RetrogeneDB ID: retro_sscr_744

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 3:120248184..120248446(-)
• Located in intron of: ENSSSCG00000008576

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCBD1
• Ensembl ID: ENSSSCG00000010275
• Aliases: None
• Description: pterin-4 alpha-carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha [Source:HGNC Symbol;Acc:8646]

Sequence

>retro_sscr_744
ATGGCTGGCAAAGCACACAGGCTAAGTGCTGAGGAGAGGGACCAGCTGCAGCCAAACCCGCGGGCAGTAGGGTGGAACGA
GCTGGAAGGCTGGATGCCATCTTCAAGCAGTTTCATTTCAAAGACTTCAATGGGGCTTTTGGCTTTACGACGAGAGGGGC
TCTGCAGGCTGAGACACTGGGCCACACTCTGAATGGTTTAACCTGTGCAAGGTCCACCACACCCTGAGCAGCCTCGAGTG
TGTGGGCCTTTCGGAATGGGAC

Alignment

ORF - retro_sscr_744 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.12 %
• Parental protein coverage: 85.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAGKAHRLSAEERDQLLPNLRAVGWNELEG-RDAIFKQFHFKDFNRAFGFMTRVALQAEKLDH-HPEWFN
          MAGKAHRLSAEERDQL.PN.RAVGWNELEG..DAIFKQFHFKDFN.AFGF.TR.ALQAE.L.H.H.EWFN
Retrocopy MAGKAHRLSAEERDQLQPNPRAVGWNELEG<LDAIFKQFHFKDFNGAFGFTTRGALQAETLGH<HSEWFN

Parental  VYNKVHITLSTHECAGLSERD
          ...KVH.TLS..EC.GLSE.D
Retrocopy LC-KVHHTLSSLECVGLSEWD

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	18.45 RPM
SRP014902_testis	0.00 RPM	54.88 RPM
SRP018288_heart	0.00 RPM	21.79 RPM
SRP018288_kidney	0.00 RPM	81.76 RPM
SRP018288_liver	0.00 RPM	308.15 RPM
SRP018288_lung	0.00 RPM	34.32 RPM
SRP018856_adipose	0.00 RPM	97.91 RPM
SRP035408_brain	0.00 RPM	19.18 RPM
SRP035408_liver	0.00 RPM	183.18 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_744 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_744 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_744 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011866	1 retrocopy	retro_btau_1478,
Cavia porcellus	ENSCPOG00000012703	1 retrocopy	retro_cpor_61,
Felis catus	ENSFCAG00000001235	1 retrocopy	retro_fcat_1478,
Loxodonta africana	ENSLAFG00000001397	1 retrocopy	retro_lafr_1028,
Myotis lucifugus	ENSMLUG00000016074	3 retrocopies	retro_mluc_1534, retro_mluc_2459, retro_mluc_462,
Procavia capensis	ENSPCAG00000007201	1 retrocopy	retro_pcap_46,
Sus scrofa	ENSSSCG00000010275	1 retrocopy	retro_sscr_744 ,
Takifugu rubripes	ENSTRUG00000017869	1 retrocopy	retro_trub_26,
Tursiops truncatus	ENSTTRG00000005775	1 retrocopy	retro_ttru_1541,
Vicugna pacos	ENSVPAG00000004496	1 retrocopy	retro_vpac_69,