RetrogeneDB ID: retro_hsap_3164

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 5:37209465..37212480(+)
• Located in intron of: ENSG00000197603

Retrocopy information

• Ensembl ID: ENSG00000228212
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: OFD1
• Ensembl ID: ENSG00000046651
• Aliases: OFD1, 71-7A, CXorf5, JBTS10, RP23, SGBS2
• Description: oral-facial-digital syndrome 1 [Source:HGNC Symbol;Acc:2567]

Sequence

>retro_hsap_3164
ATGATGGCTCAGTCCAACATGCTCCCCGTGGCTGATGTGTTGAGTCAAAATGAACTGCGCAAAAAGCTATACCAGACATT
TAAGGATCGGGGTATACTGGAAACACTCAAGATACAACTTCGAAACCAGCTAATTCATGAGTTAATGCACCCTGTATTGA
GTGGAGAACTGCAACCTCAGTCCATTTCAGTGCAAGGGAGCTCCCTCTTAATAAGTGCCTCTAACTCTTTAGTGGCAGAT
CACTTACAAAGATGTGGCTGTGAATATTCACTTTCTGTTTTCTTTCTAGAAAGTGGTTTGGCAAAAGAAAAGGTATTTAC
TATGCAGGATCTATTACAACTCATTAAAATCAACCCTACTTCCAGTCTGTACAAATCACTGGTTTCAGGAGCTGATAAAG
AAAACCAAAAAGGTTTTCTTATGCATTTTTTAAAAGGATTGGCAGAATATCATCAAGCTAAAGAAAGTTGTAATATGGAA
ACTCAGACAAGTTCGACATTTAGCAGAGATTCTCTGGCTGAGAAGCTTCAGCTTATTGATGATCAGTTTGCAGATGCTTA
CCCTCAGCGTATCAAGTTTGAGTCTTTAGAAATAAAGCTAAATGAATATAAGAGAGAAATAGAAGAGCAACTTCGGGAAG
AAATATGTCAAAAGTTGAAGTTTTTTAAAGATACCGAAATAGGAAAAATTAAAATGGAAGCAAAAAAAAAGTATGAGAAG
GAATTAGCCGTGTTCCAGAATGATTTTGAGAAAGCTTGTCAAGCAAAATCTGAAGCCCTTGTTATTCGGGAAAAGAGCAC
CCTTGAGAGAATTCAAAAGCACCAAGAGATTGAAACAAAAGAGATTTATGCTCAAAGGCAACTTTTACTAAAAGATATGG
ATTTGCTAAGAGGAAGAGAAGCAGAGCTGAAGCAAAGAGTTGAAGCTTTTGAACTGAACCAGAAGCTCCAGGAAGAAAAA
CATAAAAGTATGACTGAGGCACTTAGGAGACGGGAGCAGAATATAAAGAGTTTTGAGAAGACCTATGACCAAAAACTCAA
GAATGAACTCCTAAAGTATCAACTTGAACTAAAGGACGACTACATCATTAGAACTAATCGACTGATTGAAGATGAAAGGA
AGAATAAAGAAAAAGCTGTTCATTTGCAAGAGGAGCTCATAGCTTTTAATTCAAAAAAGGAGGAACTCAATCAATCTATA
AATCGCATGAAAGAACTTGAGCTTGAATTAGAGTCTGTCAAAGCCCAGTCTTTGGCAATAACAAAACAAAACCATATGCT
GAATGAAAAGGTTAAAGTGATGAGTGACTATTCACTACTAAAAGAAGAGAGACTGGAGCTTCTGGCACAAAATAAATTAC
TTAAACAACAACTGGAAGAGAGTAGAAATGAAAACTTGCGTCTCCTAAACCGCCTAGCTCAGCTGGCTCCTGAACTTGCG
GTCTTTCAGAAAGAACTAAGGAGAGCAGAAAAGGCTACAGTGGTTGAGCATGAGGAGTTCGAAAGCCGCAAACAAGCTCT
GCACAAACAACTGCAAGATGAAATTGAGCATACTACACAGTTGAAGGCCCAGATACTAGGTTACAAAGTTTCCATAAAGA
GGTTAACTATTCAGGTTGCCGATTTAAAATCGCAATTGAAGCAAACTCAGACAGCCCTAGAGAATGAAGTGTACTGCAAT
CCAAAGCAGTCTGTGATCCATCATTCTGCCAATGGATTAATAAATGGCAACATGGTGCTTCACAATGGTGAGATAAGTGG
GGATTTCTTGAACAATCCTTTTAAACAGGAAAAAGTTCTAGCAGGTACGGTTGCATCAAGGATCACAAATTATCCAAATG
CAGGGATGGAGGGTAGTTCCCCTGATTCTGACCTTGAGTTTGTCGCCAATACTAATGCAAGGGTCAAACAGCTTCAGCAA
GAGGCGGAACGCTTGGAAAAGGCTTTCAGAAGTTACCATCGGAGAGACATTAAAAACTCTGCCAAAGGCCCACTACCAGC
AAAGAGCCCACCATCTCTGCACTTGCTGGAAGCCTTCAAAAACATTACTTCCAGTTCCCCGGAAAGACGTATTTTTGCAG
AGGACAGAGTTGTCTCTGAGCAGCCTCAAGTGGGCACACTTAAAGAAGAAAGGAATGACATCTTGGAAGCCCTGACAGGC
AGTGCAGCCTCAAGGCTATGCGGGGGCACTTCCTCCAGACGCCTCTCCTCCACACCCCTTCCAAAAGCAAAAAGAAGCCT
TGAAAGTGAAATATATCTGGAAGGTCTGGGCAGATCACACATTGCTTCCCCCAGTCCTTATCCTGACAGAATGCCCCCGC
CATCACCCGCTGAGTCTAGGCACAACCTCTCCATCCCTCCCTTCTCCAGCCCTCCGGAGCAGAAAGCGGGTCTTTACTGG
AGACAAAATGAACTTCAAGACAAAAGTGAATTTTCAGATGCGGACAAGCTAGCTTTTAAGGATAACGAGGAATTTGAATC
ATCTTTTGAATATGCACGGAATGTGCCAAGGCAGTTTGAAATGGATGGGCCCTCTCCTGCCGGGGATATGCTTCATATGG
GCGCAGCTGTAGCTGCTGTGCCCCTCTCATATCAGCACCCAAGTGTAGATCAGAAACAAATTGAAGAACAAAAGGAAGAA
GAAAAAATATGGGAACAGCAAGTGAAAGAACGAAAGCAGAGAGAAGAAAGAAGGCAGAGTAACCTACAAGAAATTTTAGA
AAGGGAAAGAAGAGAACTAGAAAAACTGTATCAGGAAAGGAGGATGACTGAAGAATCACTGAAGATTGAAATGGAAAATG
AATTAGAAATGAGTAATCAAGAAATGAAAGACAAATCTGCTCACAGTGAAAATCCTTTAGAGAAATACATGAAAATCATC
CAGCAAGACCAGGAGTCGGCAGATAAGAGCTCAAAAAAGATGGTCCAGGAAGGCTCCCTAGTGGACACACTGCAATGTAG
TGACAAAGTCGAAAGTTTAACACGCTTTTCTCATGAAGAACCAGATGACTCTTGG

Alignment

ORF - retro_hsap_3164 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.07 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MMAQSNMFTVADVLSQDELRKKLYQTFKDRGILDTLKTQLRNQLIHELMHPVLSGELQPRSISVEGSSLL
          MMAQSNM..VADVLSQ.ELRKKLYQTFKDRGIL.TLK.QLRNQLIHELMHPVLSGELQP.SISV.GSSLL
Retrocopy MMAQSNMLPVADVLSQNELRKKLYQTFKDRGILETLKIQLRNQLIHELMHPVLSGELQPQSISVQGSSLL

Parental  IGASNSLVADHLQRCGYEYSLSVFFPESGLAKEKVFTMQDLLQLIKINPTSSLYKSLVSGSDKENQKGFL
          I.ASNSLVADHLQRCG.EYSLSVFF.ESGLAKEKVFTMQDLLQLIKINPTSSLYKSLVSG.DKENQKGFL
Retrocopy ISASNSLVADHLQRCGCEYSLSVFFLESGLAKEKVFTMQDLLQLIKINPTSSLYKSLVSGADKENQKGFL

Parental  MHFLKELAEYHQAKESCNMETQTSSTFNRDSLAEKLQLIDDQFADAYPQRIKFESLEIKLNEYKREIEEQ
          MHFLK.LAEYHQAKESCNMETQTSSTF.RDSLAEKLQLIDDQFADAYPQRIKFESLEIKLNEYKREIEEQ
Retrocopy MHFLKGLAEYHQAKESCNMETQTSSTFSRDSLAEKLQLIDDQFADAYPQRIKFESLEIKLNEYKREIEEQ

Parental  LRAEMCQKLKFFKDTEIAKIKMEAKKKYEKELTMFQNDFEKACQAKSEALVLREKSTLERIHKHQEIETK
          LR.E.CQKLKFFKDTEI.KIKME....YEKEL..FQNDFEKACQAKSEALV.REKSTLERI.KHQEIETK
Retrocopy LREEICQKLKFFKDTEIGKIKMEXXXXYEKELAVFQNDFEKACQAKSEALVIREKSTLERIQKHQEIETK

Parental  EIYAQRQLLLKDMDLLRGREAELKQRVEAFELNQKLQEEKHKSITEALRRQEQNIKSFEETYDRKLKNEL
          EIYAQRQLLLKDMDLLRGREAELKQRVEAFELNQKLQEEKHKS.TEALRR.EQNIKSFE.TYD.KLKNEL
Retrocopy EIYAQRQLLLKDMDLLRGREAELKQRVEAFELNQKLQEEKHKSMTEALRRREQNIKSFEKTYDQKLKNEL

Parental  LKYQLELKDDYIIRTNRLIEDERKNKEKAVHLQEELIAINSKKEELNQSVNRVKELELELESVKAQSLAI
          LKYQLELKDDYIIRTNRLIEDERKNKEKAVHLQEELIA.NSKKEELNQS.NR.KELELELESVKAQSLAI
Retrocopy LKYQLELKDDYIIRTNRLIEDERKNKEKAVHLQEELIAFNSKKEELNQSINRMKELELELESVKAQSLAI

Parental  TKQNHMLNEKVKEMSDYSLLKEEKLELLAQNKLLKQQLEESRNENLRLLNRLAQPAPELAVFQKELRKAE
          TKQNHMLNEKVK.MSDYSLLKEE.LELLAQNKLLKQQLEESRNENLRLLNRLAQ.APELAVFQKELR.AE
Retrocopy TKQNHMLNEKVKVMSDYSLLKEERLELLAQNKLLKQQLEESRNENLRLLNRLAQLAPELAVFQKELRRAE

Parental  KAIVVEHEEFESCRQALHKQLQDEIEHSAQLKAQILGYKASVKSLTTQVADLKLQLKQTQTALENEVYCN
          KA.VVEHEEFES..QALHKQLQDEIEH..QLKAQILGYK.S.K.LT.QVADLK.QLKQTQTALENEVYCN
Retrocopy KATVVEHEEFESRKQALHKQLQDEIEHTTQLKAQILGYKVSIKRLTIQVADLKSQLKQTQTALENEVYCN

Parental  PKQSVIDRSVNGLINGNVVPCNGEISGDFLNNPFKQENVLARMVASRITNYPTAWVEGSSPDSDLEFVAN
          PKQSVI..S.NGLINGN.V..NGEISGDFLNNPFKQE.VLA..VASRITNYP.A..EGSSPDSDLEFVAN
Retrocopy PKQSVIHHSANGLINGNMVLHNGEISGDFLNNPFKQEKVLAGTVASRITNYPNAGMEGSSPDSDLEFVAN

Parental  TKARVKELQQEAERLEKAFRSYHRRVIKNSAKSPLAAKSPPSLHLLEAFKNITSSSPERHIFGEDRVVSE
          T.ARVK.LQQEAERLEKAFRSYHRR.IKNSAK.PL.AKSPPSLHLLEAFKNITSSSPER.IF.EDRVVSE
Retrocopy TNARVKQLQQEAERLEKAFRSYHRRDIKNSAKGPLPAKSPPSLHLLEAFKNITSSSPERRIFAEDRVVSE

Parental  QPQVGTL-EERNDVVEALTGSAASRLRGGTSSRRLSSTPLPKAKRSLESEMYLEGLGRSHIASPSPCPDR
          QPQVGTL.EERND..EALTGSAASRL.GGTSSRRLSSTPLPKAKRSLESE.YLEGLGRSHIASPSP.PDR
Retrocopy QPQVGTLKEERNDILEALTGSAASRLCGGTSSRRLSSTPLPKAKRSLESEIYLEGLGRSHIASPSPYPDR

Parental  MPLPSPTESRHSLSIPPVSSPPEQKVGLYRRQTELQDKSEFSDVDKLAFKDNEEFESSFESAGNMPRQLE
          MP.PSP.ESRH.LSIPP.SSPPEQK.GLY.RQ.ELQDKSEFSD.DKLAFKDNEEFESSFE.A.N.PRQ.E
Retrocopy MPPPSPAESRHNLSIPPFSSPPEQKAGLYWRQNELQDKSEFSDADKLAFKDNEEFESSFEYARNVPRQFE

Parental  MGGLSPAGDMSHVDAAAAAVPLSYQHPSVDQKQIEEQKEEEKIREQQVKERRQREERRQSNLQEVLERER
          M.G.SPAGDM.H..AA.AAVPLSYQHPSVDQKQIEEQKEEEKI.EQQVKER.Q...R.........E...
Retrocopy MDGPSPAGDMLHMGAAVAAVPLSYQHPSVDQKQIEEQKEEEKIWEQQVKERKQ---REERRQSNLQEILE

Parental  RELEKLYQERKMIEESLKIKIKKELEMENELEMSNQEIKDKSAHSENPLEKYMKIIQQEQDQESADKSSK
          RE...L....K...E..........EMENELEMSNQE.KDKSAHSENPLEKYMKIIQ..QDQESADKSSK
Retrocopy RERREL---EKLYQERRMTEESLKIEMENELEMSNQEMKDKSAHSENPLEKYMKIIQ--QDQESADKSSK

Parental  KMVQEGSLVDTLQSSDKVESLTGFSHEELDDSW
          KMVQEGSLVDTLQ.SDKVESLT.FSHEE.DDSW
Retrocopy KMVQEGSLVDTLQCSDKVESLTRFSHEEPDDSW

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	14.31 RPM
bodymap2_adrenal	0.31 RPM	42.70 RPM
bodymap2_brain	0.23 RPM	17.16 RPM
bodymap2_breast	0.19 RPM	19.63 RPM
bodymap2_colon	0.00 RPM	14.85 RPM
bodymap2_heart	0.11 RPM	11.08 RPM
bodymap2_kidney	0.10 RPM	30.83 RPM
bodymap2_liver	0.02 RPM	5.92 RPM
bodymap2_lung	0.00 RPM	19.09 RPM
bodymap2_lymph_node	0.00 RPM	25.95 RPM
bodymap2_ovary	0.06 RPM	40.15 RPM
bodymap2_prostate	0.16 RPM	24.58 RPM
bodymap2_skeletal_muscle	0.00 RPM	7.26 RPM
bodymap2_testis	0.77 RPM	43.17 RPM
bodymap2_thyroid	0.23 RPM	58.53 RPM
bodymap2_white_blood_cells	0.00 RPM	25.40 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3164 was not detected

EST

No EST(s) were mapped for retro_hsap_3164 retrocopy.

TSS

No TSS is located nearby retro_hsap_3164 retrocopy 5' end.

Lab

retro_hsap_3164 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3164 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2274
Gorilla gorilla	retro_ggor_1352

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003979	1 retrocopy	retro_cjac_2845,
Callithrix jacchus	ENSCJAG00000035427	1 retrocopy	retro_cjac_2844,
Homo sapiens	ENSG00000046651	1 retrocopy	retro_hsap_3164 ,
Gorilla gorilla	ENSGGOG00000006453	1 retrocopy	retro_ggor_1352,
Nomascus leucogenys	ENSNLEG00000009180	1 retrocopy	retro_nleu_2496,
Pan troglodytes	ENSPTRG00000021675	1 retrocopy	retro_ptro_2274,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.06 RPM
CEU_NA11843	0.06 RPM
CEU_NA11930	0.20 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.07 RPM
CEU_NA12751	0.10 RPM
CEU_NA12760	0.04 RPM
CEU_NA12827	0.09 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.10 RPM
FIN_HG00183	0.03 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.03 RPM
FIN_HG00321	0.03 RPM
FIN_HG00328	0.05 RPM
FIN_HG00338	0.02 RPM
FIN_HG00349	0.09 RPM
FIN_HG00375	0.10 RPM
FIN_HG00377	0.10 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.03 RPM
GBR_HG00111	0.06 RPM
GBR_HG00114	0.03 RPM
GBR_HG00119	0.12 RPM
GBR_HG00131	0.09 RPM
GBR_HG00133	0.02 RPM
GBR_HG00134	0.04 RPM
GBR_HG00137	0.08 RPM
GBR_HG00142	0.06 RPM
GBR_HG00143	0.03 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.12 RPM
TSI_NA20518	0.08 RPM
TSI_NA20532	0.17 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.03 RPM
TSI_NA20765	0.04 RPM
TSI_NA20771	0.09 RPM
TSI_NA20786	0.05 RPM
TSI_NA20798	0.06 RPM
YRI_NA18870	0.03 RPM
YRI_NA18907	0.03 RPM
YRI_NA18916	0.04 RPM
YRI_NA19093	0.05 RPM
YRI_NA19099	0.03 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.04 RPM
YRI_NA19213	0.02 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.08 RPM

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Indel association:

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