RetrogeneDB ID: retro_sscr_979

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 8:112925257..112925869(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OSTF1
• Ensembl ID: ENSSSCG00000005273
• Aliases: None
• Description: Sus scrofa osteoclast stimulating factor 1 (OSTF1), mRNA. [Source:RefSeq mRNA;Acc:NM_214005]

Sequence

>retro_sscr_979
AAACCAGGGCAAGTTAGAGTGTTGAGAGCTCTTTGTACAATTTGAACCCAGAACTCAAAATGAATTGAACTGTGAAGAAG
GTGATATTATCTATATTACTGATACGAGTGATACCAGTTGGTGGAAAGGCACCTCCAAAGGCAGGACTGGACTCATCCCA
AGCAACTATGTGGCTGAGCAGGTGGAATCCATTGATAATCCATTGCATGAAGCTGCAGAAGAGGCAACCTGAGCTGGTTG
AGAGGGTGTTTGGATGACTAAGTCCATGTTACCAGCTTGGACAAAGCCTTGTACTTTGCTTGTACTGGGCTTGTCATGGG
GGTCACAAAGATATAGTGGAAATGCTATTTACTCAACCAAACATTTAACTGAACCAATGGAACAAGTTGGTAGACTCAGC
TTTGCATGCTGCTGCTTTGAAGGGTTATGCAGATACTGTCTAGTTGCTTCTGGCAAAAAGGTGCTGGAACAGATTTAAGA
AACAATGAGAAGAAACTGACCCTGGACATGGCTACTAATGCTGCCTGTGCATCTCTCCTGAAAAAGAAACAGGGAACACA
TGCATTTTGAACATTAAGCAACACCGAGGACTGTCTTGATGATGAAGACTCA

Alignment

ORF - retro_sscr_979 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.25 %
• Parental protein coverage: 95.33 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KPGQVKVFRALYT-FEPRTPDELYFEEGDIIYITDMSDTNWWKGTSKGRTGLIPSNYVAEQAESIDNPLH
          KPGQV.V.RAL.T.FEPRT..EL..EEGDIIYITD.SDT.WWKGTSKGRTGLIPSNYVAEQ.ESIDNPLH
Retrocopy KPGQVRVLRALCT>FEPRTQNELNCEEGDIIYITDTSDTSWWKGTSKGRTGLIPSNYVAEQVESIDNPLH

Parental  EAA-KRGNLSWLRECLDNRVGVNGLDKAGSTA-LYWACHGGHKDIVDMLFTQPNIELNQQNKLGDTALHA
          EAA..RGNLSWLR.CLD..V.V..LDKA...A.LYWACHGGHKDIV.MLFTQPNI.LNQ.NKL.D.ALHA
Retrocopy EAA<RRGNLSWLRGCLDD*VHVTSLDKALYFA<LYWACHGGHKDIVEMLFTQPNI*LNQWNKLVDSALHA

Parental  AAWKGYADIVQLLLA-KGARTDLRNNEKKLALDMATNAACASLLKKKQGTDAVRTLSNAEDYLDDEDS
          AA.KGYAD.V.LLLA.KGA.TDLRNNEKKL.LDMATNAACASLLKKKQGT.A..TLSN.ED.LDDEDS
Retrocopy AALKGYADTV*LLLA>KGAGTDLRNNEKKLTLDMATNAACASLLKKKQGTHAF*TLSNTEDCLDDEDS

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
SRP014902_placenta	0.00 RPM	71.41 RPM
SRP014902_testis	0.00 RPM	31.83 RPM
SRP018288_heart	0.00 RPM	28.32 RPM
SRP018288_kidney	0.00 RPM	25.51 RPM
SRP018288_liver	0.00 RPM	52.13 RPM
SRP018288_lung	0.00 RPM	58.75 RPM
SRP018856_adipose	0.00 RPM	93.08 RPM
SRP035408_brain	0.00 RPM	18.07 RPM
SRP035408_liver	0.00 RPM	41.10 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_979 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_979 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_979 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,