RetrogeneDB ID: retro_pabe_268

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:82722382..82723437(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: QRSL1
• Ensembl ID: ENSPPYG00000016883
• Aliases: None
• Description: glutaminyl-tRNA synthase (glutamine-hydrolyzing)-like 1 [Source:HGNC Symbol;Acc:21020]

Sequence

>retro_pabe_268
ATGCTGGGCCGGACCCTCTGAGAAGTTTCTGCAGCACTGAAACAAGGCCAGATTACACCAACAGAGCTCTGTCAAAAATG
TCTCTCTCTTATCAAGAAGACCAAGTTTCTACATGCCTACATTACTGTATCAGAAGAGGTGGCCTTAAAACAAGCTGAAG
AATCAGAAAAGAGATATAAGCATGAATAGTCACTTAGGGATTTAGATGGAATTCCTATTGCAGTAAAAGACCACTTTAGC
ACATCTGGCATTGAGACAATATGTGCATCAAATATGCTGAAAGGTTATATACCACCTTATAATGCTAGAGTAGTTTCAAA
GTTGTTGGATCAGGGAGCTCTACTAATGGGAAAAACAAATTTAGATGAGTTTGCTATGGGATCTGGAAGCACAGATGGTG
TGTTTGGACCGGTTAAAAACCCCTGAGTTATTCAAAATAATATAGAGAAAAGAGGAAGCAGAATCCCCACAGCAAGAATG
AAGATTCAGACTGGCTGATAACTGGAGGAAGCTCAGGTGGGAGTGCAGCTGCTATGTCGGCTTTAGGATCAGCTACAGGA
GGATCGACCAGAAATCCTGCTGCCCACTGCAGGCTTGCTGGTTTCAAACCAAGCTATGGTTTAGTTTCCCATCATGGTCT
CATTCCCCTGGTGAATTTGATGGATGTGCCAGGAATCTTAACCAGATGTGTGGATGATGCAGCAATTGTGTTGAGTATAC
TGGCTGGACATGACACCAATGATTGTACCACAGTACAGGACCCTATTAAACCATTCATTTGGTTTGGCAGATGTGAGCAA
ACTATGAATAGAAATTCCAAAGGAATATCTTGTGCCAGAATTATTAAGTGAAGTACAGTCTTTTTGGTCCAAAGCTGCTG
ACCTCTTTGAGTCTGAAAGGGCCAAAGTAATTGAAGTATCCATTCCTCACACCAGTTATTCAATTGTCTGCTATCATGTA
TCGTGCACATCAGGATGGCATTAAATATGGCAAGACTTGGTGGGCTACAATATAGTCACAGATGTGACATTGATGTGTCC
ACGCAATGTGTCCAC

Alignment

ORF - retro_pabe_268 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.14 %
• Parental protein coverage: 68.37 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MLGRTLREVSAALKQGQITPTELCQKCLSLIKKTKFLNAYITVSEEVALKQAEESEKRYKNGQSLGDLDG
          MLGRTL.EVSAALKQGQITPTELCQKCLSLIKKTKFL.AYITVSEEVALKQAEESEKRYK...SL.DLDG
Retrocopy MLGRTL*EVSAALKQGQITPTELCQKCLSLIKKTKFLHAYITVSEEVALKQAEESEKRYKHE*SLRDLDG

Parental  IPIAVKDNFSTSGIETTCASNMLKGYIPPYNATVVQKLLDQGALLMGKTNLDEFAMGSGSTDGVFGPVKN
          IPIAVKD.FSTSGIET.CASNMLKGYIPPYNA.VV.KLLDQGALLMGKTNLDEFAMGSGSTDGVFGPVKN
Retrocopy IPIAVKDHFSTSGIETICASNMLKGYIPPYNARVVSKLLDQGALLMGKTNLDEFAMGSGSTDGVFGPVKN

Parental  P-WSYSKQYREKRKQNPHSKNEDSDWLITGGSSGGSAAAVSAFTCYAALGSDTGGSTRNPAAHCGLVGFK
          P..SYSK.YREKRKQNPHSKNEDSDWLIT....GGS.....A.....ALGS.TGGSTRNPAAHC.L.GFK
Retrocopy P<LSYSK*YREKRKQNPHSKNEDSDWLIT----GGSSGGSAA--AMSALGSATGGSTRNPAAHCRLAGFK

Parental  PSYGLVSRHGLIPLVNSMDVPGILTRCVDDAAIVLGALAGPDPRDSTTVHDP-INKPFMLPSLADVSKLC
          PSYGLVS.HGLIPLVN.MDVPGILTRCVDDAAIVL..LAG.D..D.TTV.DP..N..F....LADVSKL.
Retrocopy PSYGLVSHHGLIPLVNLMDVPGILTRCVDDAAIVLSILAGHDTNDCTTVQDP>LNHSF---GLADVSKL*

Parental  IGIPKEYLVPELSSEVQSLWSKAADLFESEGAKVIEVSLPHTSYSIVCYHVLCTS-EVASNMARFDGLQY
          I.IPKEYLVPEL.SEVQS.WSKAADLFESE.AKVIEVS.PHTSYSIVCYHV.CTS...A.NMAR..GLQY
Retrocopy IEIPKEYLVPELLSEVQSFWSKAADLFESERAKVIEVSIPHTSYSIVCYHVSCTS<RMALNMARLGGLQY

Parental  GHRCDIDVSTEAMY
          .HRCDIDVST....
Retrocopy SHRCDIDVSTQCVH

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	3.76 RPM
SRP007412_cerebellum	0.00 RPM	7.42 RPM
SRP007412_heart	0.06 RPM	10.54 RPM
SRP007412_kidney	0.03 RPM	12.16 RPM
SRP007412_liver	0.03 RPM	7.34 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_268 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_268 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_268 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_466
Pan troglodytes	retro_ptro_351
Gorilla gorilla	retro_ggor_445

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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,