RetrogeneDB ID: retro_cjac_4119

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:116332005..116332860(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RUVBL2
• Ensembl ID: ENSCJAG00000000222
• Aliases: None
• Description: None

Sequence

>retro_cjac_4119
ATGGCAACTGTGATGGCCATGACCAAAGTCCTGGGAATCTAAGATGTGAGGAGGATTGAGCATAGAGGTGTTCACTCTCC
CGTCTAAGGATTGGGCCTGGATGATGCTTTGGAGTCTCGACAGACCTCCCAGGGCATAGTGGGTCAGCTTAGCTGCACAG
TGGGCACTGATGTGGAGCTGGAGATGATCCACAAAGGGAAGACCATCAAGTAGGAAGTTCTCATTGCTCATCAACTGGGC
AAAGGAAAGATAGCCATTGTTGTAGGCATGGCATAGGTCCTGGGACCTAACACCTTGTTCACAGCCATCACTGGCAGTGA
GATCTTCCTGGAAATGAGCCAGACTGAGGCACTGACACAGGCTTTCTGGCCACCTTTTGGCATTTGCTTCAATGAGAAGA
TGGAGAACATCGAAGGTGAAGAGGTTGAGATCCAGATCGATAGAACAGTGAGAGGAATGGGCTCCAAGGTGAGCAAACCG
GCCATCAAAACCACAAAGATGGAGACCATCTATGACCTGGGAATCAAGATGATTGAGTCCCCGACCAAAGACAAGGTCCA
TGCTGGTGACATGATCACCGCTGACAAAGCAATGGTCAAGATCTCCAAGTTGGACCATTCCTTCACATGCTCCTGTGATT
ACAACACCATGGATTCCCAGAACAAATTCAGGCGGTGCCCAGATAGGAAGCTCCAGAAATGCAAGGTGCACACTGTGTCC
CTTGCATAAGATCAACATCATCAACTCCCACACCCATGGCTTCCTGGCTTCTTCTCATGTGATGCAAGAGAGATAAAGAC
AGAAGTTGGCAAGGAGATCAATGTCAAGGTGGCCAAGTGGATGAAACAAAATAGA

Alignment

ORF - retro_cjac_4119 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.41 %
• Parental protein coverage: 62.12 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MATVTA-TKVPEIRDVTRIERIGAHSHIRGLGLDDALEPRQASQGMVGQLAARRAAGVVLEMIREGKIAG
          MATV.A.TKV..I.DV.RIE..G.HS...GLGLDDALE.RQ.SQG.VGQL.......V.LEMI..GK...
Retrocopy MATVMAMTKVLGI*DVRRIEHRGVHSPV*GLGLDDALESRQTSQGIVGQLSCTVGTDVELEMIHKGKTIK

Parental  RAVLIAGQPGTGKTAIAMGMAQALGPDTPFTAIAGSEIFSLEMSKTEALTQAFRRSIGVRIKEETEIIEG
          ..VLIA.Q.G.GK.AI..GMA..LGP.T.FTAI.GSEIF.LEMS.TEALTQAF....G....E..E.IEG
Retrocopy *EVLIAHQLGKGKIAIVVGMA*VLGPNTLFTAITGSEIF-LEMSQTEALTQAFWPPFGICFNEKMENIEG

Parental  EVVEIQIDRPATGTGSKVGKLTLKTTEMETIYDLGTKMIESLTKDKVQAGDVITIDKATGKISKLGRSFT
          E.VEIQIDR...G.GSKV.K...KTT.METIYDLG.KMIES.TKDKV.AGD.IT.DKA..KISKL..SFT
Retrocopy EEVEIQIDRTVRGMGSKVSKPAIKTTKMETIYDLGIKMIESPTKDKVHAGDMITADKAMVKISKLDHSFT

Parental  RARDYDAMGSQTKFVQCPDGELQKRKEVVHTVS-LHEIDVINSRTQGFLA-LFSGDTGEIKSEVREQINA
          ...DY..M.SQ.KF..CPD..LQK.K..VHTVS.LH.I..INS.T.GFLA..FS.D..EIK.EV...IN.
Retrocopy CSCDYNTMDSQNKFRRCPDRKLQKCK--VHTVS>LHKINIINSHTHGFLA<FFSCDAREIKTEVGKEINV

Parental  KVAEWREEGK
          KVA.W.....
Retrocopy KVAKWMKQNR

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	11.49 RPM
SRP051959_heart	0.00 RPM	9.51 RPM
SRP051959_kidney	0.00 RPM	11.38 RPM
SRP051959_liver	0.06 RPM	10.83 RPM
SRP051959_lung	0.00 RPM	10.80 RPM
SRP051959_lymph_node	0.00 RPM	9.34 RPM
SRP051959_skeletal_muscle	0.00 RPM	16.60 RPM
SRP051959_spleen	0.00 RPM	7.58 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4119 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4119 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4119 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000222	2 retrocopies	retro_cjac_329, retro_cjac_4119 ,
Homo sapiens	ENSG00000183207	1 retrocopy	retro_hsap_4755,
Gorilla gorilla	ENSGGOG00000009245	1 retrocopy	retro_ggor_2961,
Macropus eugenii	ENSMEUG00000000069	1 retrocopy	retro_meug_2099,
Macaca mulatta	ENSMMUG00000003915	1 retrocopy	retro_mmul_2536,
Nomascus leucogenys	ENSNLEG00000004769	1 retrocopy	retro_nleu_1251,
Otolemur garnettii	ENSOGAG00000007519	2 retrocopies	retro_ogar_2473, retro_ogar_3246,
Pongo abelii	ENSPPYG00000010225	1 retrocopy	retro_pabe_3701,
Pan troglodytes	ENSPTRG00000011270	1 retrocopy	retro_ptro_3168,