RetrogeneDB ID: retro_ptro_3180

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:5142359..5143738(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HADHB
• Ensembl ID: ENSPTRG00000011733
• Aliases: None
• Description: Pan troglodytes hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), beta subunit (HADHB), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001034119]

Sequence

>retro_ptro_3180
CTTATCACTGCATCAGAATGGTCCCTCAGATTTTCCATAAGACCTCTGAGCTGTTCCTCCCAGTTGCGAGCTGCCCAGCC
ATCCAGACCGAAACGAGGAAGACATTAGCCAAACCCAATATAAGGAATATTGTGGTGGTGGATTGTGTTGGCACTCCATT
TTTGCTGTCAGGCACTTCTTATAAAGACCTGATACCACATGATTTGGCTAGAGCAACACTTACGGGTTTGTTGCATCAGC
CCAGTGTCCCCAAGGAAGTAGCTGATTATATCATCTTTGGCACAGTCATTCAGGAAGTGAAAACAAGCCATGTGGCTAGA
GAGGCTGCCCTTGGAGCTGCCTTCTCTGACAAGACTCCTGCTCACACTGTCACCATGGCTTGTATCTCTGCCAACCAAGC
CATGACCACAGGTGTTGGTTTGATTGCTTCTGGCCAGTGTGATGTGATCATGGCAGGTGGTGTCGAGTTGATGTTCCATG
TCCCTATTCGTCAGTCAAGGAAAATGAGAAAACTGATGCTTGATCTAAGTAAGGCCAAATTTGTGGGCCAGTGACTGTCT
TCAATCTCTAAATGCCAGTTGAATTTCTTAGCACCTGAGCTCCCTGCGGTTTCTGAGTTCTCCACCAGTGAGACCACGGG
CCACTCTGCAGACCAATTGGCTGTTTCTCGACTGGAACAGGATGAATATGCACTGCGCTGTCCCAGTCTGGCCAAGAAGG
CACAGGATGAAGGACTCCTTTCTGATGTCGTACCCTTCAAAGTACCAGGAAAAGATACAGTTACCAAACATAATGGCATC
CGTCCTTCCTCACTGGAGCAAATGGCTAAACTAAAACCTGCATTCATCAAGCCCTACGGCACAGCGAAAGCTGCAAATTC
TTCTTTCTTGACTGATGGCGCATCTGCCATGTTGATTATGGCAGAGGAAAAGGCTCTGGCAATGGGTTATAAGCCGAAGG
AGTGTTTGAGGGATTTTATGTACGTGTCTCACAATCTGAAAGATCAACTATTATTCAGACCAACATATGCGACTCCAAAA
ATTCTAGAAAAGGCAGGATTAACCATGAGTGATATTGATGCTTTTGAATTTCACAAAGCTTTCTCAGGTAAGATTTTAGC
TAATTTTAAAGCCATGGATTCTGATTAGTTTGCACAAAATTACATGGGTAGAAAAAGCAAGGTTACATTGCTTCCTTCGG
AGAAGTTTAATAACTGGGGTGGATCTCTGTCCCTGAAACACCCATTTGGAGCTACTGGCTGCAGGTTGGTCGTGGCAGCT
GCCAACAGATTACGGAAGGAAGGAGGCCAGTATGCCTTAGCGGCTGCCTGTGCAGCTGGAGGGCAGGGCCATGGTATGAT
AGTGGAAGCTTACCCAAAA

Alignment

ORF - retro_ptro_3180 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.67 %
• Parental protein coverage: 97.68 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LPTASKWALRFSIRPLSCSSQLRAA-PAVQTKTKKTLAKPNIRNVVVVDGVRTPFLLSGTSYKDLMPHDL
          L.TAS.W.LRFSIRPLSCSSQLRAA.PA.QT.T.KTLAKPNIRN.VVVD.V.TPFLLSGTSYKDL.PHDL
Retrocopy LITASEWSLRFSIRPLSCSSQLRAA<PAIQTETRKTLAKPNIRNIVVVDCVGTPFLLSGTSYKDLIPHDL

Parental  ARAALTGLLHRTSVPKEVVDYIIFGTVIQEVKTSNVAREAALGAGFSDKTPAHTVTMACISANQAMTTGV
          ARA.LTGLLH..SVPKEV.DYIIFGTVIQEVKTS.VAREAALGA.FSDKTPAHTVTMACISANQAMTTGV
Retrocopy ARATLTGLLHQPSVPKEVADYIIFGTVIQEVKTSHVAREAALGAAFSDKTPAHTVTMACISANQAMTTGV

Parental  GLIASGQCDVIVAGGVELMSDVPIRHSRKMRKLMLDLNKAKSMGQRLSLISKFRFNFLAPELPAVSEFST
          GLIASGQCDVI.AGGVELM..VPIR.SRKMRKLMLDL.KAK..GQ.LS.ISK...NFLAPELPAVSEFST
Retrocopy GLIASGQCDVIMAGGVELMFHVPIRQSRKMRKLMLDLSKAKFVGQ*LSSISKCQLNFLAPELPAVSEFST

Parental  SETMGHSADRLAAAFAVSRLEQDEYALRSHSLAKKAQDEGLLSDVVPFKVPGKDTVTKDNGIRPSSLEQM
          SET.GHSAD.L....AVSRLEQDEYALR..SLAKKAQDEGLLSDVVPFKVPGKDTVTK.NGIRPSSLEQM
Retrocopy SETTGHSADQL----AVSRLEQDEYALRCPSLAKKAQDEGLLSDVVPFKVPGKDTVTKHNGIRPSSLEQM

Parental  AKLKPAFIKPYGTVTAANSSFLTDGASAMLIMAEEKALAMGYKPKAYLRDFMYVSQDPKDQLLLGPTYAT
          AKLKPAFIKPYGT..AANSSFLTDGASAMLIMAEEKALAMGYKPK..LRDFMYVS...KDQLL..PTYAT
Retrocopy AKLKPAFIKPYGTAKAANSSFLTDGASAMLIMAEEKALAMGYKPKECLRDFMYVSHNLKDQLLFRPTYAT

Parental  PKVLEKAGLTMNDIDAFEFHEAFSGQILANFKAMDSDWFAENYMGRKTKVGLPPLEKFNNWGGSLSLGHP
          PK.LEKAGLTM.DIDAFEFH.AFSG.ILANFKAMDSD.FA.NYMGRK.KV.L.P.EKFNNWGGSLSL.HP
Retrocopy PKILEKAGLTMSDIDAFEFHKAFSGKILANFKAMDSD*FAQNYMGRKSKVTLLPSEKFNNWGGSLSLKHP

Parental  FGATGCRLVMAAANRLRKEGGQYGLVAACAAGGQGHAMIVEAYPK
          FGATGCRLV.AAANRLRKEGGQY.L.AACAAGGQGH.MIVEAYPK
Retrocopy FGATGCRLVVAAANRLRKEGGQYALAAACAAGGQGHGMIVEAYPK

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	0.00 RPM	50.60 RPM
SRP007412_cerebellum	0.00 RPM	49.36 RPM
SRP007412_heart	0.12 RPM	544.95 RPM
SRP007412_kidney	0.03 RPM	198.18 RPM
SRP007412_liver	0.00 RPM	73.10 RPM
SRP007412_testis	0.00 RPM	75.67 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3180 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3180 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3180 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4778
Gorilla gorilla	retro_ggor_2976
Pongo abelii	retro_pabe_3718

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002288	1 retrocopy	retro_amel_1473,
Canis familiaris	ENSCAFG00000029395	1 retrocopy	retro_cfam_2114,
Choloepus hoffmanni	ENSCHOG00000010050	3 retrocopies	retro_chof_122, retro_chof_1869, retro_chof_911,
Homo sapiens	ENSG00000138029	1 retrocopy	retro_hsap_4778,
Gorilla gorilla	ENSGGOG00000025829	1 retrocopy	retro_ggor_2976,
Microcebus murinus	ENSMICG00000006750	1 retrocopy	retro_mmur_1315,
Mus musculus	ENSMUSG00000059447	2 retrocopies	retro_mmus_1427, retro_mmus_1961,
Otolemur garnettii	ENSOGAG00000005444	1 retrocopy	retro_ogar_167,
Pongo abelii	ENSPPYG00000012582	1 retrocopy	retro_pabe_3718,
Pan troglodytes	ENSPTRG00000011733	1 retrocopy	retro_ptro_3180 ,
Tarsius syrichta	ENSTSYG00000003570	2 retrocopies	retro_tsyr_1316, retro_tsyr_1951,