RetrogeneDB ID: retro_rnor_936

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 13:90162566..90162899(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000049231
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ostf1
• Ensembl ID: ENSRNOG00000012156
• Aliases: Ostf1, Sh3d3
• Description: Osteoclast-stimulating factor 1 [Source:UniProtKB/Swiss-Prot;Acc:Q6P686]

Sequence

>retro_rnor_936
CTGGACGAAGCTGGAAGCACAGCCCTGTACTGCCACGGTGGCCACAAAGACATAGTGGAGGTTCTGTTTACTCAGCCGAA
TGTGGAACTGAACCAGCAGAACAAGCTGGGAGACACGGCTCTGCACGCAGCTGCCTGGAAGGGTTATGCAGACACTGTCC
AGTTGCTACTTGCAAAAGGTGTGAGGACAGTCTTGAGAAACAATGAGAAGAAGCTAGCCTTGGACATGGCCACCAACGCT
GCCTGTGCATCGCTCCTGAAGAAGAAGCAGGCAACAGATGGGTCTCGAACGTTAAGCAATGCTGAGGACTACCTCGATGA
TGAAGACTCAGAC

Alignment

ORF - retro_rnor_936 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.81 %
• Parental protein coverage: 55.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LDKAGSTALYWACHGGHKDIVEVLFTQPNVELNQQNKLGDTALHAAAWKGYADIVQLLLAKGARTDLRNN
          LD.AGSTALY..CHGGHKDIVEVLFTQPNVELNQQNKLGDTALHAAAWKGYAD.VQLLLAKG.RT.LRNN
Retrocopy LDEAGSTALY--CHGGHKDIVEVLFTQPNVELNQQNKLGDTALHAAAWKGYADTVQLLLAKGVRTVLRNN

Parental  EKKLALDMATNAACASLLKKKQATDGARTLSNAEDYLDDEDSD
          EKKLALDMATNAACASLLKKKQATDG.RTLSNAEDYLDDEDSD
Retrocopy EKKLALDMATNAACASLLKKKQATDGSRTLSNAEDYLDDEDSD

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	0.00 RPM	10.57 RPM
SRP017611_kidney	0.00 RPM	29.24 RPM
SRP017611_liver	0.00 RPM	12.17 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_936 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_936 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_936 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012808	1 retrocopy	retro_cjac_3249,
Cavia porcellus	ENSCPOG00000007226	1 retrocopy	retro_cpor_1049,
Dipodomys ordii	ENSDORG00000002933	1 retrocopy	retro_dord_698,
Erinaceus europaeus	ENSEEUG00000008320	2 retrocopies	retro_eeur_545, retro_eeur_683,
Felis catus	ENSFCAG00000022374	1 retrocopy	retro_fcat_1869,
Homo sapiens	ENSG00000134996	1 retrocopy	retro_hsap_1058,
Gorilla gorilla	ENSGGOG00000011920	1 retrocopy	retro_ggor_836,
Macaca mulatta	ENSMMUG00000010401	1 retrocopy	retro_mmul_836,
Nomascus leucogenys	ENSNLEG00000001854	1 retrocopy	retro_nleu_2502,
Otolemur garnettii	ENSOGAG00000002603	1 retrocopy	retro_ogar_2962,
Pongo abelii	ENSPPYG00000019300	1 retrocopy	retro_pabe_883,
Pan troglodytes	ENSPTRG00000021031	1 retrocopy	retro_ptro_720,
Rattus norvegicus	ENSRNOG00000012156	2 retrocopies	retro_rnor_936 , retro_rnor_937,
Sus scrofa	ENSSSCG00000005273	1 retrocopy	retro_sscr_979,
Tursiops truncatus	ENSTTRG00000003081	1 retrocopy	retro_ttru_492,