RetrogeneDB ID: retro_ptro_2397

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:145879249..145879811(+)
• Located in intron of: ENSPTRG00000018680

Retrocopy information

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

Parental gene information

• Parental gene symbol: RHBDD1
• Ensembl ID: ENSPTRG00000012990
• Aliases: None
• Description: rhomboid domain containing 1 [Source:HGNC Symbol;Acc:23081]

Sequence

>retro_ptro_2397
TTTCTGGATGAACCTGGCTTTGGAAGGTACTGTGCTGTAGGTTTTTCCAGGAGTTTTGTTTGCTTTGGAGTTTCTTAACA
ACCATCATTGCCTTAGAGGCTTTGTCAACATTTTGGGCTTCCTTGTCCTCAACAGATTTGCTTGTTGGGCCACACTTGTG
CCTTTTCACTTATTCTCACCAGGGACTTCCTTCACTGGGCATCTGGCTGGGATTCTTGTTGCATTAATGCACACTCAAGG
GCCTCTGAAGAACATCATGGAAGCATGTGCTGGCATTTTTTTCCCTCCAATTATTGGTTATCCAGGACAGTGATATTACT
TCAATTGTTCAGGCTAGTCTGGATATCAGGATCATTATCTTTATGGCAGGCCAGGTTATTATGAAGAAGCACCCAGGAGC
TATGATATATACACAGCAGTATGGAGAGAAAAAGAACAGCTGGTGAGAGCATGAAGAGCCAGCCCCTGGGATCAAGAAAA
TACCAGGAATAGCTCACTGCCCTGCGGGCTTCTTCTCTCAGAAGAAATGAGACTATAATGGCTTCACAGGTTTGATAGCC
AG

Alignment

ORF - retro_ptro_2397 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.84 %
• Parental protein coverage: 59.37 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

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

Parental  GILVGLMYTQGPLKKIMEACAG-GFSSSAGYPGRQYYFNSSGSSGYQDYYPHGRPDHYEEAPGNYDTYTA
          GILV.LM.TQGPLK.IMEACAG..F....GYPG..YYFN.SG.SGYQD.Y..GRP..YEEAP..YD.YTA
Retrocopy GILVALMHTQGPLKNIMEACAGIFFPPIIGYPGQ*YYFNCSG*SGYQDHYLYGRPGYYEEAPRSYDIYTA

Parental  GLSEEEQLERALQASLWDRGNTRNSPPPYGFHLSPEEMRRQRLHRFDSQ
          ...E.EQL.RA..AS.WD..NTRNS..P.G..LS.EEMR...LHRFDSQ
Retrocopy VWREKEQLVRA*RASPWDQENTRNSSLPCGLLLS-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	4.52 RPM
SRP007412_cerebellum	0.00 RPM	4.34 RPM
SRP007412_heart	0.09 RPM	8.63 RPM
SRP007412_kidney	0.00 RPM	16.34 RPM
SRP007412_liver	0.00 RPM	15.35 RPM
SRP007412_testis	0.00 RPM	44.58 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2397 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2397 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2397 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3529
Gorilla gorilla	retro_ggor_2386
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 ,