RetrogeneDB ID: retro_ggor_2976

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:5017826..5019238(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HADHB
• Ensembl ID: ENSGGOG00000025829
• Aliases: None
• Description: None

Sequence

>retro_ggor_2976
ATGACTACCGTCTTGACTTAAACTTTTAAAAATCTTCTCACTGCATCAGAATGGTCCCTCAGATTTTCCATAAGACCTCT
GAGCTGTTCCTCCCAGTTGCGAGCTGCCCAGCCATCCAGACCGAAACAAGGAAGACATTAGCCAAACCCAATATAAGGAA
TGTTGTGGTGGTGGATGGTGTTCGCACTCCATTTTTGCTGTCAGGCACTTTGTATAAAGACCTGACACCACATGATTTGG
CTAGAGCAACACTTACGGGTTGGTTGCATTAGCCCAGTGTCCCCAAGGAAGTAGTTGATTATATCATCTTTGGCACAGTC
ATTCAGGAAGTGAAAACAAGCTATGTGGCTAGAGACGCTGCCCTTGGAGCTGCCTTCTGTGACAAGACTCCTGCTCACAC
TGTCACCATGGCTTGTATCTCTGCCAACCAAGCCATGACCACAGGTGTTGGTTTGATTGCTTCTGGCCAGTGTGATGTGA
TCATGGCAGGTGGTGTCGAGTTGATGTTCCATGTCCCTATTCGTCAGTCAAGGAAAATGAGAAAACTGATGCTTGATCTA
AGTAAGGCCAAATTTGTGGGCCAGTGACTGTCTTCAATCTCTAAATGCCAATTGAATTTCCTAGCACCTGACCTCCCTGC
GGTTTCTGAGTTCTCCACCAGTGAGACCACGGGCCACTCTGCAGACCAATTGGCTGTTTCTTGACTGGAACAGGATGAAT
ATGCACTGCGCTGTCCCAGTCTGGCCAAGAAGGCACAGGATGAAGGACTCCTTTCTGATGTCGTACCTTTCAAAGTACCA
GGAAAAGATACAGTTACCAAACATAACGGCATCCGTCCTTCCTCACTGGAGCAGATGGCTAAACTAAAACCTGCATTCAT
CAAGCCCTACGGCACAGCGACAGCTGCAAATTCTTCTTTCTTGACTGATGGCGCATCTGCCATGTTGATTATGGCAGAGG
AAAAGGCTCTGGCAATGGGTTATAAGCCGAAGGAGTGTTTGAAGGATTTTATGTACGTGTCTCACGATCTAAAAGATCAA
CTATTACTCAGACCAACATATGCGACTCCAAAAGTTCTAGAAAAGGCAGGATTAACCATGAGTGATATTGATGCTTTTGA
ATTTCACGAAGCTTTCTCAGGTAAGATTTTAGCTAATTTTAAAGCCATGGATTCTGATTAGTTTGCACAAAATTACATGG
ATAGAAAAAGCAAGGTTAGATTGCTTCCTTTGGAGAAGTTTAATAACTGAGGTGGATCTCTGTCCCTGGAACACCCATTT
GGAGCTACTGGCTGCAGGTTGGTCGTGGCAGCTGCCAACAGATTAAGGAAGGAAGGAGGCCAGTATGGCTTAGCGGCTGC
CTGTGCAGCTGGAGGGCAGGGCCATGGTATGATAGTGGAAGCTTACCCAAAA

Alignment

ORF - retro_ggor_2976 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.34 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTTILTYPFKNLPTASKWALRFSIRPLSCSSQLRAA-PAVQTKTKKTLAKPNIRNVVVVDGVRTPFLLSG
          MTT.LT..FKNL.TAS.W.LRFSIRPLSCSSQLRAA.PA.QT.T.KTLAKPNIRNVVVVDGVRTPFLLSG
Retrocopy MTTVLT*TFKNLLTASEWSLRFSIRPLSCSSQLRAA<PAIQTETRKTLAKPNIRNVVVVDGVRTPFLLSG

Parental  TSYKDLMPHDLARAALTGLLHQTSVPKEVVDYIIFGTVIQEVKTSNVAREAALGAGFSDKTPAHTVTMAC
          T.YKDL.PHDLARA.LTG.LH..SVPKEVVDYIIFGTVIQEVKTS.VAR.AALGA.F.DKTPAHTVTMAC
Retrocopy TLYKDLTPHDLARATLTGWLH*PSVPKEVVDYIIFGTVIQEVKTSYVARDAALGAAFCDKTPAHTVTMAC

Parental  ISANQAMTTGVGLIASGQCDVIVAGGVELMSDVPIRHSRKMRKLMLDLNKAKSMGQRLSLISKFRFNFLA
          ISANQAMTTGVGLIASGQCDVI.AGGVELM..VPIR.SRKMRKLMLDL.KAK..GQ.LS.ISK...NFLA
Retrocopy ISANQAMTTGVGLIASGQCDVIMAGGVELMFHVPIRQSRKMRKLMLDLSKAKFVGQ*LSSISKCQLNFLA

Parental  PELPAVSEFSTSETMGHSADRLAAAFAVSRLEQDEYALRSHSLAKKAQDEGLLSDVVPFKVPGKDTVTKD
          P.LPAVSEFSTSET.GHSAD.L....AVS.LEQDEYALR..SLAKKAQDEGLLSDVVPFKVPGKDTVTK.
Retrocopy PDLPAVSEFSTSETTGHSADQL----AVS*LEQDEYALRCPSLAKKAQDEGLLSDVVPFKVPGKDTVTKH

Parental  NGIRPSSLEQMAKLKPAFIKPYGTVTAANSSFLTDGASAILIMAEEKALAMGYKPKAYLRDFMYVSQDPK
          NGIRPSSLEQMAKLKPAFIKPYGT.TAANSSFLTDGASA.LIMAEEKALAMGYKPK..L.DFMYVS.D.K
Retrocopy NGIRPSSLEQMAKLKPAFIKPYGTATAANSSFLTDGASAMLIMAEEKALAMGYKPKECLKDFMYVSHDLK

Parental  DQLLLGPTYATPKVLEKAGLTMNDIDAFEFHEAFSGQILANFKAMDSDWFAENYMGRKTKVGLPPLEKFN
          DQLLL.PTYATPKVLEKAGLTM.DIDAFEFHEAFSG.ILANFKAMDSD.FA.NYM.RK.KV.L.PLEKFN
Retrocopy DQLLLRPTYATPKVLEKAGLTMSDIDAFEFHEAFSGKILANFKAMDSD*FAQNYMDRKSKVRLLPLEKFN

Parental  NWGGSLSLGHPFGATGCRLVMAAANRLQKEGGQYGLVAACAAGGQGHAMIVEAYPK
          N.GGSLSL.HPFGATGCRLV.AAANRL.KEGGQYGL.AACAAGGQGH.MIVEAYPK
Retrocopy N*GGSLSLEHPFGATGCRLVVAAANRLRKEGGQYGLAAACAAGGQGHGMIVEAYPK

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	47.76 RPM
SRP007412_cerebellum	0.04 RPM	35.85 RPM
SRP007412_heart	0.06 RPM	112.45 RPM
SRP007412_kidney	0.08 RPM	132.60 RPM
SRP007412_liver	0.05 RPM	97.47 RPM
SRP007412_testis	0.00 RPM	244.81 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2976 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2976 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4778
Pan troglodytes	retro_ptro_3180
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,