RetrogeneDB ID: retro_cjac_988

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:78971382..78971724(+)
• Located in intron of: ENSCJAG00000008495

Retrocopy information

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

Parental gene information

• Parental gene symbol: SDHC
• Ensembl ID: ENSCJAG00000004757
• Aliases: None
• Description: succinate dehydrogenase complex, subunit C, integral membrane protein, 15kDa [Source:HGNC Symbol;Acc:10682]

Sequence

>retro_cjac_988
ATCACTATCTACAGTTGGTCTCTTCCCACGGTAATGTCCATCTACCACCGTGGCACTGGCATTGCTTTGAACGCAGGGGT
CTCTCTTTTTGGCATATTGGCCCTGTTACTCCCTGGGAACTTTGAGTCTTACATGGAACTCGTGAAGTCCCTGTGTCTGG
GGCCAGCACTGATCCATGCAGCTAAGTTTGCACTTGTCTTCCCTCTCATGTATCATACCTGGAATGGGATCTGCCACTTG
ATGTGGGACCTAGGAAAAGGCATGAAGATTCCCTAGCTATACCAGTCTGGAGTGGTTGTCCTGGTTCTTACTGTGTTGTC
CTCTGTAGAGCTGGCAGCCATG

Alignment

ORF - retro_cjac_988 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.72 %
• Parental protein coverage: 67.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ITIYSWSLPMAMSICHRGTGIALSAGVSLFGMSALLLPGNFESYLELVKSLYLGPALIHTAKFALVFPLM
          ITIYSWSLP..MSI.HRGTGIAL.AGVSLFG..ALLLPGNFESY.ELVKSL.LGPALIH.AKFALVFPLM
Retrocopy ITIYSWSLPTVMSIYHRGTGIALNAGVSLFGILALLLPGNFESYMELVKSLCLGPALIHAAKFALVFPLM

Parental  YHTWNGIRHLMWDLGKGLKIPQLYQSGVVVLVLTVLSSLGLAAM
          YHTWNGI.HLMWDLGKG.KIP.LYQSGVVVLVLTVLSS..LAAM
Retrocopy YHTWNGICHLMWDLGKGMKIP*LYQSGVVVLVLTVLSSVELAAM

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
SRP051959_colon	0.29 RPM	21.63 RPM
SRP051959_heart	0.33 RPM	32.13 RPM
SRP051959_kidney	0.44 RPM	36.05 RPM
SRP051959_liver	0.35 RPM	37.82 RPM
SRP051959_lung	0.44 RPM	12.98 RPM
SRP051959_lymph_node	0.53 RPM	12.05 RPM
SRP051959_skeletal_muscle	0.35 RPM	34.59 RPM
SRP051959_spleen	0.44 RPM	14.96 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_988 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_988 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_988 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_609
Gorilla gorilla	retro_ggor_536
Macaca mulatta	retro_mmul_2416

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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,