RetrogeneDB ID: retro_cjac_2690

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:7300037..7300763(+)
• Located in intron of: ENSCJAG00000017150

Retrocopy information

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

Parental gene information

• Parental gene symbol: WDR12
• Ensembl ID: ENSCJAG00000005171
• Aliases: None
• Description: None

Sequence

>retro_cjac_2690
GAGGCTTCTCAGATCTGGTCCTTGGAAGGAAAGTCAACACTGACAATTGTGGGACATATGGACGTTGTAAAAGATGGGGC
CCGGGTGAAAAAAAGACAGTTTGTCTTCCTTGTTACTGAGTGCCTCTATGGATCAGACTATTCTCTTACGGGAGTGGAAT
GTCAAAAGAAACAAAGTGAAAACCCTACACTGTTGCACAGGTCATGCTGGAAGTGTCTATTCTACCCCTGCTGATAGCTC
AGGAACTAAACTTTGCATCGGCTCCTGGGATAAGATACAAAGGATCTGATCTACTGTCCCTACAGAAGAAAATGAAATGG
AGGAATCCACAAATTGACCAAGAAAGAGACAGAAAACAGAGTAGCTGGGACTAACAAGGACTCCCATACTGACCCTCTCT
GGCCACAAGGAAGCAACTTCCTCAGTTCTGTGGTCAGATGCTACAGAAATCTGCAGTGCATCATGGGATCATACAATTAG
CATGTGGGATGTTCTGTCTGCCAATCTTAAGTCAACTTTACAGGAAATAAACTGTTTAATTGTATTTCCTATTCTCCACT
TTGCATATGTTTAGCATCTGGAAGCAGAGAGAGGCATATCAGACTGTGGGATCCCCAAACTAGAGATGGTTCTTTGGTGT
TGCCGTCTCTAACCTCACATACTGGTTGGGAGACATCAGTAGCATGGTCTCCTACCCATGAACAGCGGCTGGTTTCAGCA
TCCTTG

Alignment

ORF - retro_cjac_2690 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.14 %
• Parental protein coverage: 57.45 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KTSRIWSLEGKLIMTTVGHTDVVKDVAWVKK-DSLSCLLLSASMDQTILLWEWNVERNKVKALHCCRGHA
          ..S.IWSLEGK...T.VGH.DVVKD.A.VKK.DSLS.LLLSASMDQTILL.EWNV.RNKVK.LHCC.GHA
Retrocopy EASQIWSLEGKSTLTIVGHMDVVKDGARVKK>DSLSSLLLSASMDQTILLREWNVKRNKVKTLHCCTGHA

Parental  GSVDSIAVDGSGTKFCSGSWDKMLKIWSTVPTDEEDEMEESTNRPRKKQKTEQLGLTRTPIVTLSGHKEA
          GSV.S...D.SGTK.C.GSWDK...I.STVPT.EE.EMEESTN.PRK.QKTE.LGLTRTPI.TLSGHKEA
Retrocopy GSVYSTPADSSGTKLCIGSWDKIQRI*STVPT-EENEMEESTN*PRKRQKTE*LGLTRTPILTLSGHKEA

Parental  VSSVLWSDAEEICSASWDHTIRVWDVESGSLKSTL-TGNKVFNCISYSPICKRLASGSTDRHIRLWDPRT
          .SSVLWSDA.EICSASWDHTI..WDV.S..LKSTL.TGNK.FNCISYSP.C..LASGS..RHIRLWDP.T
Retrocopy TSSVLWSDATEICSASWDHTISMWDVLSANLKSTL<TGNKLFNCISYSPLCICLASGSRERHIRLWDPQT

Parental  KDGSLVSLSLTSHTGWVTSVKWSPTHEQQLISGSL
          .DGSLV..SLTSHTGW.TSV.WSPTHEQ.L.S.SL
Retrocopy RDGSLVLPSLTSHTGWETSVAWSPTHEQRLVSASL

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	0.27 RPM	11.34 RPM
SRP051959_heart	0.32 RPM	9.47 RPM
SRP051959_kidney	0.38 RPM	13.47 RPM
SRP051959_liver	0.15 RPM	7.30 RPM
SRP051959_lung	0.36 RPM	11.66 RPM
SRP051959_lymph_node	0.37 RPM	8.97 RPM
SRP051959_skeletal_muscle	0.15 RPM	12.29 RPM
SRP051959_spleen	0.29 RPM	9.29 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2690 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2690 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2690 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012519	1 retrocopy	retro_cfam_1759,
Choloepus hoffmanni	ENSCHOG00000013851	1 retrocopy	retro_chof_118,
Callithrix jacchus	ENSCJAG00000005171	1 retrocopy	retro_cjac_2690 ,
Cavia porcellus	ENSCPOG00000008824	1 retrocopy	retro_cpor_1107,
Homo sapiens	ENSG00000138442	1 retrocopy	retro_hsap_1615,
Gorilla gorilla	ENSGGOG00000026073	1 retrocopy	retro_ggor_1222,
Loxodonta africana	ENSLAFG00000011955	1 retrocopy	retro_lafr_1102,
Mus musculus	ENSMUSG00000026019	3 retrocopies	retro_mmus_1394, retro_mmus_2649, retro_mmus_2897,
Nomascus leucogenys	ENSNLEG00000007018	1 retrocopy	retro_nleu_2743,
Pongo abelii	ENSPPYG00000013089	1 retrocopy	retro_pabe_1327,
Pan troglodytes	ENSPTRG00000012823	1 retrocopy	retro_ptro_1083,
Tursiops truncatus	ENSTTRG00000001231	1 retrocopy	retro_ttru_1380,