RetrogeneDB ID: retro_cjac_692

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:60270028..60270890(+)
• Located in intron of: ENSCJAG00000006821

Retrocopy information

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

Parental gene information

• Parental gene symbol: QRSL1
• Ensembl ID: ENSCJAG00000006200
• Aliases: None
• Description: Glutamyl-tRNA(Gln) amidotransferase subunit A, mitochondrial [Source:UniProtKB/TrEMBL;Acc:F7HUD4]

Sequence

>retro_cjac_692
AATGCTACAGTATTTCAGAAGTTGTTGGATCAGGGAGCTCTACTAATGGAAAAAGAAATTTTGATGAGTTTGCTATGGGA
TCTACAAAAGCAGATGGTGTATTTGGACTAGTTAAAAATCCCTGGAATTATTCAAAACAATATAGAGAAAAGAGGAAGCA
AAATCTCCACTTTGAGAATGAAGATTCAGACTGGCTGATAACTGGAGGAAGTTCAGGTGGGAGTGCAGGTGCCATATCAG
CATCCACATGCTATGAGGCTTTAGGATCAGATACAGGAGGATTGACCAGAAATCCTGCTGCCCACTGTAGGCTTCCTGGT
TTCAAATCAAGCTATGGCTTAGTTTCCCATCATGGTCTCATTCCCCTGAAGAATTTGATAGATGTGCAAGGAATCTTAAC
CAGATGGGTGGATGATGCAGCAATTGTGTTGGGTGTACTGCTGGACATGACCCTACGGATTCTACCACAGTATAGGATTC
TGTTAAACCATTCTGGCTTCCCAGTTTGACAGATGTCAGCAAACTATGTATAGGAATTCCAAAGGAATATCTTATACCAG
AATTATAAAGTGAAGTACAGTCTCTTTGGTCCAAAGCTGCTGACCTCTTTGAGTCTGAAGGGGCCAAAATAACTGAAGTA
TCCTTTCCTCACACCAGTTATTCAATTGACTGCTACCATGTATTGTGCACATCGAAAGCAGCATCAAATATAGCAAGATT
TGATGGGCTACAATATGGTCACAAATGTGACACTGATGTGCCTACTGCAGCCATGCATGCTGCCACCAGATGAGAAAGGT
TCAATCATTTGGTAAGAGGAAGAATTCTCTTGGGAAATCTTTTCTTATTAAAAGAAAAGTAT

Alignment

ORF - retro_cjac_692 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.31 %
• Parental protein coverage: 54.56 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NATVVQKLLDQGALLM-GKTNLDEFAMGSGSTDGVFGPVKNPWSYSKQYREKRKQNPHSESGDSDWLITG
          NATV.QKLLDQGALLM.GK.N.DEFAMGS...DGVFG.VKNPW.YSKQYREKRKQN.H.E..DSDWLITG
Retrocopy NATVFQKLLDQGALLM<GKRNFDEFAMGSTKADGVFGLVKNPWNYSKQYREKRKQNLHFENEDSDWLITG

Parental  GSSGGSAAAVSAFTCYAALGSDTGGSTRNPAAHCGLVGFKPSYGLVSRHGLIPLVNSMDVPGILTRYVDD
          GSSGGSA.A.SA.TCY.ALGSDTGG.TRNPAAHC.L.GFK.SYGLVS.HGLIPL.N..DV.GILTR.VDD
Retrocopy GSSGGSAGAISASTCYEALGSDTGGLTRNPAAHCRLPGFKSSYGLVSHHGLIPLKNLIDVQGILTRWVDD

Parental  AAIVLGVL-AGHDPKDSTTV-PINKPLVLSSLEDVSKLCIGIPKEYLVPELSSEIQSLWSRAADLFESEG
          AAIVLGVL.AGHDP.DSTTV....KP..L.SL.DVSKLCIGIPKEYL.PEL.SE.QSLWS.AADLFESEG
Retrocopy AAIVLGVL<AGHDPTDSTTV*DSVKPFWLPSLTDVSKLCIGIPKEYLIPEL*SEVQSLWSKAADLFESEG

Parental  AKVIEVSLPHTSYSIVCYHVLCTSEVASNMARFDGLQYGHRCDIDVSTEAMYAATRREGFNDVVRGRILS
          AK..EVS.PHTSYSI.CYHVLCTS..ASN.ARFDGLQYGH.CD.DV.T.AM.AATR.E.FN..VRGRIL.
Retrocopy AKITEVSFPHTSYSIDCYHVLCTSKAASNIARFDGLQYGHKCDTDVPTAAMHAATR*ERFNHLVRGRILL

Parental  GNFFLLKENY
          GN.FLLKE.Y
Retrocopy GNLFLLKEKY

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	1.02 RPM	6.17 RPM
SRP051959_heart	1.05 RPM	12.56 RPM
SRP051959_kidney	0.93 RPM	12.09 RPM
SRP051959_liver	0.41 RPM	7.21 RPM
SRP051959_lung	1.17 RPM	5.58 RPM
SRP051959_lymph_node	0.82 RPM	4.34 RPM
SRP051959_skeletal_muscle	1.24 RPM	37.76 RPM
SRP051959_spleen	0.71 RPM	5.13 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_692 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_692 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_692 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1321
Pan troglodytes	retro_ptro_902
Gorilla gorilla	retro_ggor_1031
Pongo abelii	retro_pabe_1100

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017557	3 retrocopies	retro_btau_476, retro_btau_493, retro_btau_616,
Choloepus hoffmanni	ENSCHOG00000001036	1 retrocopy	retro_chof_2382,
Callithrix jacchus	ENSCJAG00000006200	4 retrocopies	retro_cjac_1421, retro_cjac_3781, retro_cjac_3919, retro_cjac_692 ,
Cavia porcellus	ENSCPOG00000021670	1 retrocopy	retro_cpor_179,
Homo sapiens	ENSG00000130348	3 retrocopies	retro_hsap_1321, retro_hsap_466, retro_hsap_514,
Gorilla gorilla	ENSGGOG00000008261	3 retrocopies	retro_ggor_1031, retro_ggor_445, retro_ggor_474,
Macaca mulatta	ENSMMUG00000008330	2 retrocopies	retro_mmul_429, retro_mmul_675,
Nomascus leucogenys	ENSNLEG00000013383	2 retrocopies	retro_nleu_1403, retro_nleu_1550,
Pongo abelii	ENSPPYG00000016883	3 retrocopies	retro_pabe_1100, retro_pabe_230, retro_pabe_268,
Pan troglodytes	ENSPTRG00000018462	2 retrocopies	retro_ptro_351, retro_ptro_902,