RetrogeneDB ID: retro_cjac_3919

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286240.1:5096..6666(-)
• 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_3919
CTGCTGGGTTGGACCCTTCGATAAGTTTCTGTGGCACTGCAACAAGGACAAATTACAACAGAGCTCTGTCAAAAATGTCT
TCCTCTTATCAGGAAGACCAAGTTTCTAAATGCTTACATTACTGTGTCGGAAGAGTTAGCCTTAAAACAAGCTGAAAAAT
TAGAAAAGAGATATAAGAACAGACAGTCACTTGGGGATTAAATGGAATTCCTATTGCAGTAAAAGACAACCTTAACATGT
CTGGCATTGAGAAAACATGTGCATCAAATATGCTGAAGGGTTATGTGCCACCTTATAATGCTGCAGTAGTTCAGAAGTTG
TTGGATCAGGGAGCTCTACTAACAGGAAAAACAAATTTAGATGACTTTGCTATGGGATCTGGAAGCACAGATGGTGTATT
TGGACCAGTTAAAAACCCCTGAAGTTATTCAAAACAATATAGATAAAAGAGGAAGCAGAATCCCCACAGCAAGAATCAAG
ATTCAGACTGGCTGATAACTGGAGGAAGCTCAGATGGGAGTGCAGCTGCTGTGTCAGCACTCACATGCTATGCGGCTTTA
GGATCAGATACAGGAAGATCGACCAGAAATCCTGCTGCCCACTGTGGGCTTGTTGGTTTCAAACCAAGCTATGTCTTAGT
TTCCCATCATGGCCTCATTCTCCTGGTGAATTTGATGGATGTGTCAGGAATCTTAACCAGATGTGTGGATGATGCAGCAA
TTGTATTGGGTGTCCTGGCTGGACATGACCCCAGGGATTCTACCACAGTACATGATCCTATTAATAAGCCACTCGTGCTT
TCCAGTTAGACAGATGTGAGCAAACTATGAATGGGAATTTTGAAGGAATATCTTGTAACAGAATTATCAAGTGAAATACA
GTCTCTCTGGTCCAGAGCTGCTAAGCTCTTTTAGTCTGAGGGGGCCAAAGTGATTGAGAAGTATCCCTTCCTCACACCAG
TTATTCAGTTGTCTGCTACCATGTATTGTGCACATTGGAAGTGGCATTGAATATGGCAAGATTTGATGGGCTACAATATG
GTCACACATGTGACATTGATGTGTCCACTGAAGCCATGTATGCTGCGACCAGATGAGAAGAGTTCAATGATGTGGTGAGA
AGAAGAATTCTCTCAGGAAACATTTTCTTATTAAAAGAAAACTATGAAAATTATTTTGTCAAAGCACAGAAAGTGAGACA
CCTCACTGCTAATGACTTTGTGATTCCTTTTAACTCTGGAGTAGATGTCTTGTTAACTCCTACCACCGTGAGTGAGGCAG
TACCATACTTGGAGTTCATCAAAGAGGACAACAGAACACAAAGTGCCCAGGATGCTATTTTTACACAAGCTGTAAATAAG
GCAGGATTGCCAGCAGTGAGTATCCCTGTTGCACTCTCAAACCAAGGGCTGCCAATAGGACTGAAGTTTATTGGATGTGC
ATTTTATGACCAGCAGCTTCTTACAGTGGCCAAATGGTTTGAAAAACAAGTGCAGTTTCCTGTTATTCCACTTCAAGATT
TCATGGATGATTGGTCAGCAATCCTTGAAAATGATTAACTTCTGTCTCTC

Alignment

ORF - retro_cjac_3919 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.06 %
• Parental protein coverage: 99.24 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MLGQTLREVSAALKQGQITPTELCQKCLSLIKKTKFLNAYITVSEEVALKQAEESEKRYKNGQSLGD-LD
          .LG.TLR.VS.AL.QGQIT.TELCQKCL.LI.KTKFLNAYITVSEE.ALKQAE..EKRYKN.QSLGD.L.
Retrocopy LLGWTLR*VSVALQQGQIT-TELCQKCLPLIRKTKFLNAYITVSEELALKQAEKLEKRYKNRQSLGD<LN

Parental  GIPIAVKDNFSTSGIETTCASNMLKGYVPPYNATVVQKLLDQGALLMGKTNLDEFAMGSGSTDGVFGPVK
          GIPIAVKDN...SGIE.TCASNMLKGYVPPYNA.VVQKLLDQGALL.GKTNLD.FAMGSGSTDGVFGPVK
Retrocopy GIPIAVKDNLNMSGIEKTCASNMLKGYVPPYNAAVVQKLLDQGALLTGKTNLDDFAMGSGSTDGVFGPVK

Parental  NPWSYSKQYREKRKQNPHSESGDSDWLITGGSSGGSAAAVSAFTCYAALGSDTGGSTRNPAAHCGLVGFK
          NP.SYSKQYR.KRKQNPHS...DSDWLITGGSS.GSAAAVSA.TCYAALGSDTG.STRNPAAHCGLVGFK
Retrocopy NP*SYSKQYR*KRKQNPHSKNQDSDWLITGGSSDGSAAAVSALTCYAALGSDTGRSTRNPAAHCGLVGFK

Parental  PSYGLVSRHGLIPLVNSMDVPGILTRYVDDAAIVLGVLAGHDPKDSTTV--PINKPLVLSSLEDVSKLCI
          PSY.LVS.HGLI.LVN.MDV.GILTR.VDDAAIVLGVLAGHDP.DSTTV..PINKPLVLSS..DVSKL..
Retrocopy PSYVLVSHHGLILLVNLMDVSGILTRCVDDAAIVLGVLAGHDPRDSTTVHDPINKPLVLSS*TDVSKL*M

Parental  GIPKEYLVPELSSEIQSLWSRAADL-FESEGAKVI-EVSLPHTSYSIVCYHVLCTSEVASNMARFDGLQY
          GI.KEYLV.ELSSEIQSLWSRAA.L.F...G.K...EVSLPHTSYS.VCYHVLCT.EVA.NMARFDGLQY
Retrocopy GILKEYLVTELSSEIQSLWSRAAKL>FSLRGPK*L>EVSLPHTSYSVVCYHVLCTLEVALNMARFDGLQY

Parental  GHRCDIDVSTEAMYAATRREGFNDVVRGRILSGNFFLLKENYENYFVKAQKVRRLIANDFVNAFNSGVDV
          GH.CDIDVSTEAMYAATR.E.FNDVVR.RILSGN.FLLKENYENYFVKAQKVR.L.ANDFV..FNSGVDV
Retrocopy GHTCDIDVSTEAMYAATR*EEFNDVVRRRILSGNIFLLKENYENYFVKAQKVRHLTANDFVIPFNSGVDV

Parental  LLTPTTLSEAVPYLEFIKEDNRTRSAQDDIFTQAVNMAGLPAVNIPIALSNQGLPIGLQFIGRAFCDQQL
          LLTPTT.SEAVPYLEFIKEDNRT.SAQD.IFTQAVN.AGLPAV.IP.ALSNQGLPIGL.FIG.AF.DQQL
Retrocopy LLTPTTVSEAVPYLEFIKEDNRTQSAQDAIFTQAVNKAGLPAVSIPVALSNQGLPIGLKFIGCAFYDQQL

Parental  LTVAKWFEKQVQFPVIQLQELVDNCSAILENEKLASV
          LTVAKWFEKQVQFPVI.LQ...D..SAILEN..L.S.
Retrocopy LTVAKWFEKQVQFPVIPLQDFMDDWSAILEND*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	0.02 RPM	6.17 RPM
SRP051959_heart	0.07 RPM	12.56 RPM
SRP051959_kidney	0.02 RPM	12.09 RPM
SRP051959_liver	0.00 RPM	7.21 RPM
SRP051959_lung	0.00 RPM	5.58 RPM
SRP051959_lymph_node	0.02 RPM	4.34 RPM
SRP051959_skeletal_muscle	0.04 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_3919 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3919 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3919 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,