RetrogeneDB ID: retro_ggor_2386

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 6:145307178..145307740(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RHBDD1
• Ensembl ID: ENSGGOG00000000723
• Aliases: None
• Description: None

Sequence

>retro_ggor_2386
TTTCTGGATGAACCTGGCTTCGGAAGGTACTGTGCTGTAGGTTTTTCCAGGAGTTTTGTTTGCTTTGGAGTTTCTTAACA
ACCATCATTGCCTTGGAGGCTTTGTCAACATTTTGGGCTTCCTTGTCCTCAACAGATTTGCTTGTTGGGCCACACTTGTG
CCTTTTCACTTATTCTCACCAGGGACTTCCTTCACTGGGCATCTGGCTGGGATTCTTGTTGCATTAATGCACACTCAAGG
GCCTCTGAAGAACATCATGGAAGCATGTGCCGGCATTTTTTCCCCTCCAATTATTGGTTATCCAGGACAGTGATATTACT
TCAATTGTTCAGGCTAGTCTAGTTATCAGGATCATTATCTTTATGGCAGGCCAGGTTATTAGGAAGAAGCACCCAGGAGC
TATGATATATACACAGCAGTACGGAGAGAAAAAGAACAGCTGGTGAGAGCATGAAGAGCCAGCCCCTGGGATTGAGAAAA
TACCAGGAATAGCTCACTGCCCTGTGGGCTTCTTCTCTCAGAAGAAATGAGACTATAATGGCTTCACAGGTTTGATAGCC
AG

Alignment

ORF - retro_ggor_2386 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.9 %
• Parental protein coverage: 59.37 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FMDEPDFKRSCAVGFS-GVLFALKVLNNHYCPGGFVNILGFPVPNRFACWVELVAIHLFSPGTSFAGHLA
          F.DEP.F.R.CAVGFS.GVLFAL..LNNH.C.GGFVNILGF.V.NRFACW..LV..HLFSPGTSF.GHLA
Retrocopy FLDEPGFGRYCAVGFS>GVLFALEFLNNHHCLGGFVNILGFLVLNRFACWATLVPFHLFSPGTSFTGHLA

Parental  GILVGLMYTQGPLKKIMEACAGGFSSS-VGYPGQQYYFNSSGSSGYQDYYPHGRPDHYEEAPRNYDTYTA
          GILV.LM.TQGPLK.IMEACAG.FS....GYPGQ.YYFN.SG.S.YQD.Y..GRP...EEAPR.YD.YTA
Retrocopy GILVALMHTQGPLKNIMEACAGIFSPPIIGYPGQ*YYFNCSG*SSYQDHYLYGRPGY*EEAPRSYDIYTA

Parental  GLSEEEQLERALQASLWDRGNTRNSPPPYGFHLSPEEMRRQRLHRFDSQ
          ...E.EQL.RA..AS.WD..NTRNS..P.G..LS.EEMR...LHRFDSQ
Retrocopy VRREKEQLVRA*RASPWD*ENTRNSSLPCGLLLS-EEMRL*WLHRFDSQ

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	5.75 RPM
SRP007412_cerebellum	0.00 RPM	4.02 RPM
SRP007412_heart	0.00 RPM	3.19 RPM
SRP007412_kidney	0.00 RPM	13.37 RPM
SRP007412_liver	0.00 RPM	11.32 RPM
SRP007412_testis	0.00 RPM	41.44 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_2386 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2386 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3529
Pan troglodytes	retro_ptro_2397
Pongo abelii	retro_pabe_2915
Callithrix jacchus	retro_cjac_2386

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012767	1 retrocopy	retro_cjac_2386,
Homo sapiens	ENSG00000144468	1 retrocopy	retro_hsap_3529,
Gorilla gorilla	ENSGGOG00000000723	1 retrocopy	retro_ggor_2386 ,
Pongo abelii	ENSPPYG00000013235	1 retrocopy	retro_pabe_2915,
Pan troglodytes	ENSPTRG00000012990	1 retrocopy	retro_ptro_2397,