RetrogeneDB ID: retro_cjac_2454

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:92232804..92233434(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COPS5
• Ensembl ID: ENSCJAG00000004632
• Aliases: None
• Description: None

Sequence

>retro_cjac_2454
ATGGCAGCCTCTGGGAGTGGTATGGTCCAGAAAACCTGGGAACTGGCCAAAAACATGCATGAAGCTCAGAGTATCAATGA
AATCTACAAATATGACAAGAAGTAGCAGCAAGAAATACTGGCAGCAAAACCCTGGGTTAGCAATCACTATTACTTTAAAG
TACTGCAAAATCTCAGCATTGGCTCTACTGAAGATGGTGATGCATGCCAGATCAGGGGGCAACTCGGAAGTTGTGGGTTG
GATGCCAGGAAAGGTGGATGGCAAAACCACAATTGTTATGGGCTGTTTTACTTTGCTTGTAGAAGGCACTGAAACCTGAG
AAAATGCTTAGGCTGTTGCATATGAGTACACAGCCACATACATAGAAAATGCCAACCAGGTTGGCTGCCTTAACAATGCA
GTCGGATGGTATTATAGGCACCCTGGCCATGGCTGCTGGCTTTCTGGGATCATGTTAGTACTCAGCTGCTCAATAAGCAG
TTCCGGAAACCATTTACAGCAGTGGCGATTGATCCAACAAGAACAGTATCTGCAGGGAAAGTGAATCTTGATGCCTTTAG
GGCATACCCAAAGGGCTGCAAACCTCCTAATAAAGGACCTTCTGAGTACCAGACTATCCCGCTTAGTAAA

Alignment

ORF - retro_cjac_2454 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.89 %
• Parental protein coverage: 62.87 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAASGSGMAQKTWELANNMQEAQSIDEIYKYDKKQQQEILAAKPWTKDHHYF-KYCKISALALLKMVMHA
          MAASGSGM.QKTWELA.NM.EAQSI.EIYKYDKK.QQEILAAKPW...H.YF.KYCKISALALLKMVMHA
Retrocopy MAASGSGMVQKTWELAKNMHEAQSINEIYKYDKK*QQEILAAKPWVSNHYYF>KYCKISALALLKMVMHA

Parental  RSGGNLEVMGLMLGKVDGETMIIMDSFALPVEGTETRVNAQAAAYEYMAAYIENAKQVGRLENAIGWYHS
          RSGGN.EV.G.M.GKVDG.T.I.M..F.L.VEGTET..NA.A.AYEY.A.YIENA.QVG.L.NA.GWY..
Retrocopy RSGGNSEVVGWMPGKVDGKTTIVMGCFTLLVEGTET*ENA*AVAYEYTATYIENANQVGCLNNAVGWYYR

Parental  HPGYGCWLSGI-DVSTQMLNQQFQEPFVAVVIDPTRTISAGKVNLGAFRTYPKGYKPPDEGPSEYQTIPL
          HPG.GCWLSGI..VSTQ.LN.QF..PF.AV.IDPTRT.SAGKVNL.AFR.YPKG.KPP..GPSEYQTIPL
Retrocopy HPGHGCWLSGI<HVSTQLLNKQFRKPFTAVAIDPTRTVSAGKVNLDAFRAYPKGCKPPNKGPSEYQTIPL

Parental  NK
          .K
Retrocopy SK

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	10.41 RPM
SRP051959_heart	0.00 RPM	14.10 RPM
SRP051959_kidney	0.00 RPM	14.40 RPM
SRP051959_liver	0.00 RPM	16.59 RPM
SRP051959_lung	0.00 RPM	11.18 RPM
SRP051959_lymph_node	0.00 RPM	10.94 RPM
SRP051959_skeletal_muscle	0.00 RPM	25.73 RPM
SRP051959_spleen	0.00 RPM	11.13 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2454 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2454 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2454 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3634
Pan troglodytes	retro_ptro_2457
Gorilla gorilla	retro_ggor_2451
Pongo abelii	retro_pabe_2980

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002028	1 retrocopy	retro_chof_556,
Callithrix jacchus	ENSCJAG00000004632	1 retrocopy	retro_cjac_2454 ,
Homo sapiens	ENSG00000121022	1 retrocopy	retro_hsap_3634,
Gorilla gorilla	ENSGGOG00000016289	1 retrocopy	retro_ggor_2451,
Microcebus murinus	ENSMICG00000011042	1 retrocopy	retro_mmur_834,
Myotis lucifugus	ENSMLUG00000011697	1 retrocopy	retro_mluc_1528,
Monodelphis domestica	ENSMODG00000007838	1 retrocopy	retro_mdom_1460,
Mustela putorius furo	ENSMPUG00000010175	1 retrocopy	retro_mputfur_397,
Nomascus leucogenys	ENSNLEG00000010914	1 retrocopy	retro_nleu_815,
Pongo abelii	ENSPPYG00000018648	1 retrocopy	retro_pabe_2980,
Pan troglodytes	ENSPTRG00000020317	2 retrocopies	retro_ptro_2457, retro_ptro_638,
Tupaia belangeri	ENSTBEG00000008440	7 retrocopies	retro_tbel_1083, retro_tbel_1833, retro_tbel_1853, retro_tbel_2528, retro_tbel_3147, retro_tbel_3896, retro_tbel_3914,