RetrogeneDB ID: retro_pabe_3718

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:4905790..4907200(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HADHB
• Ensembl ID: ENSPPYG00000012582
• Aliases: None
• Description: hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), beta subunit [Source:HGNC Symbol;Acc:4803]

Sequence

>retro_pabe_3718
ATGACTACCGTCTTGACTTACACTTTTAAAAATCTTCTCACTGCATCAAAATGGGCCCTCAGATTTTCCATAAGACCTCT
GAGCTGTTCCTCCCAGCTGCGAGCTGCCCAGCCATCCAGACCAAAACGAAGAAGACATTAGCCAAACCCAATATAAGGAA
TGTTGTGGTGGTGGATGGTGTTCGCACTCCATTTTTGCTGTCAGGCACTTCATATAAAGACCTGATACCACATGATTTGG
CTAGAGCAACGCTTACGGGTTTGTTGCATCAGCCCAGTGTCCCCAAGGAAGTAGTTGATTATATCATCTTTGGCACAGTT
ATTCAGGAAGTGAAAACAAGCAATGTGGCTAAAGAGGCTGCCCTTGGAGCTGCCTTCTCTGGCAAGACTCCTGCTCACAC
TGTCACCATGGCTTGTATCTCTCCCAACCAAGCCATGACCACAGGTGTTGGTTTGATTCCTTCTGGCCAGTGTGATGTGA
TCATGGCAGGTGGTGTCGAGTTGATGTCCCAGTCCCTATTCGTCAGTCAAGGAAAATGAGAAAACTGATGCTTGATCTAA
GTAAGACCAAATTTGTGGGCCAGTGACTGTCTTCAATCTCTAAATTCTGATTGAATTTCCTAGCACCTGAGCTCCTGCCG
TTTCTGAGTTCTCCAACAGTGAGACCACGGGCCACTCTGCAGACCAATTGACTGTTTCTCGACTGGAACAGGATGAATAT
GCACTGCGCTCTCCCAGTCTGGCCAAGAAGGCACAGGATGAAGGACTCCTTTCTGATGTCATACCCTTCAAAGTACCAGG
AAAAGATACAGTTACCAAACATAACGGCATCCGTCCTTCTTCACTGGAGCAGATGGCTAAACTAAAACCTGCATTCATCA
AGCCCTACGGCACAGTGACAGCTGCAAATTCTTCTTTCTTGACTGATGGCGCATCTGCCATGTTGATTATGGCAGAGGAA
AAGGCTCTGGCAATGGGTTATAAGCCGAAGGAGTGTTTGAGGGATCTTATGTACGTGTCTCACAATCTAAAAGATCAACT
ATTACTCAGACCAACATATGCGACTCCAAAAGTTCTAGAAAAGGCAGGATTAACCATGAGTGATATTGATGCTTTTGAGT
TTCACGAAGCTTTCTCAGGTAAGATTTTAGCAAATTTTAAAACCATGGATTCTGATTGGTTTGCACAAAATTACATGGGT
AGAAAAACCAAGATTAGATTGTGTCCTTTGGAGAAGTTTAATAACTGGGGTGGATCTCTGTCCCTGGGATACCCATTTGG
AGCTACTGGCTGCGGGCTGGTCGTGGCAGCTGCCAACAGATTACGGAAGGAAGGAGGCCAGTATGGCTTAGCGGCTGCCT
GTGCAGCTGGAGGGCAGGGCCATGCTATGATACTGGAAGCTTACCCAAAA

Alignment

ORF - retro_pabe_3718 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.98 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MTTILTYPFKNLPAASKWALRFSIRPLSCSSQLRAA-PAVQTKTKKTLAKPNIRNVVVVDGVRTPFLLSG
          MTT.LTY.FKNL..ASKWALRFSIRPLSCSSQLRAA.PA.QTKTKKTLAKPNIRNVVVVDGVRTPFLLSG
Retrocopy MTTVLTYTFKNLLTASKWALRFSIRPLSCSSQLRAA<PAIQTKTKKTLAKPNIRNVVVVDGVRTPFLLSG

Parental  TSYKDLMPHDLARAALTGLLHRTSVPKEVVDYIIFGTVIQEVKTSNVAREAALGAGFSDKTPAHTVTMAC
          TSYKDL.PHDLARA.LTGLLH..SVPKEVVDYIIFGTVIQEVKTSNVA.EAALGA.FS.KTPAHTVTMAC
Retrocopy TSYKDLIPHDLARATLTGLLHQPSVPKEVVDYIIFGTVIQEVKTSNVAKEAALGAAFSGKTPAHTVTMAC

Parental  ISANQAMTTGVGLIASGQCDVIVAGGVELMSD-IPIRHSRKMRKLMLDLNKAKSMGQRLSLISKFRFNFL
          IS.NQAMTTGVGLI.SGQCDVI.AGGVELMS...PIR.SRKMRKLMLDL.K.K..GQ.LS.ISKF..NFL
Retrocopy ISPNQAMTTGVGLIPSGQCDVIMAGGVELMSQ<VPIRQSRKMRKLMLDLSKTKFVGQ*LSSISKF*LNFL

Parental  APEL-PAVAEFSTNETMGHSADRLAAAFAVSRLEQDEYALRSHSLAKKAQDEGLLSDVVPFKVPGKDTVT
          APEL.PAV.EFS..ET.GHSAD.L.....VSRLEQDEYALRS.SLAKKAQDEGLLSDV.PFKVPGKDTVT
Retrocopy APEL<PAVSEFSNSETTGHSADQLT----VSRLEQDEYALRSPSLAKKAQDEGLLSDVIPFKVPGKDTVT

Parental  KDNGIRPSSLEQMAKLKPAFIKPYGTVTAANSSFLTDGAS----MAEEKALAMGYKPKAYLRDFMYVSQD
          K.NGIRPSSLEQMAKLKPAFIKPYGTVTAANSSFLTDGAS....MAEEKALAMGYKPK..LRD.MYVS..
Retrocopy KHNGIRPSSLEQMAKLKPAFIKPYGTVTAANSSFLTDGASAMLIMAEEKALAMGYKPKECLRDLMYVSHN

Parental  PKDQLLLGPTYATPKVLEKAGLTINDIDAFEFHEAFSGQILANFKAMDSDWFAENYMSRKTKVGLPPLEK
          .KDQLLL.PTYATPKVLEKAGLT..DIDAFEFHEAFSG.ILANFK.MDSDWFA.NYM.RKTK..L.PLEK
Retrocopy LKDQLLLRPTYATPKVLEKAGLTMSDIDAFEFHEAFSGKILANFKTMDSDWFAQNYMGRKTKIRLCPLEK

Parental  FNNWGGSLSLGHPFGATGCRLVMAAANRLRKEGGQYGLVAACAAGGQGHAMIVEAYPK
          FNNWGGSLSLG.PFGATGC.LV.AAANRLRKEGGQYGL.AACAAGGQGHAMI.EAYPK
Retrocopy FNNWGGSLSLGYPFGATGCGLVVAAANRLRKEGGQYGLAAACAAGGQGHAMILEAYPK

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	0.06 RPM	29.69 RPM
SRP007412_cerebellum	0.00 RPM	27.24 RPM
SRP007412_heart	0.27 RPM	292.43 RPM
SRP007412_kidney	0.33 RPM	103.09 RPM
SRP007412_liver	0.03 RPM	67.69 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3718 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3718 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3718 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4778
Pan troglodytes	retro_ptro_3180
Gorilla gorilla	retro_ggor_2976

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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,