RetrogeneDB ID: retro_rnor_713

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 10:91519425..91519797(+)
• Located in intron of: ENSRNOG00000003506

Retrocopy information

• Ensembl ID: ENSRNOG00000028427
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Magmas
• Ensembl ID: ENSRNOG00000004608
• Aliases: Pam16, Magmas
• Description: mitochondria-associated granulocyte macrophage CSF signaling molecule [Source:RefSeq peptide;Acc:NP_001093606]

Sequence

>retro_rnor_713
ATGGCCAAGTACCTGACCCAGATCATTGTGATGGGTGTGCAGGTGGTGGGCAGAGACTTTGCCAAGGCCCTGAGGCAGGA
GTTTGCAGCAAGCCAGGCAGCCGCTGATGCTCGAGGCCATGCTGGGCACCAGTCTGCAGCTGCATCCAATCTCTCTGGCC
TCAGCCTCCAGGAAGCCCAGCAGATTCTCAACATCTCTAAGCTGAGCCCTGAGGAGGTGCAGAATTATGAACACCTGTTT
AAGGTGAATGATAAGTCCGTGGGTGACTCTTTCTACCTGCAGTCAAAGGTTGTCCGTGCAAAGGAACGCCTAGATGAGGA
ACTCCAAATACAAGCCCAGGAAGACAGAGAGAAAGGGCAGATGCCCAAAACG

Alignment

ORF - retro_rnor_713 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.6 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAKYLAQIIVMGVQVVGRAFARALRQEFAASQAAADARGRAGHQSAAASNLSGLSLQEAQQILNISKLSP
          MAKYL.QIIVMGVQVVGR.FA.ALRQEFAASQAAADARG.AGHQSAAASNLSGLSLQEAQQILNISKLSP
Retrocopy MAKYLTQIIVMGVQVVGRDFAKALRQEFAASQAAADARGHAGHQSAAASNLSGLSLQEAQQILNISKLSP

Parental  EEVQKNYEHLFKVNDKSVGGSFYLQSKVVRAKERLDEELRIQAQEDREKGQTPKT
          EEVQ.NYEHLFKVNDKSVG.SFYLQSKVVRAKERLDEEL.IQAQEDREKGQ.PKT
Retrocopy EEVQ-NYEHLFKVNDKSVGDSFYLQSKVVRAKERLDEELQIQAQEDREKGQMPKT

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	0.14 RPM	14.67 RPM
SRP017611_kidney	0.00 RPM	20.66 RPM
SRP017611_liver	0.13 RPM	8.07 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_713 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_713 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_713 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009200	1 retrocopy	retro_btau_1664,
Canis familiaris	ENSCAFG00000019226	1 retrocopy	retro_cfam_1967,
Callithrix jacchus	ENSCJAG00000019772	1 retrocopy	retro_cjac_1148,
Dasypus novemcinctus	ENSDNOG00000010921	2 retrocopies	retro_dnov_1361, retro_dnov_8,
Dipodomys ordii	ENSDORG00000014888	1 retrocopy	retro_dord_81,
Equus caballus	ENSECAG00000019387	1 retrocopy	retro_ecab_302,
Erinaceus europaeus	ENSEEUG00000007432	7 retrocopies	retro_eeur_138, retro_eeur_171, retro_eeur_213, retro_eeur_234, retro_eeur_273, retro_eeur_440, retro_eeur_673,
Echinops telfairi	ENSETEG00000006416	1 retrocopy	retro_etel_2070,
Felis catus	ENSFCAG00000027971	1 retrocopy	retro_fcat_520,
Myotis lucifugus	ENSMLUG00000008921	6 retrocopies	retro_mluc_2446, retro_mluc_2447, retro_mluc_2448, retro_mluc_2516, retro_mluc_2517, retro_mluc_429,
Mus musculus	ENSMUSG00000014301	1 retrocopy	retro_mmus_73,
Rattus norvegicus	ENSRNOG00000004608	1 retrocopy	retro_rnor_713 ,
Sus scrofa	ENSSSCG00000007947	2 retrocopies	retro_sscr_1090, retro_sscr_468,
Ictidomys tridecemlineatus	ENSSTOG00000003461	1 retrocopy	retro_itri_1732,
Tupaia belangeri	ENSTBEG00000001347	1 retrocopy	retro_tbel_3190,
Tarsius syrichta	ENSTSYG00000009306	1 retrocopy	retro_tsyr_282,