RetrogeneDB ID: retro_hsap_466

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:168419670..168420449(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000215833
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: QRSL1
• Ensembl ID: ENSG00000130348
• Aliases: QRSL1, GatA
• Description: glutaminyl-tRNA synthase (glutamine-hydrolyzing)-like 1 [Source:HGNC Symbol;Acc:21020]

Sequence

>retro_hsap_466
ATGCTGGGCCGGACCCTCTGAGAAGTTTCTGCAGCACTGAAACAAGGCCAGATTACGCCAACAGAGCTCTGTCAAAAATG
TCTCTCTCTTATCAAGAAGACCAAGTTTCTACATGCCTACATTACTGCATCAGAAGAGGTGGCCTTAAAACAAGCTGAAG
AATCAGAAAAGAGATATAAGCATGAACAGTCACTTGGGGATTTAGATGGAATTCCTATTGCAGTAAAAGACAACTTTAGC
ACATCTGGCATTGAGACAACATGTGCATCAAATATGCTGAAAGGTTATGTACCACCTTATAACGCTAGAGTAGTTCCGAA
GTTGTTGGATCAGGGAGCTCTACTAATAGGAAAAACAAATTTAGATGAGTTTGCTATTGGATCTGTAAGAACAGATGGTG
TGTTTGGACCAGTTAAAAACCCCTGAGTTATTCAAAATAATATAGAGAAAAGAGGAAGCAGAATCCCCACAGCAAGAATG
AAGATTCAGACTGGCTGATAACTGGAGGAAGCTCAGGTGGGAGTGAGGCTGCTATGTCGGCTTTAGGATCAGCTACAGAA
GGATCGACCAGAAATCCTGCTGCTCACTGCAGGCTTGTTGGTTTCAAACCAAGCTATGGTTTAGTTTCCCATCATGGTCT
CATTCTCCTGGTGAACTTGATGGATGTGCCAGGAATCTTAACCAGATGTGTGGATGATGCAGCAATTGTGTTGAGTGTAC
AGGCTGGACATGACACCAATGATTGTACCACAGTATAGGACCCTATTAAACCATTTATT

Alignment

ORF - retro_hsap_466 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.09 %
• Parental protein coverage: 50.57 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLGRSLREVSAALKQGQITPTELCQKCLSLIKKTKFLNAYITVSEEVALKQAEESEKRYKNGQSLGDLDG
          MLGR.L.EVSAALKQGQITPTELCQKCLSLIKKTKFL.AYIT.SEEVALKQAEESEKRYK..QSLGDLDG
Retrocopy MLGRTL*EVSAALKQGQITPTELCQKCLSLIKKTKFLHAYITASEEVALKQAEESEKRYKHEQSLGDLDG

Parental  IPIAVKDNFSTSGIETTCASNMLKGYIPPYNATVVQKLLDQGALLMGKTNLDEFAMGSGSTDGVFGPVKN
          IPIAVKDNFSTSGIETTCASNMLKGY.PPYNA.VV.KLLDQGALL.GKTNLDEFA.GS..TDGVFGPVKN
Retrocopy IPIAVKDNFSTSGIETTCASNMLKGYVPPYNARVVPKLLDQGALLIGKTNLDEFAIGSVRTDGVFGPVKN

Parental  P-WSYSKQYREKRKQNPHSENEDSDWLITGGSSGGSAAAVSAFTCYAALGSDTGGSTRNPAAHCGLVGFK
          P..SYSK.YREKRKQNPHS.NEDSDWLIT....GGS.....A.....ALGS.T.GSTRNPAAHC.LVGFK
Retrocopy P<LSYSK*YREKRKQNPHSKNEDSDWLIT----GGSSGGSEA--AMSALGSATEGSTRNPAAHCRLVGFK

Parental  PSYGLVSRHGLIPLVNSMDVPGILTRCVDDAAIVLGALAGPDPRDSTTVHEPINKPFM
          PSYGLVS.HGLI.LVN.MDVPGILTRCVDDAAIVL...AG.D..D.TTV..PI.KPF.
Retrocopy PSYGLVSHHGLILLVNLMDVPGILTRCVDDAAIVLSVQAGHDTNDCTTV*DPI-KPFI

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
bodymap2_adipose	0.00 RPM	10.79 RPM
bodymap2_adrenal	0.00 RPM	31.38 RPM
bodymap2_brain	0.00 RPM	17.23 RPM
bodymap2_breast	0.00 RPM	15.25 RPM
bodymap2_colon	0.00 RPM	14.27 RPM
bodymap2_heart	0.00 RPM	23.46 RPM
bodymap2_kidney	0.00 RPM	28.91 RPM
bodymap2_liver	0.00 RPM	17.07 RPM
bodymap2_lung	0.00 RPM	9.86 RPM
bodymap2_lymph_node	0.00 RPM	24.45 RPM
bodymap2_ovary	0.00 RPM	25.06 RPM
bodymap2_prostate	0.00 RPM	15.61 RPM
bodymap2_skeletal_muscle	0.00 RPM	23.52 RPM
bodymap2_testis	0.00 RPM	22.06 RPM
bodymap2_thyroid	0.00 RPM	25.82 RPM
bodymap2_white_blood_cells	0.00 RPM	25.34 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_466 was not detected

EST

No EST(s) were mapped for retro_hsap_466 retrocopy.

TSS

No TSS is located nearby retro_hsap_466 retrocopy 5' end.

Lab

retro_hsap_466 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_466 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_351
Gorilla gorilla	retro_ggor_445
Pongo abelii	retro_pabe_268

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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,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.02 RPM
YRI_NA19223	0.00 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).