RetrogeneDB ID: retro_cjac_981

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:53235001..53235867(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000014769
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cjac_981
GGCCCAAGCCACAGCAGCTTCCCAGTGGGATGCCGCCACCCCACCGTGCTGCGCATGGTGCTGGATGTGCTGCAGGCAGG
GGAGCAGTGTCGGGGCACATCGGTGGCAGCCATCAAGCTCTACATCTTGCAAAAGTACCCAGCGGTGGATGTCCTTCGCT
TCAAGTACCTGCTGAAGAAGGCGCTGGCCATTGGCATGTGCCGTGGCCTCCTCGCCAGGCCCCTCAACTCCAAAGCCAGC
GGGGCCACTGGCAGCTTCAAATTAGTTACCAAGTACAAGAGGAAAATCAAGCCCAGGAAGATGGCTTCCCCGAAGGCCCC
CAGGAGAGCAGGCGAGGCCAAGGGGAAGTCTTTAAGAAACCAGATGAGGCCAAGGAGGAGGCTTCCAAGGCAGGCAAGGT
GAAAAAGGCAGCCAAGAGGCCAACAGAGGTGCAGAAGTTTCCTCTCAAGACAGGCACAGCCACAGAAAAAGCTCACAAAC
AAGGCAGCAAGGCCAAGGACACCAAGGCACAGCCAGGCGAAGCTCAGAAGGTGCCCCCCAAGCCAGACAAGGCCATGCAG
GCCTCTTCTAATGTCAGCAGGTTCAGCAGGAAGGCAGAGGCCAAAGGAAGCAGGAGGAGCCAAGGAGATGCTGAGGCCTG
CAGGAACACCAAAACCGGGAGTAGGAGTTCAAGACCTACGGTCAGCAAGGTCAAGAATGGTGCTGCTTCCCCAACCAAAA
AGAAGTTGGTGGCCAAGGCCAAGGCCCAGGCCCCTAGAGGGGCAGCTGCCCCTGGGGCTGGGCAGGGGCTGAATGCCAAG
GGTGCTTCTGCTAAGGCCAATGGGTCCAAGGTGGTGCCTGCACACTTGTCCAGGAAGACAGAGGCC

Alignment

ORF - retro_cjac_981 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.06 %
• Parental protein coverage: 91.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GPSRSSFPVGRRHPPTLQMVLEAMQVLQAEEQRQGTSVVAIKRYILRKYPAADGPRFKYLLKNALATGMC
          GPS.SSFPVG.RHP..L.MVL....VLQA.EQ..GTSV.AIK.YIL.KYPA.D..RFKYLLK.ALA.GMC
Retrocopy GPSHSSFPVGCRHPTVLRMVLD---VLQAGEQCRGTSVAAIKLYILQKYPAVDVLRFKYLLKKALAIGMC

Parental  RGLLARPPHLKTRGATGSFQLVTNHERTIKPRKTASPKAPRRAGVAKGK-VPKKPDEAKEEPPKAGKGKK
          RGLLARP...K..GATGSF.LVT...R.IKPRK.ASPKAPRRAG.AKGK.V.KKPDEAKEE..KAGK.KK
Retrocopy RGLLARPLNSKASGATGSFKLVTKYKRKIKPRKMASPKAPRRAGEAKGK<VFKKPDEAKEEASKAGKVKK

Parental  GAKSPAEVQKPPLKPGTDTEKACKESSKAKDTEAQPGEAQKVPPKPDKAMRAPSNDSGFSRRAEVKGSWR
          .AK.P.EVQK.PLK.GT.TEKA.K..SKAKDT.AQPGEAQKVPPKPDKAM.A.SN.S.FSR.AE.KGS.R
Retrocopy AAKRPTEVQKFPLKTGTATEKAHKQGSKAKDTKAQPGEAQKVPPKPDKAMQASSNVSRFSRKAEAKGSRR

Parental  SPGGAEASRKTKAGSKSLRPTVSKVKSGTASLTEKKSVARAKAQS-QAPAPTGAGQGPNAKGASAKAGGS
          S.G.AEA.R.TK.GS.S.RPTVSKVK.G.AS.T.KK.VA.AKAQ.....A..GAGQG.NAKGASAKA.GS
Retrocopy SQGDAEACRNTKTGSRSSRPTVSKVKNGAASPTKKKLVAKAKAQAPRGAAAPGAGQGLNAKGASAKANGS

Parental  KVVPAHLSRKTEA
          KVVPAHLSRKTEA
Retrocopy KVVPAHLSRKTEA

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	0.02 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_981 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_981 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_981 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,