RetrogeneDB ID: retro_pcap_46

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: GeneScaffold_2401:8423..8732(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCBD1
• Ensembl ID: ENSPCAG00000007201
• Aliases: None
• Description: pterin-4 alpha-carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha [Source:HGNC Symbol;Acc:8646]

Sequence

>retro_pcap_46
ATGGCTGGCAAAGCACAAAAGCTAAGTATCAAGGAGAGCAACCAATTGCTACCACATATGAGTGCCGTGGGATGGAATGA
GATGGAAGGTCATGATGCTATCTTCAAGCAGTTCCATTTCTCAGACTTCAATAGGGCATCTGGGTTCACGACAAAGGTGG
TCCTGCAGGCCGAGAAACTGGACCACTACCCTGAATCGTTTCAAGTGTACAAGGGTGATATCACCCTGAGCATCCATGAC
TATGCAGGCCTTTCAAAGTAGGGCATAAATCTAACCATCTTCATCAAATAAGTAGCGTTGTCCATGACA

Alignment

ORF - retro_pcap_46 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.27 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGKAHRLSAEERDQLLPNLRAVGWNELEGRDAIFKQFHFKDFNRAFGFMTRVALQAEKLDHHPEWFNVY
          MAGKA..LS..E..QLLP...AVGWNE.EG.DAIFKQFHF.DFNRA.GF.T.V.LQAEKLDH.PE.F.VY
Retrocopy MAGKAQKLSIKESNQLLPHMSAVGWNEMEGHDAIFKQFHFSDFNRASGFTTKVVLQAEKLDHYPESFQVY

Parental  NKVHITLSTHECAGLSERDINLASFIEQVAVSMT
          .K..ITLS.H..AGLS...INL..FI..VA.SMT
Retrocopy -KGDITLSIHDYAGLSK*GINLTIFIK*VALSMT

Legend:

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

Expression

RNA-Seq

Procavia capensis was not studied using RNA-Seq expression data.

ChIP-Seq

Procavia capensis was not studied using ChIP-Seq data.

EST

Procavia capensis was not studied using EST data.

TSS

Procavia capensis was not studied using FANTOM5 data.

Lab

retro_pcap_46 was not experimentally validated.

Homology

Retrocopy orthology:

Procavia capensis 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 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,