RetrogeneDB ID: retro_cfam_275

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 1:91757519..91757995(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SDHC
• Ensembl ID: ENSCAFG00000012992
• Aliases: None
• Description: succinate dehydrogenase complex, subunit C, integral membrane protein, 15kDa [Source:HGNC Symbol;Acc:10682]

Sequence

>retro_cfam_275
CACACTGGCTGTCATTACTTCTGTGCCGACCTTACTCTGTGGCTTTGTATCTAAAATGCTGTTCCTTTGTGAACCACAGC
CAAATAAGAAGTGGAGCAGTTCTGGAATCAGAACAGAGGCTCACATGGTCCTCTGTCTCCCCATATCACTAGCTACAGCT
GGTCTCTTCCCATGAGGATGCCTACCTGCCACAGTGGCTCTAAAAAGGTTGCATTTTCAGGGGTTGCTTTTTGACTTGTC
AGCCCTGTGGCTCCTGGGAATTATGAATATCATTTGGAACTTGTGAAGTCCCCGTGTCTGGGGTAGCACTGATCCACAGA
GCTCAGTTTGCACTTCTTTGCCTTCTCATGTATCACACCAGCAATGAGATCGTACGCTGGATGAGGGACTCAGTAAAAGA
CCTGAAGACACCCCAGCTATACCAGTCCGGAACGGTGGACTTGATTACTGTGTTTTGCTCTGTAGGATTGGCAGCT

Alignment

ORF - retro_cfam_275 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.79 %
• Parental protein coverage: 95.83 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HVGRHCLRAHLSPQLCIRNAVPLGTTAKEEMERFWNKNTDLNRPLSPHITIYSWSLPMAMSICHRGTGVA
          H.G.H...A.L...LCI.NAVPL.TTAK.E.E.FWN.N.....PLSPHIT.YSWSLPM.M..CH.G....
Retrocopy HTGCHYFCADLTLWLCI*NAVPL*TTAK*EVEQFWNQNRGSHGPLSPHITSYSWSLPMRMPTCHSGSKKV

Parental  LSAGVSLFGLSALLVPGNFESHLELVKSLCL-GPSLIYTAKFALVFPLMYHTWNGIRHLIWDLGKGLKIP
          ...GV..F.L.....PGN.E.HLELVKS.CL.G..LI..A.FAL...LMYHT.N.I.....D..K.LK.P
Retrocopy AFSGVA-F*LVSPVAPGNYEYHLELVKSPCL<GVALIHRAQFALLCLLMYHTSNEIVRWMRDSVKDLKTP

Parental  QLYQSGVAVLVLTVLSSVGLAA
          QLYQSG...L..TV..SVGLAA
Retrocopy QLYQSGTVDLI-TVFCSVGLAA

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
SRP012049_cerebellum	0.00 RPM	33.64 RPM
SRP017611_brain	0.00 RPM	34.93 RPM
SRP017611_kidney	0.00 RPM	188.60 RPM
SRP017611_liver	0.00 RPM	53.88 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_275 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_275 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_275 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 18 parental genes, and 45 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,
Homo sapiens	ENSG00000143252	4 retrocopies	retro_hsap_1794, retro_hsap_1896, retro_hsap_609, retro_hsap_854,
Gorilla gorilla	ENSGGOG00000008017	3 retrocopies	retro_ggor_1390, retro_ggor_536, retro_ggor_697,
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,
Nomascus leucogenys	ENSNLEG00000014367	3 retrocopies	retro_nleu_1476, retro_nleu_420, retro_nleu_439,
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,