RetrogeneDB ID: retro_ogar_2962

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873690.1:3742599..3743233(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000031040
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: OSTF1
• Ensembl ID: ENSOGAG00000002603
• Aliases: None
• Description: osteoclast stimulating factor 1 [Source:HGNC Symbol;Acc:8510]

Sequence

>retro_ogar_2962
ATGTCCAAACCACTACCCAAACCAGTCAAACCAGGGCAAGTTAAAGTTTTCAGAGCTCTGTATACATTTGAACCCAGAAC
TCCAGATGAATTGTACTTTGAAGAAGGTGATATTATTTATGTTACTGACATGAGTGATACCAATTGGTGGAAAGGCACCT
CCAAAGGCAGGACTGGACTAATTCCAAGCAACTATGTGGCTGAGCGGGCAGAATCCATTGACAATCCATTGCATGAAGCT
GCAAAAAGAGGCAACTTGAACTGGTTGAGAGAGTGTTTGGACAACCGAGTGGGTGTTAACGGCTTAGACAAAGCTGGGAG
CACAGCCTTATATCGGGCTTGTCACAGGGGCCACAAAGATATAGTGGAAATGTTATTTACTCAACCAAACATTGAACTGA
ACCAACAGAACAAGTTGGGAGACACGGCTTTGCACGCTGCTACCCGGAAGGGTTATGCAGATATTGTTCAGTTGCTTCTG
GAAAAAAGGTGCTAGAATGGACTTAAGAAACAATGAGAAGAAACTGGCCTTCGACATGGCTGCCTGTGCATCTCTCCTGA
AAAAGAAACAGGAAACAGATGCTATTCGAACATTAAGCAATGCCGAGGACTATCTTGATGATGACGACTCAGAT

Alignment

ORF - retro_ogar_2962 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.56 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSKPPPKPVKPGQVKVFRALYTFEPRTPDELYFEEGDIIYITDMSDTNWWKGTSKGRTGLIPSNYVAEQA
          MSKP.PKPVKPGQVKVFRALYTFEPRTPDELYFEEGDIIY.TDMSDTNWWKGTSKGRTGLIPSNYVAE.A
Retrocopy MSKPLPKPVKPGQVKVFRALYTFEPRTPDELYFEEGDIIYVTDMSDTNWWKGTSKGRTGLIPSNYVAERA

Parental  ESIDNPLHEAAKRGNLSWLRECLDNRVGVNGLDKAGSTALYWACHGGHKDIVEMLFTQPNIELNQQNKLG
          ESIDNPLHEAAKRGNL.WLRECLDNRVGVNGLDKAGSTALY.ACH.GHKDIVEMLFTQPNIELNQQNKLG
Retrocopy ESIDNPLHEAAKRGNLNWLRECLDNRVGVNGLDKAGSTALYRACHRGHKDIVEMLFTQPNIELNQQNKLG

Parental  DTALHAAAWKGYADIVQLLLE-KGARTDLRNNEKKLAFDMATNAACASLLKKKQGTDAIRTSSNAEDYLD
          DTALHAA..KGYADIVQLLLE.KGAR.DLRNNEKKLAFDMA...ACASLLKKKQ.TDAIRT.SNAEDYLD
Retrocopy DTALHAATRKGYADIVQLLLE>KGARMDLRNNEKKLAFDMA---ACASLLKKKQETDAIRTLSNAEDYLD

Parental  DEDSD
          D.DSD
Retrocopy DDDSD

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_2962 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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 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,