RetrogeneDB ID: retro_cpor_509

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_176:318455..318752(+)
• Located in intron of: ENSCPOG00000003259

Retrocopy information

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

Parental gene information

• Parental gene symbol: ANP32B
• Ensembl ID: ENSCPOG00000020118
• Aliases: None
• Description: None

Sequence

>retro_cpor_509
CAGGGCTTCACAACTGGAATCTGTGAACTTCAAGAGTTCCTTAGTTTAATAAATATATGCTTGATTTTAGCCTCAAATTT
CCCCAAGCTATTTAAATTGAAAAGGCTTGAACTCTGTGACAGTAAACTCTTCTAAAGTTTAGATTCACTAACAGAAAAAC
TTCTAAACCTCACACACATAAACTTCTTGAGTGGAAATAAACTGAAAAACAACAGTATCCTGAAATCTTTGAAAAAACTA
GATTGTCTGAAAAGCCTGGATCTGTCCAACTGGGAGGTTGCCAACCTGAGAACCTAT

Alignment

ORF - retro_cpor_509 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.64 %
• Parental protein coverage: 57.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EGLTAEFVNL-EFLSLINVCLLSVSNLPKLPKLKKLELSDNRIFGGLDMLAEKLPNLTHLN-LSGNKLKD
          .G.T.....L.EFLSLIN.CL...SN.PKL.KLK.LEL.D...F..LD.L.EKL.NLTH.N.LSGNKLK.
Retrocopy QGFTTGICELQEFLSLINICLILASNFPKLFKLKRLELCDSKLF*SLDSLTEKLLNLTHINFLSGNKLKN

Parental  ISTLEPLKKLDCLKSLDLFNCEVTNLNDY
          .S.L..LKKLDCLKSLDL.N.EV.NL..Y
Retrocopy NSILKSLKKLDCLKSLDLSNWEVANLRTY

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
SRP017611_brain	0.06 RPM	18.52 RPM
SRP017611_kidney	0.10 RPM	40.51 RPM
SRP017611_liver	0.00 RPM	22.81 RPM
SRP040447_lung	0.03 RPM	37.48 RPM
SRP040447_skeletal_muscle	0.00 RPM	20.37 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_509 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_509 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005149	6 retrocopies	retro_chof_1293, retro_chof_1456, retro_chof_19, retro_chof_2244, retro_chof_588, retro_chof_681,
Cavia porcellus	ENSCPOG00000020118	3 retrocopies	retro_cpor_1336, retro_cpor_493, retro_cpor_509 ,
Equus caballus	ENSECAG00000012310	2 retrocopies	retro_ecab_246, retro_ecab_826,
Echinops telfairi	ENSETEG00000015514	4 retrocopies	retro_etel_2053, retro_etel_2167, retro_etel_510, retro_etel_677,
Homo sapiens	ENSG00000136938	2 retrocopies	retro_hsap_1597, retro_hsap_1603,
Myotis lucifugus	ENSMLUG00000004844	2 retrocopies	retro_mluc_1787, retro_mluc_1788,
Macaca mulatta	ENSMMUG00000012242	1 retrocopy	retro_mmul_2600,
Monodelphis domestica	ENSMODG00000003261	1 retrocopy	retro_mdom_763,
Mustela putorius furo	ENSMPUG00000006433	1 retrocopy	retro_mputfur_1392,
Mus musculus	ENSMUSG00000028333	1 retrocopy	retro_mmus_2399,
Nomascus leucogenys	ENSNLEG00000016941	1 retrocopy	retro_nleu_3009,
Otolemur garnettii	ENSOGAG00000006091	2 retrocopies	retro_ogar_1915, retro_ogar_3282,
Pongo abelii	ENSPPYG00000019430	2 retrocopies	retro_pabe_1312, retro_pabe_1316,
Pan troglodytes	ENSPTRG00000021172	3 retrocopies	retro_ptro_1073, retro_ptro_1075, retro_ptro_40,
Pteropus vampyrus	ENSPVAG00000006569	1 retrocopy	retro_pvam_699,
Sorex araneus	ENSSARG00000000804	1 retrocopy	retro_sara_549,
Tupaia belangeri	ENSTBEG00000002189	8 retrocopies	retro_tbel_1659, retro_tbel_2710, retro_tbel_2772, retro_tbel_3770, retro_tbel_3863, retro_tbel_4351, retro_tbel_4361, retro_tbel_491,
Tursiops truncatus	ENSTTRG00000010825	2 retrocopies	retro_ttru_1899, retro_ttru_341,