RetrogeneDB ID: retro_cjac_3781

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01201113.1:600..2170(-)
• Located in intron of: None

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_3781
ATGCTGGGCTGGACCCTTTGATAAGTTTCTGTGGCACTGCAACAAGGACAAATTACAACAGAGCTCTGTCAAAAATGTCT
TCCTCTTATCAGGAAGACCAACTTTCTAAATGCTTACATTACTGTATCGGAAGAGTTGGCCTTAAAACAAGCTGTACAAT
TAGAAAAGAGATATAAGAACAGACAGTCACTTGGGGATTAAATGGAATTCCTATTGCAGTAAAAGACAACCTTAACATGT
CTGGCATTGAGACAGCATGTGTGTCAAATATGCTGAAGGGTTATGTGCCACCTTATAATGCTGCAGTAGTTCAGAAGTTG
TTGGATCAGGGAGCTCTACTAACAGGAAAAACAAATTTAGATGACTTTGCTATGGGATCTGGAAGCACAGATGGTGTATT
TGGACCAGTTAAAAACCCCTGAAGTTATTCAAAACAATATAGATAAAAGAGGAAGCAGAATCCCCACAGCAAGAATCAAG
ATTCAGACTGGCTGATAACTGGAGGAAGCTCAGATGGGAGTGCAGCTGCTGTGTCAGCACTCACATGCTATGCGGCTTTA
GGATCAGATACAGGAGGATCGACCAGAAATCCTGCTGCCCACTGTGGGCTTGTTGGTTTCAAACCAAACTATGTCTTAGT
TTCCCATCATGGCCTCATTCTCCTGCTGAATTTGATGGATGTGTCAGGAATTTTAACCAGATGTGTGGATGATGCAGCAA
TTGTATTGGGTGTCCTGGCTGGACATGACCCCAGGGATTCTACCACAGTACATGATCCTATTAATAAGCCACTCGTGCTT
TCCAGTTAGACAGATGTGAGCAAACTATGAATGGGAATTTTGAAGGAATATATTGTAACAGAATTATCAAGTGAAATACA
GTCTCTCTGGTCCAGAGCTGCTAAGCTCTTTTAGTCTGAGGGGGCCAAAGTGATTGAGAAGTATCCCTTCCTCACACCAG
TTATTCAGTTGTCTGCTACCATGTATTGTGCACAATGGAAGTGGCATCGAATATGGCAAGATTTGATGGGCTACAATATG
GTCACAGGTGTGACATTGATGTGTCCACTGAAGCCATGTATGCTGCGACCAGATGAGAAGGGTTCAATGATGTGGTGAGA
AGAAGAATTCTCTCAGGAAACATTTTCTTATTAAAAGAAAACTATGAAAATTATTTTGTCAAAGCACAGAAAGTGAGACA
GCTCACTGCTAATGACTTTGTGATTCCTTTTAACTATGGAGTAGATGTCTTGCTAACTCCTACCACCGTGAGTGAGGCAG
TACCATACTTGGAGTTCATCAAAGAGGACAACAGAACACAAAGTGCCCAGGATGCTATTTTTACACAAGCTGTAAATAAG
GCAGGATTGCCAGCAGTGAGTATCCCTGTTGCACTCTCAAACCAAGGGCTGCCAATAGGACTGCAGTTTATTGGATGTGC
ATTTTATGACCAGCAGCTTCTTACAGTGGCCAAATGGTTTGAAAAACAAGTGCAGTTTCCTGTTATTCCACTTCAAGAAT
TCATGAATGATTGGTCAGCAATCCTTGAAAATGATTAACTTCTGTCTCTC

Alignment

ORF - retro_cjac_3781 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.68 %
• Parental protein coverage: 99.24 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MLGQTLREVSAALKQGQITPTELCQKCLSLIKKTKFLNAYITVSEEVALKQAEESEKRYKNGQSLGD-LD
          MLG.TL..VS.AL.QGQIT.TELCQKCL.LI.KT.FLNAYITVSEE.ALKQA...EKRYKN.QSLGD.L.
Retrocopy MLGWTL**VSVALQQGQIT-TELCQKCLPLIRKTNFLNAYITVSEELALKQAVQLEKRYKNRQSLGD<LN

Parental  GIPIAVKDNFSTSGIETTCASNMLKGYVPPYNATVVQKLLDQGALLMGKTNLDEFAMGSGSTDGVFGPVK
          GIPIAVKDN...SGIET.C.SNMLKGYVPPYNA.VVQKLLDQGALL.GKTNLD.FAMGSGSTDGVFGPVK
Retrocopy GIPIAVKDNLNMSGIETACVSNMLKGYVPPYNAAVVQKLLDQGALLTGKTNLDDFAMGSGSTDGVFGPVK

Parental  NPWSYSKQYREKRKQNPHSESGDSDWLITGGSSGGSAAAVSAFTCYAALGSDTGGSTRNPAAHCGLVGFK
          NP.SYSKQYR.KRKQNPHS...DSDWLITGGSS.GSAAAVSA.TCYAALGSDTGGSTRNPAAHCGLVGFK
Retrocopy NP*SYSKQYR*KRKQNPHSKNQDSDWLITGGSSDGSAAAVSALTCYAALGSDTGGSTRNPAAHCGLVGFK

Parental  PSYGLVSRHGLIPLVNSMDVPGILTRYVDDAAIVLGVLAGHDPKDSTTV--PINKPLVLSSLEDVSKLCI
          P.Y.LVS.HGLI.L.N.MDV.GILTR.VDDAAIVLGVLAGHDP.DSTTV..PINKPLVLSS..DVSKL..
Retrocopy PNYVLVSHHGLILLLNLMDVSGILTRCVDDAAIVLGVLAGHDPRDSTTVHDPINKPLVLSS*TDVSKL*M

Parental  GIPKEYLVPELSSEIQSLWSRAADL-FESEGAKVI-EVSLPHTSYSIVCYHVLCTSEVASNMARFDGLQY
          GI.KEY.V.ELSSEIQSLWSRAA.L.F...G.K...EVSLPHTSYS.VCYHVLCT.EVASNMARFDGLQY
Retrocopy GILKEYIVTELSSEIQSLWSRAAKL>FSLRGPK*L>EVSLPHTSYSVVCYHVLCTMEVASNMARFDGLQY

Parental  GHRCDIDVSTEAMYAATRREGFNDVVRGRILSGNFFLLKENYENYFVKAQKVRRLIANDFVNAFNSGVDV
          GHRCDIDVSTEAMYAATR.EGFNDVVR.RILSGN.FLLKENYENYFVKAQKVR.L.ANDFV..FN.GVDV
Retrocopy GHRCDIDVSTEAMYAATR*EGFNDVVRRRILSGNIFLLKENYENYFVKAQKVRQLTANDFVIPFNYGVDV

Parental  LLTPTTLSEAVPYLEFIKEDNRTRSAQDDIFTQAVNMAGLPAVNIPIALSNQGLPIGLQFIGRAFCDQQL
          LLTPTT.SEAVPYLEFIKEDNRT.SAQD.IFTQAVN.AGLPAV.IP.ALSNQGLPIGLQFIG.AF.DQQL
Retrocopy LLTPTTVSEAVPYLEFIKEDNRTQSAQDAIFTQAVNKAGLPAVSIPVALSNQGLPIGLQFIGCAFYDQQL

Parental  LTVAKWFEKQVQFPVIQLQELVDNCSAILENEKLASV
          LTVAKWFEKQVQFPVI.LQE.....SAILEN..L.S.
Retrocopy LTVAKWFEKQVQFPVIPLQEFMNDWSAILEND*LLSL

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	6.17 RPM
SRP051959_heart	0.02 RPM	12.56 RPM
SRP051959_kidney	0.00 RPM	12.09 RPM
SRP051959_liver	0.00 RPM	7.21 RPM
SRP051959_lung	0.02 RPM	5.58 RPM
SRP051959_lymph_node	0.00 RPM	4.34 RPM
SRP051959_skeletal_muscle	0.00 RPM	37.76 RPM
SRP051959_spleen	0.00 RPM	5.13 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3781 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3781 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3781 has 0 orthologous retrocopies within eutheria group .

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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,