTKSDGPETTTQCKFDRGSKSPKTPTGLRRGRQCIRPAEIVASLLEGEENTCGKQKP
          EQLAGS..KV.NEDT.SDGPETTTQCKFDRGS.SPKTPTGL.R.R.CI.P...VA.LLEGEE.TCGKQKP
Retrocopy EQLAGSEQKVSNEDTESDGPETTTQCKFDRGSNSPKTPTGLHRRRHCICPDDTVAFLLEGEESTCGKQKP

Parental  KENNLKPKFQAFKGVGCLYE-KESMKKSLKDSVASN--NKDQNSMKHEDPSIISMEDGSPYVNGSLGEVT
          KENN.KP.FQ.FKGVGCLYE.KES.KKSLKD.VASN..NKDQNSMKH.DP.IISMEDGSPYVNGS.GE.T
Retrocopy KENN*KPEFQVFKGVGCLYE>KESIKKSLKDNVASNNINKDQNSMKHVDPRIISMEDGSPYVNGSSGELT

Parental  PCQHAKKANG-PNYIQPQKRQTTFESQDRKAVSPSSSEKRSKNPISR--PLEGKKSLSLSAKTHNIGFDK
          .CQHAKKANG.PNYIQPQKR..T.ESQD.KA.S.SSSEKRSKN.IS...PL.GKKSLSLSAKTHNIGFDK
Retrocopy LCQHAKKANG<PNYIQPQKR*NTSESQDCKAMSTSSSEKRSKNSISSLLPLKGKKSLSLSAKTHNIGFDK

Parental  DSCHSTT-KTEASQEERSDSSGLTSLKKSPKVSSKDTREIKTDFSLSISNSSDVSAKDKHAEDNEKRLAA
          DSCHSTT.KTEAS.EERSDSS.LTSL.KSPK.SSKDT.EIKTDFSLSISNSSD.SAKDKHAED.EK.L.A
Retrocopy DSCHSTT<KTEASEEERSDSSSLTSLEKSPKFSSKDTQEIKTDFSLSISNSSDLSAKDKHAEDDEKHLVA

Parental  LEARQKAKEVQKKLVHNALANLDGHPEDKPTHIIFGSDSECETEETSTQEQSHPGEEWVKESMGKTSGKL
          LE.RQKAKEVQKKLV.NALA.LDGHPEDK.T.IIFGSDSECETEE.STQEQ.HPGEEWVK.SMGKT.GKL
Retrocopy LEVRQKAKEVQKKLVDNALASLDGHPEDKLTYIIFGSDSECETEEISTQEQRHPGEEWVK*SMGKTLGKL

Parental  FDSSDDDESDSEDDSNRFKIKPQFEGRAGQKLMDLQSHFGTDDRFRMDSRFLETDSEEEQEEVNEKKTAE
          .DSSDD.ESDSEDDSNRFKIKPQFEGRAGQKLMDLQSHFGTDDRF.M.SRFLE.DSE.EQEEVNEKK.A.
Retrocopy PDSSDDEESDSEDDSNRFKIKPQFEGRAGQKLMDLQSHFGTDDRFCMNSRFLESDSEDEQEEVNEKKPAR

Parental  -EEELAEEKKKA-LNVVQSVLQINLSNST
          .EEELAEEKKKA.L.VVQSVL.INLSNST
Retrocopy <EEELAEEKKKA<LDVVQSVLKINLSNST

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	0.02 RPM	22.78 RPM
bodymap2_adrenal	0.00 RPM	53.67 RPM
bodymap2_brain	0.00 RPM	23.28 RPM
bodymap2_breast	0.00 RPM	27.98 RPM
bodymap2_colon	0.00 RPM	37.28 RPM
bodymap2_heart	0.00 RPM	14.12 RPM
bodymap2_kidney	0.00 RPM	35.96 RPM
bodymap2_liver	0.00 RPM	13.94 RPM
bodymap2_lung	0.00 RPM	12.15 RPM
bodymap2_lymph_node	0.00 RPM	37.74 RPM
bodymap2_ovary	0.00 RPM	54.50 RPM
bodymap2_prostate	0.00 RPM	44.91 RPM
bodymap2_skeletal_muscle	0.00 RPM	17.75 RPM
bodymap2_testis	0.00 RPM	39.63 RPM
bodymap2_thyroid	0.06 RPM	48.75 RPM
bodymap2_white_blood_cells	0.00 RPM	35.63 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3121 was not detected

EST

No EST(s) were mapped for retro_hsap_3121 retrocopy.

TSS

No TSS is located nearby retro_hsap_3121 retrocopy 5' end.

Lab

retro_hsap_3121 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3121 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2110
Pongo abelii	retro_pabe_2577

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000198000	1 retrocopy	retro_hsap_3121 ,
Nomascus leucogenys	ENSNLEG00000016357	1 retrocopy	retro_nleu_773,
Pongo abelii	ENSPPYG00000019375	1 retrocopy	retro_pabe_2577,
Pan troglodytes	ENSPTRG00000021109	1 retrocopy	retro_ptro_2110,