RetrogeneDB ID: retro_cjac_3976

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286459.1:167928..168873(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000023352
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000017209
• Aliases: None
• Description: None

Sequence

>retro_cjac_3976
CCAAGCCACAGCAGCTTCCCAGTGGGATGCCACCACCACCCCATGCTGCACATGGTGCTGGAGGCACTGCAGGCAGGGGA
GCAGTGCCAGGGCACATAGGTGGTAGCCATCAAGCTCTACATTCTGCAAAAGTACCCAGCAGTGGATGTCCTTTGCTTCA
AGTACCTGCTGAAGCAGGTGCTGGCCACTGGCATGCTCCATGGCCTCCTTGCCAGGCCTCTCAATTTCAAAGCCAGGGGG
GCCACTAGCAACTTCAAATTAGTTACCAAGCACAAGAGGAAAATTAAGCCCAGGAAGATGGCCCCCCAGAAGGCCCCCAG
GAGAGCAGGCGAGACCAAGGGGAAGGTCCCAAAGAAACCAGATGAGGCCAAGGAGGAGCCTCCCAAGGCAGGAAAGGTGA
AAAAGGCAGCCAAGAGGCCAGGGGAGGTGCAGAAGTATTCTCTCAAGCCAGGCACAGTCACAGAAAAAGCTTACGAGCAA
GGCAGCAAGTCCAAGGACATCAAGGCACAGCCAGGTGAGGCTCAGAAGGTGCCCACCAAGCCAGACAAGGCCATGGGGGC
CCCTTATAGTGCCAGTGGGTTCAGCAGGAAGGCAGAGGCCAAAGGCAGCAGGAGGAGCCAAAGAGATGCTGAGGCCTGCA
GGAAAAGCAAACCTGGGAGTAAGAGTTCAAGACCCACGGTCAGTAAGGTCAAGAATGGTGCTGCTTCCACAACCAAAAAG
AAGTTGGCAGCCAAGGCCAAGGCCCAGGGCCCTAGAGGGGCAGCTGGCCCTGGGGCTGGGCAGGGGCCAAATGCCAAGGG
TGCTTCTGCTAAGGCCGGTGGGTCCAAGGTGGTGCCTACACACCTGTCCCAGAAGACAGAGGCCCCTAAGGGCTTGAGAC
AGGCTGGGCTGCTCATCAACATCAAGTCCTCATCATCCAAAGTGCCCAGCCAGAGGGCTAAAGCT

Alignment

ORF - retro_cjac_3976 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.7 %
• Parental protein coverage: 99.69 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PSRSSFPVGRRHPPTLQMVLEAMQVLQAEEQRQGTSVVAIKRYILRKYPAADGPRFKYLLKNALATGMCR
          PS.SSFPVG..H.P.L.MVLEA...LQA.EQ.QGT.VVAIK.YIL.KYPA.D...FKYLLK..LATGM..
Retrocopy PSHSSFPVGCHHHPMLHMVLEA---LQAGEQCQGT*VVAIKLYILQKYPAVDVLCFKYLLKQVLATGMLH

Parental  GLLARPPHLKTRGATGSFQLVTNHERTIKPRKTASPKAPRRAGVAKGKVPKKPDEAKEEPPKAGKGKKGA
          GLLARP...K.RGAT..F.LVT.H.R.IKPRK.A..KAPRRAG..KGKVPKKPDEAKEEPPKAGK.KK.A
Retrocopy GLLARPLNFKARGATSNFKLVTKHKRKIKPRKMAPQKAPRRAGETKGKVPKKPDEAKEEPPKAGKVKKAA

Parental  KSPAEVQKPPLKPGTDTEKACKESSKAKDTEAQPGEAQKVPPKPDKAMRAPSNDSGFSRRAEVKGSWRSP
          K.P.EVQK..LKPGT.TEKA....SK.KD..AQPGEAQKVP.KPDKAM.AP...SGFSR.AE.KGS.RS.
Retrocopy KRPGEVQKYSLKPGTVTEKAYEQGSKSKDIKAQPGEAQKVPTKPDKAMGAPYSASGFSRKAEAKGSRRSQ

Parental  GGAEASRKTKAGSKSLRPTVSKVKSGTASLTEKKSVARAKAQS-QAPAPTGAGQGPNAKGASAKAGGSKV
          ..AEA.RK.K.GSKS.RPTVSKVK.G.AS.T.KK..A.AKAQ.....A..GAGQGPNAKGASAKAGGSKV
Retrocopy RDAEACRKSKPGSKSSRPTVSKVKNGAASTTKKKLAAKAKAQGPRGAAGPGAGQGPNAKGASAKAGGSKV

Parental  VPAHLSRKTEAPKGSRTAGLPIDIKFPSSKVSSQRAEA
          VP.HLS.KTEAPKG.R.AGL.I.IK..SSKV.SQRA.A
Retrocopy VPTHLSQKTEAPKGLRQAGLLINIKSSSSKVPSQRAKA

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	0.00 RPM
SRP051959_heart	0.00 RPM	0.00 RPM
SRP051959_kidney	0.00 RPM	0.00 RPM
SRP051959_liver	0.00 RPM	0.00 RPM
SRP051959_lung	0.00 RPM	0.00 RPM
SRP051959_lymph_node	0.00 RPM	0.02 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.00 RPM
SRP051959_spleen	0.00 RPM	0.02 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3976 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3976 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3976 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017209	2 retrocopies	retro_cjac_3976 , retro_cjac_981,
Felis catus	ENSFCAG00000000094	2 retrocopies	retro_fcat_1139, retro_fcat_416,
Homo sapiens	ENSG00000178804	1 retrocopy	retro_hsap_2799,
Gorilla gorilla	ENSGGOG00000000735	1 retrocopy	retro_ggor_1946,
Myotis lucifugus	ENSMLUG00000025226	2 retrocopies	retro_mluc_1278, retro_mluc_1318,
Oryctolagus cuniculus	ENSOCUG00000029379	1 retrocopy	retro_ocun_1483,
Ochotona princeps	ENSOPRG00000010371	2 retrocopies	retro_opri_403, retro_opri_624,
Pongo abelii	ENSPPYG00000013414	1 retrocopy	retro_pabe_2225,
Pan troglodytes	ENSPTRG00000015380	1 retrocopy	retro_ptro_1896,
Pteropus vampyrus	ENSPVAG00000007110	1 retrocopy	retro_pvam_808,
Tursiops truncatus	ENSTTRG00000011276	1 retrocopy	retro_ttru_1111,