RetrogeneDB ID: retro_cjac_1867

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:161856040..161856946(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TCP1
• Ensembl ID: ENSCJAG00000011792
• Aliases: None
• Description: T-complex protein 1 subunit alpha [Source:UniProtKB/TrEMBL;Acc:F6TE24]

Sequence

>retro_cjac_1867
CTTGGTGTACACATGGTCATTACAAACCCTGAAAAACTGGACCAAATTAGACAGAATCAGATATTATCAAGAAGAGAATT
CCAAAGATCCTGGCAACTGATGCCAATATTATTCTAATCAGTGGTGGAATTGATGATATGTGTCAAAGTATTTCATAGAG
GCTGGTGTTATAGCAATTAGGAGAGCTTTAAAAAGGGACCTTAAATGCATTGTTAAAGCTCCTAGAGGGACTACTCTGTC
AACCCTGGCCAATTTGAAGGGTGAAGAAACTTTTCAAGCTGTAATTTTGGGACAGGTAGAGAAGTGGTACAGGAGACAAT
TTGTGATGATGAGCTGATCTTAATGAAAACCAGTAAGACTTGTGCATCTGCATCAATTATCTTACATGGGGAAAATGACT
TAATGTGTGATGAGATGGAACACTCTCTACATGATGCTCTTTGCGTAGTGAACAAAGTTTTGGAGTCAAAATCTGTGATG
CCAGCTGGGGCTGCTGTAGAAGCAGCCTTTTCCATCTACCCAGAAAACTATGCAACCAGCATGAGTTCTTGGGAACAGCT
TGCTATTGCAGAATTTGCAAGACTTCTTCTTGTTATTGCTAATACACTGGCAGTTGATGCTGCCCAGAACTCCACAGATC
TGCTTGCAAAGTTAAGAGCTTTTCATAATGAGGCTCAAGTTAACCCAGAACGTAAAAATCTAAAATGGATGGGTCTTGAT
TTGAGCAATGGTAAACTGGGACACAACCAACAAGCAGGAGTGTTTGAACCAACCATAGCTAAAGTTAAAAGTTTGAAATT
AGCAACAGAAGCTGCAGTTATCATTCTTCAAATTGATGATCTTATAAAATTATACCCAGAGAGTAAAGGCGTTAAACATG
GAGGTTATGAAGATGCTGTTCATAAC

Alignment

ORF - retro_cjac_1867 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.59 %
• Parental protein coverage: 54.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LGVQVVITDPEKLDQIRQRESDITKERIQ-KILATGANVILTTGGIDDMC-LKYFVEAGAMAVRRVLKRD
          LGV..VIT.PEKLDQIRQ..........Q.KILAT.AN.IL..GGIDDMC..KYF.EAG..A.RR.LKRD
Retrocopy LGVHMVITNPEKLDQIRQNQI-LSRREFQ<KILATDANIILISGGIDDMC<SKYFIEAGVIAIRRALKRD

Parental  LKRIAKASGASILSTLANLEGEETFEAAMLGQAE-EVVQERICDDELILIKNTKARTSASIILRGANDFM
          LK.I.KA.....LSTLANL.GEETF.A..LGQ.E.EVVQE.ICDDELIL.K..K...SASIIL.G.ND.M
Retrocopy LKCIVKAPRGTTLSTLANLKGEETFQAVILGQVE<EVVQETICDDELILMKTSKTCASASIILHGENDLM

Parental  CDEMERSLHDALCVVKRVLESKSVVPGGGAVEAALSIYLENYATSMGSREQLAIAEFARSLLVIPNTLAV
          CDEME.SLHDALCVV..VLESKSV.P.G.AVEAA.SIY.ENYATSM.S.EQLAIAEFAR.LLVI.NTLAV
Retrocopy CDEMEHSLHDALCVVNKVLESKSVMPAGAAVEAAFSIYPENYATSMSSWEQLAIAEFARLLLVIANTLAV

Parental  NAAQDSTDLVAKLRAFHNEAQVNPERKNLKWIGLDLSNGKPRDNKQAGVFEPTIVKVKSLKFATEAAITI
          .AAQ.STDL.AKLRAFHNEAQVNPERKNLKW.GLDLSNGK...N.QAGVFEPTI.KVKSLK.ATEAA..I
Retrocopy DAAQNSTDLLAKLRAFHNEAQVNPERKNLKWMGLDLSNGKLGHNQQAGVFEPTIAKVKSLKLATEAAVII

Parental  LRIDDLIKLHPESKDDKHGSYEDAVHS
          L.IDDLIKL.PESK..KHG.YEDAVH.
Retrocopy LQIDDLIKLYPESKGVKHGGYEDAVHN

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	0.00 RPM	70.76 RPM
SRP051959_heart	0.19 RPM	52.67 RPM
SRP051959_kidney	0.00 RPM	56.91 RPM
SRP051959_liver	0.02 RPM	71.55 RPM
SRP051959_lung	0.02 RPM	42.59 RPM
SRP051959_lymph_node	0.02 RPM	46.21 RPM
SRP051959_skeletal_muscle	0.02 RPM	53.24 RPM
SRP051959_spleen	0.02 RPM	46.16 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1867 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1867 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1867 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015405	1 retrocopy	retro_amel_828,
Callithrix jacchus	ENSCJAG00000011792	2 retrocopies	retro_cjac_1867 , retro_cjac_2193,
Equus caballus	ENSECAG00000017953	1 retrocopy	retro_ecab_798,
Homo sapiens	ENSG00000120438	1 retrocopy	retro_hsap_3722,
Gorilla gorilla	ENSGGOG00000014063	1 retrocopy	retro_ggor_2514,
Microcebus murinus	ENSMICG00000007998	1 retrocopy	retro_mmur_795,
Macaca mulatta	ENSMMUG00000012846	1 retrocopy	retro_mmul_1696,
Oryctolagus cuniculus	ENSOCUG00000013847	1 retrocopy	retro_ocun_1577,
Pongo abelii	ENSPPYG00000017146	1 retrocopy	retro_pabe_3135,
Pan troglodytes	ENSPTRG00000018760	1 retrocopy	retro_ptro_2617,
Pteropus vampyrus	ENSPVAG00000005316	1 retrocopy	retro_pvam_522,
Sorex araneus	ENSSARG00000002463	1 retrocopy	retro_sara_624,
Sarcophilus harrisii	ENSSHAG00000015128	1 retrocopy	retro_shar_830,
Ictidomys tridecemlineatus	ENSSTOG00000005572	1 retrocopy	retro_itri_1274,