RetrogeneDB ID: retro_ptro_1274

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 18:65088523..65088770(+)
• Located in intron of: ENSPTRG00000010100

Retrocopy information

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

Parental gene information

• Parental gene symbol: SDHC
• Ensembl ID: ENSPTRG00000001585
• Aliases: None
• Description: succinate dehydrogenase complex, subunit C, integral membrane protein, 15kDa [Source:HGNC Symbol;Acc:10682]

Sequence

>retro_ptro_1274
ATGGTTGTACTCTTGCAAAGACATGTTGGCTGTCCTTGCCTCTGAGCCCAATTTAGCCCTCTGCTCTGTATCAGAAAAGC
TGCTCCTTTGGGAACCTTAGTCAAAAAAGAGATGGAGTGGTTCTGGAATAAGAACATAGATTCAAACCGCCCTTTATCTT
GCCATAGCACTGTCTACAGTTTGGCCTCTTCCCATGACGATGTCCATTTGCCACCGTGGGTCTGGTATTGCTTTGAGTAC
ACGGGTC

Alignment

ORF - retro_ptro_1274 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.08 %
• Parental protein coverage: 54.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAALLLRHVGRHCLRAHFSPQLCIRNAVPLGTTAKEEMERFWNKNIGSNRPLSPHITIYS-WSLPMAMSI
          M..LL.RHVG..CL.A.FSP.LCIR.A.PLGT..K.EME.FWNKNI.SNRPLS.H.T.YS.W.LPM.MSI
Retrocopy MVVLLQRHVGCPCL*AQFSPLLCIRKAAPLGTLVKKEMEWFWNKNIDSNRPLSCHSTVYS>WPLPMTMSI

Parental  CHRGTGIALSADV
          CHRG.GIALS..V
Retrocopy CHRGSGIALSTRV

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	0.02 RPM	52.62 RPM
SRP007412_cerebellum	0.00 RPM	39.54 RPM
SRP007412_heart	0.00 RPM	90.53 RPM
SRP007412_kidney	0.00 RPM	137.85 RPM
SRP007412_liver	0.00 RPM	52.15 RPM
SRP007412_testis	0.00 RPM	26.14 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1274 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1274 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1274 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015351	2 retrocopies	retro_amel_468, retro_amel_803,
Bos taurus	ENSBTAG00000015853	1 retrocopy	retro_btau_835,
Canis familiaris	ENSCAFG00000012992	2 retrocopies	retro_cfam_1529, retro_cfam_275,
Callithrix jacchus	ENSCJAG00000004757	3 retrocopies	retro_cjac_1119, retro_cjac_2455, retro_cjac_988,
Echinops telfairi	ENSETEG00000015767	1 retrocopy	retro_etel_675,
Felis catus	ENSFCAG00000000499	1 retrocopy	retro_fcat_1609,
Macaca mulatta	ENSMMUG00000012411	11 retrocopies	retro_mmul_1063, retro_mmul_1323, retro_mmul_1338, retro_mmul_1686, retro_mmul_1845, retro_mmul_2002, retro_mmul_2087, retro_mmul_239, retro_mmul_2416, retro_mmul_369, retro_mmul_672,
Mustela putorius furo	ENSMPUG00000014439	1 retrocopy	retro_mputfur_1201,
Pan troglodytes	ENSPTRG00000001585	4 retrocopies	retro_ptro_1274 , retro_ptro_2458, retro_ptro_449, retro_ptro_593,
Pteropus vampyrus	ENSPVAG00000005544	2 retrocopies	retro_pvam_879, retro_pvam_974,
Rattus norvegicus	ENSRNOG00000003163	2 retrocopies	retro_rnor_1486, retro_rnor_1487,
Sarcophilus harrisii	ENSSHAG00000016835	1 retrocopy	retro_shar_205,
Sus scrofa	ENSSSCG00000030318	2 retrocopies	retro_sscr_1050, retro_sscr_1061,
Takifugu rubripes	ENSTRUG00000001873	1 retrocopy	retro_trub_41,
Tursiops truncatus	ENSTTRG00000009234	1 retrocopy	retro_ttru_196,