RetrogeneDB ID: retro_ggor_1196

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 15:35253493..35254323(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HADH
• Ensembl ID: ENSGGOG00000004423
• Aliases: None
• Description: None

Sequence

>retro_ggor_1196
ATGATGGTCATCAGCATCACACAGGTTGCTGCAGTGACCGGCCACACAGTAGTGTTGCTAGACCAGACAGAGGACATCTT
GGCAAAATATAAAGAGGGAATTGAGAAAAGCCTTAGGAAAGTGACAAAGAAGTTGTTTGTAGAAAACCCTAAGGCTTTTG
ATGAATTTGTGGAGAAAACCGTAAGCAGCATATCAACCAGCACAGATGCAATATCCGTAGTCCACAGCACAGAGCTGGTG
GTAGAGGCCGTTGTAGAAAATCTAAAGGTGAAAATCAAGCTCTCCAAGAGGTTGGACAAGTTTGTTGCTGAACATACAAC
TTTGCCAGCAGCACTTCCTCTTTGCAAATTACAAGCATAGCCAATGCTACCACCAAACAAGACCGATTTGCTGGCCTCCG
TTTACTCAACCCAGTGCCCCTGATGAAATTTGTAGAGGTCTTTAAAACACCAATGACCACCCGAAAGACATTTGAATCTT
TGGTAAACTTGAGCAAAACCCTGGGAAAGCATCCTGTTCCTTGCAAGGACACTCCTGGGTTTATTGTCAGCTGTCTCAGG
CTTCAACACCTCATGGAAGCAGTCAGGCTGCATGAATGAGGTGACGTATCCAAGGAGAACACTGACACTGCTATGAAGTT
AGGAGCCAGGTACCCCATGGGCTCACTTGAGCTTCTAGTTTATGTTGGGCTGGATTCTGTGCAGTTCGTCATGGATGGAT
GGCATGAAATAGATACAAAGAACCCCATATTTCAGCCCAGCCCATCCTTGAAAAGGCTGATGGCAGAGAAGAAGCTTGGC
AAGAAGTCTGGAGAAGGATTTTACAAATAC

Alignment

ORF - retro_ggor_1196 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.1 %
• Parental protein coverage: 87.94 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LMGAGIAQVAAATGHTVVLVDQTEDILAKSKKGIEESLRKVAKKKFAENPKAGDEFVEKTLSTIATSTDA
          .M...I.QVAA.TGHTVVL.DQTEDILAK.K.GIE.SLRKV.KK.F.ENPKA.DEFVEKT.S.I.TSTDA
Retrocopy MMVISITQVAAVTGHTVVLLDQTEDILAKYKEGIEKSLRKVTKKLFVENPKAFDEFVEKTVSSISTSTDA

Parental  ASVVHSTDLVVEAIVENLKVKNELFKRLDKFAAEHTI-FASNTSSLQITSIANATTRQDRFGGLHFFNPV
          .SVVHST.LVVEA.VENLKVK..L.KRLDKF.AEHT..FAS.TSSLQITSIANATT.QDRF.GL...NPV
Retrocopy ISVVHSTELVVEAVVENLKVKIKLSKRLDKFVAEHTT<FASSTSSLQITSIANATTKQDRFAGLRLLNPV

Parental  PVMKLVEVIKTPMTSQKTFESLVDFSKALGKHPVSCKDTPGFIVNRLLVPYLMEAIRLYERGDASKEDID
          P.MK.VEV.KTPMT..KTFESLV..SK.LGKHPV.CKDTPGFIV..L....LMEA.RL.E.GD.SKE..D
Retrocopy PLMKFVEVFKTPMTTRKTFESLVNLSKTLGKHPVPCKDTPGFIVSCLRLQHLMEAVRLHE*GDVSKENTD

Parental  TAMKLGAGYPMGPFELLDYVGLDTTKFIVDGWHEMDTENPLHQPSPSLNKLVAENKFGKKTGEGFYKY
          TAMKLGA.YPMG..ELL.YVGLD...F..DGWHE.DT.NP..QPSPSL..L.AE.K.GKK.GEGFYKY
Retrocopy TAMKLGARYPMGSLELLVYVGLDSVQFVMDGWHEIDTKNPIFQPSPSLKRLMAEKKLGKKSGEGFYKY

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	0.10 RPM	18.85 RPM
SRP007412_cerebellum	0.12 RPM	15.88 RPM
SRP007412_heart	0.00 RPM	62.20 RPM
SRP007412_kidney	0.00 RPM	116.74 RPM
SRP007412_liver	0.00 RPM	118.94 RPM
SRP007412_testis	0.00 RPM	49.52 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_1196 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1196 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002049	2 retrocopies	retro_btau_1111, retro_btau_1685,
Callithrix jacchus	ENSCJAG00000015938	1 retrocopy	retro_cjac_772,
Echinops telfairi	ENSETEG00000013807	1 retrocopy	retro_etel_1694,
Felis catus	ENSFCAG00000022260	1 retrocopy	retro_fcat_1225,
Homo sapiens	ENSG00000138796	1 retrocopy	retro_hsap_1571,
Gorilla gorilla	ENSGGOG00000004423	1 retrocopy	retro_ggor_1196 ,
Gorilla gorilla	ENSGGOG00000004918	1 retrocopy	retro_ggor_772,
Macaca mulatta	ENSMMUG00000023254	1 retrocopy	retro_mmul_2217,
Nomascus leucogenys	ENSNLEG00000012951	1 retrocopy	retro_nleu_1738,
Pongo abelii	ENSPPYG00000014986	1 retrocopy	retro_pabe_1296,
Pan troglodytes	ENSPTRG00000016351	1 retrocopy	retro_ptro_1058,