RetrogeneDB ID: retro_cjac_4000

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286894.1:215166..215827(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000017665
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PRDX6
• Ensembl ID: ENSCJAG00000009355
• Aliases: None
• Description: peroxiredoxin 6 [Source:HGNC Symbol;Acc:16753]

Sequence

>retro_cjac_4000
GGTCTGTTTCTTGGTAACTTGGCTCCCAACTTTGAGGCCAATACCACCGTCGGCTGCATCCGTTTCCAGGAACTTTCTGG
GAGACTCAAGGGACATTCTCTTTCCCACTCTCGGGACTTTATCCCAGTGTGTACCACAGAGCTTGGCAGAGCTGAAAAGC
TGGCACCAGAATTTGCCAAGGGGAATGTCGAGCTGATTCCCCTTTCAATAGACAGTGTTGAGGAAGGCCTTGCCTGGAGC
AAGGTCACCAATGCTTCCAGTGGTGAAGAGCCCAGAGAAGTCACCTTTTCCCATCACTGATGATAAGAATCGGGACCTTG
CCATCCTGTTGGGCATGCTGGGTCCAGCAGAGAAGGATGAAAAGGGGGTGCCTGTGACAGCTCATGTGGTGGTGTTTGTT
TTCAGTCCCGATAAGAAGCTGAAAATCTCTATCCTCTACCCAGCTACCACTGGCAGGAACTTTGATGACATTCTCAGGGT
ACTCATCTCTCTTCAGCTGACAGCAGAAAAGAGGGTTGCCACCCCAGTTGACAGGAAAGATGGGGATAATGTGATGGTCC
TTCCAACCATCCCTGAAAAAGAAGCCAAGAGACTTCTCACAAAAGGAGTCTTCACTAAAGAGCTCCCATCTGGCAAGAAA
TACCTCCACTACACCCCTCAG

Alignment

ORF - retro_cjac_4000 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.8 %
• Parental protein coverage: 98.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GLLLGDVAPNFEANTTVGPIRFHD-FLGDSWGILF-SHPRDFTPVCTTELGRAAKLAPEFAKRNVKLIAL
          GL.LG..APNFEANTTVG.IRF...FLGDS..ILF.SH.RDF.PVCTTELGRA.KLAPEFAK.NV.LI.L
Retrocopy GLFLGNLAPNFEANTTVGCIRFQE>FLGDSRDILF<SHSRDFIPVCTTELGRAEKLAPEFAKGNVELIPL

Parental  SIDSVEDHLAWSKDINAYNG-EEPTEKLPFPIIDDKNRDLAILLGMLDPAEKDEKGMPVTARVV-FVFGP
          SIDSVE..LAWSK..NA..G...P.EK.PFPI.DDKNRDLAILLGML.PAEKDEKG.PVTA.VV.FVF.P
Retrocopy SIDSVEEGLAWSKVTNASSG>KSP-EKSPFPITDDKNRDLAILLGMLGPAEKDEKGVPVTAHVVVFVFSP

Parental  DKKLKLSILYPATTGRNFDEILRVVISLQLTAEKRVATPVDWKDGDSVMVLPTIPEEEAKKLFPKGVFTK
          DKKLK.SILYPATTGRNFD.ILRV.ISLQLTAEKRVATPVD.KDGD.VMVLPTIPE.EAK.L..KGVFTK
Retrocopy DKKLKISILYPATTGRNFDDILRVLISLQLTAEKRVATPVDRKDGDNVMVLPTIPEKEAKRLLTKGVFTK

Parental  ELPSGKKYLRYTPQ
          ELPSGKKYL.YTPQ
Retrocopy ELPSGKKYLHYTPQ

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	55.91 RPM
SRP051959_heart	0.00 RPM	33.94 RPM
SRP051959_kidney	0.00 RPM	52.16 RPM
SRP051959_liver	0.00 RPM	77.55 RPM
SRP051959_lung	0.00 RPM	32.83 RPM
SRP051959_lymph_node	0.00 RPM	21.73 RPM
SRP051959_skeletal_muscle	0.00 RPM	21.44 RPM
SRP051959_spleen	0.00 RPM	27.42 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4000 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4000 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4000 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015560	1 retrocopy	retro_amel_493,
Bos taurus	ENSBTAG00000004855	2 retrocopies	retro_btau_1325, retro_btau_1477,
Canis familiaris	ENSCAFG00000014579	1 retrocopy	retro_cfam_492,
Choloepus hoffmanni	ENSCHOG00000011367	6 retrocopies	retro_chof_1143, retro_chof_1361, retro_chof_1364, retro_chof_225, retro_chof_2483, retro_chof_2598,
Callithrix jacchus	ENSCJAG00000009355	6 retrocopies	retro_cjac_1903, retro_cjac_2188, retro_cjac_3008, retro_cjac_3239, retro_cjac_3830, retro_cjac_4000 ,
Cavia porcellus	ENSCPOG00000011091	1 retrocopy	retro_cpor_623,
Equus caballus	ENSECAG00000022468	1 retrocopy	retro_ecab_215,
Erinaceus europaeus	ENSEEUG00000004040	1 retrocopy	retro_eeur_475,
Homo sapiens	ENSG00000117592	2 retrocopies	retro_hsap_1046, retro_hsap_3017,
Gorilla gorilla	ENSGGOG00000026357	1 retrocopy	retro_ggor_2086,
Macaca mulatta	ENSMMUG00000008776	1 retrocopy	retro_mmul_1928,
Monodelphis domestica	ENSMODG00000004032	2 retrocopies	retro_mdom_462, retro_mdom_661,
Mustela putorius furo	ENSMPUG00000004648	1 retrocopy	retro_mputfur_1328,
Mus musculus	ENSMUSG00000026701	2 retrocopies	retro_mmus_181, retro_mmus_2334,
Nomascus leucogenys	ENSNLEG00000015278	2 retrocopies	retro_nleu_2244, retro_nleu_917,
Pan troglodytes	ENSPTRG00000042455	1 retrocopy	retro_ptro_70,
Pteropus vampyrus	ENSPVAG00000002596	2 retrocopies	retro_pvam_1389, retro_pvam_805,
Rattus norvegicus	ENSRNOG00000002896	3 retrocopies	retro_rnor_2084, retro_rnor_754, retro_rnor_806,
Sarcophilus harrisii	ENSSHAG00000003248	1 retrocopy	retro_shar_478,
Tarsius syrichta	ENSTSYG00000010073	2 retrocopies	retro_tsyr_1395, retro_tsyr_193,
Tursiops truncatus	ENSTTRG00000008478	1 retrocopy	retro_ttru_1274,