RetrogeneDB ID: retro_hsap_947

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 12:3949782..3951677(+)
• Located in intron of: ENSG00000111224

Retrocopy information

• Ensembl ID: ENSG00000118976
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: OTUD4
• Ensembl ID: ENSG00000164164
• Aliases: OTUD4, DUBA6, HIN1, HSHIN1
• Description: OTU domain containing 4 [Source:HGNC Symbol;Acc:24949]

Sequence

>retro_hsap_947
GCTACTTCTCAGAGTAGCAATCCATGTGTCCAGAGAAAATCATCACACGTAAGTGATAGAAAAGGAAGCAGGCGGAGAAT
GGATACAGAAGAACGAAAAGACAAAGACTCTATTCATGGACATAGTTGGATAAAAGACCCGAACCAAGCATATTGGAGAA
TATTACTGATGATAAATATGCAACAGTTTCATCACCATCAAAGTCAAAGAAGTTAGAGTGCCCTTCTCCTGCAGAACAAA
AGCCAGCAGAACATGTGTCTTTGTCAAATCCAGCTCCCCTTCTAGTTTCTCCAGAGGTACATCTAACTCCTGCAGTGCCT
TCTTTACCAGCCACTGTGCCAGCCTGGCCAAGTGAACCTACAACTTTTGGACCAACAGGTGTCCCTGCTCCAATTCCTGG
TCGGTCAGTGACACAGACTTTGACCCCTGGACCTGATTCTGCTGTATCCCAAACTCATTTAACACCCTCTCCAGTTCCTG
TGTCAATACAGGCAGTTAACCAGCCCTTGATGCCTTTGCCTCAGACATTGAGCCTTTATCAAGACCCACTCTATCCTGGG
TTTCCTTGTAATGAAAAGGGAGATCGAGCCATTGTACCACCTTCTTCACTGTGTCAGACTGGGGAGGACCTACCTAAAGA
TAAGAATATTCTTCGATTCTTCTTCAATCTTGGTGTGAAGGCATACAGTTGTCCTGTGTGGGCCCCACATTCTTACCTGT
ACCCTCTGCACCAGGCCTACCTGGCAGCCTGCAGGATGTACCCAAAGGTCCCTGTCCCTGTTTATCTTCATAATCCCTGG
TTCAAAGAGGCTCCTGCCGCCCAGAATTAAAGTGATTGTACCTGTACTGATGCCCACTTTCCTATGCAGACTGAGGCTAG
TGTTAATGGTCAAATGCTACAGCCAGTGATTGGACCGCCGACATTTTCTTCACCTCTGGTTATCCCTCCATCTCAGGTGT
CTGAAAGTCACGGACAATTGTCTTACCAGGCTGATCTTGAATCTGAGACCCCTGGGCAGCTTCTGCATGCTGATTATGAA
GAGTCACTGAGTGGCAAGAATATGTTCCCCCAGCCATCTTTTGGACCCAATCCATTCTTAGGCCCAGTTCCTATTGCACC
TCCTTTCTTTCCTCATGTTTGGCATGGGTACCCTTTTCAGGGATTCATAGAAAATCCAGTAATGAGGCAGAATATTGTCC
TGCCCTCTGATGAGAAAGGAGAATTGGATCTGTCTCTGGAAAATCTGGATCTGTCTAAAGATTGTGGTTCAGTTTCCACA
GTAGATGAGTTTCCAGCAGCCAGGAGTGAACATGTACATTCTCTCCCTGAAGCAAGTGTGAGCAGTAAGCCAGACGAAGG
CCGGACAGAGCAATCTTCCCAGACACGAAAGGCAGATATGGCATTGGCTTCCATCCCTCCTGTAGCAGAGGGAAAGGCTC
ACCCTCCCACTCAGATTCTAAACAGAGAGAGAGAGAAATTGTGCCTGTTGAACTTGAACCTAAAAGGACCATTCAAAGTC
TGAAAGAAAAAACAGAAAAAGTAAAAGATCCTAAGACTGCTGCTGATGTGGTCAGCCCTGGGGCCAACTCTGTGGATAGC
AGAGTGCAAAGACCAAAAGAAGAGAGTTCAGAAAATGAAAATGAAGTGTCATATTTTGAGAAGTGGTAGATCCAAGCAGT
TCTATAATCAAACTTATGGGAGCAGGAAGTACAAAAGTGATTGGGGCTATTCTGGTAGGGGCGGATATCAACATGTGAGA
AGTGAGGAGTCCTGGAAAGGACAGCCAAGCAGAAGTCGGGATGAAGGTTATCAGTACCATCGAAATGTCAGAGGGCGACC
ATTTAGGGGAGATAGGAGGAGATCAGGGATGGGAGATGGCCATAGGGGACAGCAC

Alignment

ORF - retro_hsap_947 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.89 %
• Parental protein coverage: 60.34 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SASQSSNPCVQRKSSHVGDRKGSRRRMDTEE-RKDKDSIHGHSQLDKRPEPSTLENITDDKYATVSSPSK
          ..SQSSNPCVQRKSSHV.DRKGS.RR....E.R...........LDKRPEPS.LENITDDKYATVSSPSK
Retrocopy ATSQSSNPCVQRKSSHVSDRKGS-RRRMDTE<RTKRQRLYSWT*LDKRPEPSILENITDDKYATVSSPSK

Parental  SKKLECPSPAEQKPAEHVSLSNPAPLLVSPEVHLTPAVPSLPATVPAWPSEPTTFGPTGVPAPIPVLSVT
          SKKLECPSPAEQKPAEHVSLSNPAPLLVSPEVHLTPAVPSLPATVPAWPSEPTTFGPTGVPAPIP..SVT
Retrocopy SKKLECPSPAEQKPAEHVSLSNPAPLLVSPEVHLTPAVPSLPATVPAWPSEPTTFGPTGVPAPIPGRSVT

Parental  QTLTTGPDSAVSQAHLTPSPVPVSIQAVNQPLMPLPQTLSLYQDPLYPGFPCNEKGDRAIVPPYSLCQTG
          QTLT.GPDSAVSQ.HLTPSPVPVSIQAVNQPLMPLPQTLSLYQDPLYPGFPCNEKGDRAIVPP.SLCQTG
Retrocopy QTLTPGPDSAVSQTHLTPSPVPVSIQAVNQPLMPLPQTLSLYQDPLYPGFPCNEKGDRAIVPPSSLCQTG

Parental  EDLPKDKNILRFFFNLGVKAYSCPMWAPHSYLYPLHQAYLAACRMYPKVPVPVYPHNPWFQEAPAAQNES
          EDLPKDKNILRFFFNLGVKAYSCP.WAPHSYLYPLHQAYLAACRMYPKVPVPVY.HNPWF.EAPAAQN.S
Retrocopy EDLPKDKNILRFFFNLGVKAYSCPVWAPHSYLYPLHQAYLAACRMYPKVPVPVYLHNPWFKEAPAAQN*S

Parental  DCTCTDAHFPMQTEASVNGQMPQPEIGPPTFSSPLVIPPSQVSESHGQLSYQADLESETPGQLLHADYEE
          DCTCTDAHFPMQTEASVNGQM.QP.IGPPTFSSPLVIPPSQVSESHGQLSYQADLESETPGQLLHADYEE
Retrocopy DCTCTDAHFPMQTEASVNGQMLQPVIGPPTFSSPLVIPPSQVSESHGQLSYQADLESETPGQLLHADYEE

Parental  SLSGKNMFPQPSFGPNPFLGPVPIAPPFFPHVWYGYPFQGFIENPVMRQNIVLPSDEKGELDLSLENLDL
          SLSGKNMFPQPSFGPNPFLGPVPIAPPFFPHVW.GYPFQGFIENPVMRQNIVLPSDEKGELDLSLENLDL
Retrocopy SLSGKNMFPQPSFGPNPFLGPVPIAPPFFPHVWHGYPFQGFIENPVMRQNIVLPSDEKGELDLSLENLDL

Parental  SKDCGSVSTVDEFPEARGEHVHSLPEASVSSKPDEGRTEQSSQTRKADTALASIPPVAE-GKAHPP-TQI
          SKDCGSVSTVDEFP.AR.EHVHSLPEASVSSKPDEGRTEQSSQTRKAD.ALASIPPVAE.GK..P.....
Retrocopy SKDCGSVSTVDEFPAARSEHVHSLPEASVSSKPDEGRTEQSSQTRKADMALASIPPVAE<GKGSPSHSDS

Parental  LNRERETVPVELEPKRTIQSLKEKTEKVKDPKTAADVVSPGANSVDSRVQRPKEESSEDENEV-SNILRS
          ..RERE.VPVELEPKRTIQSLKEKTEKVKDPKTAADVVSPGANSVDSRVQRPK.E.S.........ILRS
Retrocopy KQREREIVPVELEPKRTIQSLKEKTEKVKDPKTAADVVSPGANSVDSRVQRPK-EESSENENE>CHILRS

Parental  GRSKQFYNQTYGSRKYKSDWGYSGRGGYQHVRSEESWKGQPSRSRDEGYQYHRNVRGRPFRGDRRRSGMG
          GRSKQFYNQTYGSRKYKSDWGYSGRGGYQHVRSEESWKGQPSRSRDEGYQYHRNVRGRPFRGDRRRSGMG
Retrocopy GRSKQFYNQTYGSRKYKSDWGYSGRGGYQHVRSEESWKGQPSRSRDEGYQYHRNVRGRPFRGDRRRSGMG

Parental  DGHRGQH
          DGHRGQH
Retrocopy DGHRGQH

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	52.18 RPM
bodymap2_adrenal	0.00 RPM	62.78 RPM
bodymap2_brain	0.00 RPM	40.83 RPM
bodymap2_breast	0.02 RPM	51.30 RPM
bodymap2_colon	0.00 RPM	58.22 RPM
bodymap2_heart	0.02 RPM	57.34 RPM
bodymap2_kidney	0.10 RPM	60.30 RPM
bodymap2_liver	0.04 RPM	27.59 RPM
bodymap2_lung	0.14 RPM	89.77 RPM
bodymap2_lymph_node	0.00 RPM	64.71 RPM
bodymap2_ovary	0.00 RPM	79.11 RPM
bodymap2_prostate	0.03 RPM	54.23 RPM
bodymap2_skeletal_muscle	0.00 RPM	120.09 RPM
bodymap2_testis	0.89 RPM	125.77 RPM
bodymap2_thyroid	0.08 RPM	84.97 RPM
bodymap2_white_blood_cells	0.10 RPM	98.10 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_947 was not detected

EST

No EST(s) were mapped for retro_hsap_947 retrocopy.

TSS

No TSS is located nearby retro_hsap_947 retrocopy 5' end.

Lab

retro_hsap_947 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_947 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000164164	1 retrocopy	retro_hsap_947 ,
Oryctolagus cuniculus	ENSOCUG00000014569	2 retrocopies	retro_ocun_1258, retro_ocun_330,