RetrogeneDB ID: retro_cpor_1049

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_40:10294826..10295452(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OSTF1
• Ensembl ID: ENSCPOG00000007226
• Aliases: None
• Description: None

Sequence

>retro_cpor_1049
ATGTTGAAGCTGCCCCCCAAACCTGTTAAACCAGGGCAAGTTAAAGTCTTTCATACAGAAATGGCAAAGAGCCCAGAACT
CCAGATGAATTGTACTGCAAGGAAGGTGAGATTATCTACATTACTGACATGAATCATAGCAGTTGATGGGAAGGAACCTC
CAAAGGCAGGGTGGGACTAATTCGAAGTGGCTGTATGCTGAGTGGGCAGAATCTGATAGCAATCTGTTGCATGATGCTGC
TGAAGAGGCAACTTGAGCTGGCTGAGGAGTGTCTGGACAGTCCAGAGGCAGTAATGGCCTAGACAAAGCGAGAAGCACTG
CCTTGTACTACGCTTGTCACGGCAGTCACAAAGATATAGTAGAAGTGCTATTTACTCAGCCAAATATTGAACTGAACCAA
CAGAACAACTTAGGGGACACAGCTTTGCACACTGCTGCTTGAAAGGGTTACGCAGATATTGTCCAGCTGCTTCTGGTGAA
GGCGATAGAAGAGACTTGTGGAACCAGGAGAAGAAGTTGGCCTTGGACGTGGCCACCAAAGTTTCCTGTGCAATGCTCCT
AAAAAACAAGCAGGGAACAGATGCAGTTTGATGATTAAGCAATGTGAGGACCATCTTGATGAAGAC

Alignment

ORF - retro_cpor_1049 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.64 %
• Parental protein coverage: 98.6 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  MSKPPPKPVKPGQVKVFRALYTFEP-RTPDELYFEEGDVIYITDMSDSNWWKGTSKGRTGLIPSN-YGGE
          M.K.PPKPVKPGQVKVF.......P.RTPDELY..EG..IYITDM..S..W.GTSKGR.GLI.S.....E
Retrocopy MLKLPPKPVKPGQVKVFHTEMAKSP<RTPDELYCKEGEIIYITDMNHSS*WEGTSKGRVGLIRSG<LYAE

Parental  QAESIDNPLHEAAK-RGNLSWLR-ECLDN-RVGVNGLDKAGSTALYWACHGGHKDIVEVLFTQPNIELNQ
          .AES..N.LH.AA..RGNLSWLR.ECLD....G.NGLDKA.STALY.ACHG.HKDIVEVLFTQPNIELNQ
Retrocopy WAESDSNLLHDAAE<RGNLSWLR<ECLDS<SRGSNGLDKARSTALYYACHGSHKDIVEVLFTQPNIELNQ

Parental  QNKLGDTALHAAAWKGYADIVQLLLEK-GARTDLLNNEKKLALDMATNAACASLLKKKQGTDAVRSLSN-
          QN.LGDTALH.AA.KGYADIVQLLL.K.G.R.DL.N.EKKLALD.AT...CA.LLK.KQGTDAV..LSN.
Retrocopy QNNLGDTALHTAA*KGYADIVQLLLVK<GDRRDLWNQEKKLALDVATKVSCAMLLKNKQGTDAV**LSN<

Parental  AEDYLDDE
          .ED.LD..
Retrocopy CEDHLDED

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	0.06 RPM	4.72 RPM
SRP017611_kidney	0.00 RPM	38.11 RPM
SRP017611_liver	0.00 RPM	20.98 RPM
SRP040447_lung	0.05 RPM	62.40 RPM
SRP040447_skeletal_muscle	0.00 RPM	7.59 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1049 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1049 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus 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,