RetrogeneDB ID: retro_pabe_883

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:116560828..116561227(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OSTF1
• Ensembl ID: ENSPPYG00000019300
• Aliases: None
• Description: osteoclast-stimulating factor 1 [Source:RefSeq peptide;Acc:NP_001127367]

Sequence

>retro_pabe_883
CAATCCATTGACAATCTATTGCATGAAGTAGCAAAAAGAGGCAACTTGAGTTGGTTGCAAGAGTGTTTGGACAACCGAGT
GGGTGTTAATGGCTTAGACAAGGCTGGAAGCACTGCCTTAGACTAGGCTTGTCATGGGGATCTCAGAGATATAGTGGAAA
TGCTATTTACTCAACCGAGTATTTAACTGAAACAACAGAACAAGTTGGAAGACACAGCTTTGCATGCTGCTGCCTGGAAG
AGTTATGCAGATATTGTCCAGTTGCTTCTGGCAAAAGGTGCCAGAACAGACTGAAGAAACAATGAGAAGAAGCTGGCTTT
GGGCATGGCTACCAATGCCCATGCGTCTCTCCTGAAAAAGAAACAGGAGACAGATGCAGTTCGAACATTAAGCAATGCT

Alignment

ORF - retro_pabe_883 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.33 %
• Parental protein coverage: 71.28 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ESIDNPLHEAAKRGNLSWLRECLDNRVGVNGLDKAGSTALYWACHGGHKDIVEMLFTQPNIELNQQNKLG
          .SIDN.LHE.AKRGNLSWL.ECLDNRVGVNGLDKAGSTAL..ACHG...DIVEMLFTQP.I.L.QQNKL.
Retrocopy QSIDNLLHEVAKRGNLSWLQECLDNRVGVNGLDKAGSTALD*ACHGDLRDIVEMLFTQPSI*LKQQNKLE

Parental  DTALHAAAWKGYADIVQLLLAKGARTDLRNIEKKLAFDMATNAACASLLKKKQGTDAVRTLSNA
          DTALHAAAWK.YADIVQLLLAKGARTD.RN.EKKLA..MATNA..ASLLKKKQ.TDAVRTLSNA
Retrocopy DTALHAAAWKSYADIVQLLLAKGARTD*RNNEKKLALGMATNAH-ASLLKKKQETDAVRTLSNA

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	20.84 RPM
SRP007412_cerebellum	0.00 RPM	13.13 RPM
SRP007412_heart	0.00 RPM	8.73 RPM
SRP007412_kidney	0.00 RPM	23.27 RPM
SRP007412_liver	0.00 RPM	24.85 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_883 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_883 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_883 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1058
Pan troglodytes	retro_ptro_720
Gorilla gorilla	retro_ggor_836
Macaca mulatta	retro_mmul_836
Callithrix jacchus	retro_cjac_3249

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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,