RetrogeneDB ID: retro_cjac_168

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:76525078..76526188(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022859
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TRAM1
• Ensembl ID: ENSCJAG00000007893
• Aliases: None
• Description: None

Sequence

>retro_cjac_168
ATGGGGCTCCGTAAGAAGGGCACCAGGAACCCCCCCGTTCTGAGTCAGGAATTCATCCTGCAGAATCATGCGGACATCGT
CTCCTGCGTGGGGATGTTCTTCCTGCTGGGGCTTGTGTTCGAGGGAACAGCAGAAGCATCCATCGTGTTTCTCACTCTTC
AGCACAGTGTTGCCGTCCCTGCAGCAGAGGAACAAGCCACGGGATCAAAGTCCCTTTATTATTATGGTGTCAAAGATTTG
GCCACGGTTTTCTTCTACATGCTGGTGGCAATCATTATTCATGCCACAATTCAGGAGTATGTGTTGGATAAAATTAACAG
GAGAATGCAGTTCACCAAAGCGAAACAAAACAAGTTTAACGAATCTGGTCAGTTTAGTGTGTTCTACTTTTTTTCTTGTA
TTTGGGGCACATTCATTTTAATCTCTGAAAACTGCCTGTCAGACCCAACTCTCATATGGAGGGCTCATCCCCATAGCATG
ATGACATTTCAAATGAAGTTTTTCTACATATCCCAGTTGGCTTACTGGTTTCATGCTTTTCCTGAACTCTACTTTCAGAA
AACCAAAAAACAAGACATCCCTCGTCAAGTTGTCTACATTGGTCTTCACCTCTTTCACATTACTGGAGCTTATCTCTTGT
ACTTGAATCATTTGGGACTTCTTCTTTTGGTACTGCATTATTTTGTTGAATTACTTTCCCATATGTGCGGTCTGTTTTAC
TTTAGTGATGAAAAGTACCAGAAAGGCATATCTCTGTGGGCCATCGTGTTTATCTTGGGTAGACTTGTGACTTTAATTGT
TTCTGTAGTCACTGTTGGGTTTCACCTAGCTGGATCGCAGAATCAGAATCCTGATGCCATTACTGGAAATGTAAATGTGT
TGGCAGCTAAAATTGCTGTTCTGTCATCTAGTTGCACTATCCAAGCCTACATAACATGGAACTTAATTACTCTCTGGCTT
CAGCGGTGGATAGAAGATTCTAATATTCAGGTCTCATGTATGAAGAAGAAACGGTCAAGGTCTTCTAAAAAAAGAACAGA
AAATGGAGTGGGAGTGGAAACTTCGAATAGAGTAGACTGTCCACCAAAGAGGAAAGAGAAATCTTCATAA

Alignment

ORF - retro_cjac_168 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.86 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAIRKKSTKSPPVLSHEFVLQNHADIVSCVAMIFLLGLMFEITAKASIIFVTLQYNVTLPATEEQATESA
          M..RKK.T..PPVLS.EF.LQNHADIVSCV.M.FLLGL.FE.TA.ASI.F.TLQ..V..PA.EEQAT.S.
Retrocopy MGLRKKGTRNPPVLSQEFILQNHADIVSCVGMFFLLGLVFEGTAEASIVFLTLQHSVAVPAAEEQATGSK

Parental  SLYYYGIKDLATVFFYMLVAIIIHAIIQEYVLDKINRRMHFSKTKHSKFNESGQLSAFYLFACVWGTFIL
          SLYYYG.KDLATVFFYMLVAIIIHA.IQEYVLDKINRRM.F.K.K..KFNESGQ.S.FY.F.C.WGTFIL
Retrocopy SLYYYGVKDLATVFFYMLVAIIIHATIQEYVLDKINRRMQFTKAKQNKFNESGQFSVFYFFSCIWGTFIL

Parental  ISENYIADPTILWRAYPHNLMTFQMKFFYISQLAYWLHAFPELYFQKTKKEDIPRQLVYIGLYLFHIAGA
          ISEN...DPT..WRA.PH..MTFQMKFFYISQLAYW.HAFPELYFQKTKK.DIPRQ.VYIGL.LFHI.GA
Retrocopy ISENCLSDPTLIWRAHPHSMMTFQMKFFYISQLAYWFHAFPELYFQKTKKQDIPRQVVYIGLHLFHITGA

Parental  YLLNLNHLGLVLLVLHYFVEFLFHISRLFYFSNEKYQKGFSLWAVLFVLGRLLTLILSVLTVGFGLARAE
          YLL.LNHLGL.LLVLHYFVE.L.H...LFYFS.EKYQKG.SLWA..F.LGRL.TLI.SV.TVGF.LA...
Retrocopy YLLYLNHLGLLLLVLHYFVELLSHMCGLFYFSDEKYQKGISLWAIVFILGRLVTLIVSVVTVGFHLAGSQ

Parental  NQKLDFSTGNFNVLAVRIAVLASICITQAFMMWKFINFQLRRWREHSAFQAPAVKKKPTVTKGRSSRKGT
          NQ..D..TGN.NVLA..IAVL.S.C..QA...W..I...L.RW.E.S..Q....KKK......RSS.K.T
Retrocopy NQNPDAITGNVNVLAAKIAVLSSSCTIQAYITWNLITLWLQRWIEDSNIQVSCMKKK----RSRSSKKRT

Parental  ENGVNGTLTSNVADSPRNRKEKSS
          ENGV.G..TSN..D.P..RKEKSS
Retrocopy ENGV-GVETSNRVDCPPKRKEKSS

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	0.04 RPM	82.23 RPM
SRP051959_heart	0.11 RPM	43.11 RPM
SRP051959_kidney	0.18 RPM	83.89 RPM
SRP051959_liver	0.00 RPM	149.72 RPM
SRP051959_lung	0.03 RPM	91.49 RPM
SRP051959_lymph_node	0.07 RPM	80.07 RPM
SRP051959_skeletal_muscle	0.00 RPM	19.13 RPM
SRP051959_spleen	0.00 RPM	87.08 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_168 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_168 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_168 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_169

---

Parental genes homology:

Parental genes homology involve 25 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006325	1 retrocopy	retro_amel_78,
Bos taurus	ENSBTAG00000007562	1 retrocopy	retro_btau_24,
Canis familiaris	ENSCAFG00000007866	1 retrocopy	retro_cfam_15,
Callithrix jacchus	ENSCJAG00000007893	1 retrocopy	retro_cjac_168 ,
Dasypus novemcinctus	ENSDNOG00000009296	2 retrocopies	retro_dnov_27, retro_dnov_906,
Dipodomys ordii	ENSDORG00000001901	1 retrocopy	retro_dord_27,
Equus caballus	ENSECAG00000018378	1 retrocopy	retro_ecab_506,
Echinops telfairi	ENSETEG00000018447	1 retrocopy	retro_etel_674,
Felis catus	ENSFCAG00000028775	1 retrocopy	retro_fcat_136,
Homo sapiens	ENSG00000067167	1 retrocopy	retro_hsap_51,
Loxodonta africana	ENSLAFG00000011625	1 retrocopy	retro_lafr_9,
Macaca mulatta	ENSMMUG00000001516	1 retrocopy	retro_mmul_235,
Monodelphis domestica	ENSMODG00000007316	1 retrocopy	retro_mdom_308,
Mustela putorius furo	ENSMPUG00000010616	1 retrocopy	retro_mputfur_558,
Mus musculus	ENSMUSG00000025935	1 retrocopy	retro_mmus_117,
Nomascus leucogenys	ENSNLEG00000011376	1 retrocopy	retro_nleu_73,
Oryctolagus cuniculus	ENSOCUG00000008734	1 retrocopy	retro_ocun_52,
Otolemur garnettii	ENSOGAG00000006379	1 retrocopy	retro_ogar_2932,
Pongo abelii	ENSPPYG00000018660	1 retrocopy	retro_pabe_169,
Pan troglodytes	ENSPTRG00000020334	1 retrocopy	retro_ptro_2081,
Rattus norvegicus	ENSRNOG00000007892	1 retrocopy	retro_rnor_287,
Sus scrofa	ENSSSCG00000006193	1 retrocopy	retro_sscr_980,
Ictidomys tridecemlineatus	ENSSTOG00000005537	1 retrocopy	retro_itri_38,
Tarsius syrichta	ENSTSYG00000013887	1 retrocopy	retro_tsyr_24,
Tursiops truncatus	ENSTTRG00000000328	1 retrocopy	retro_ttru_24,