RetrogeneDB ID: retro_pcap_40

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: GeneScaffold_1803:114368..114911(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM49B
• Ensembl ID: ENSPCAG00000002866
• Aliases: None
• Description: family with sequence similarity 49, member B [Source:HGNC Symbol;Acc:25216]

Sequence

>retro_pcap_40
ATAGGGAATCTTCTTAAAGTTTTGACATGCACAGACCTTGAGCACGGGCCAAATTTTTTCCTTGATTTTGAAAATGCCCA
GCCTACAGAATCTGAGAAGGAAATTTATAATCAGGTGAATGTAGTATTAAAAGATGCAGAAGGCATCTTGGAGGACTTGC
AGTCATATAGAGGAGCTGGCCATGAAATACGGGAGGCTATCCAGCATCCAGCATATGAGAAGTTGCAAGAGAAGGCATGG
GGTGCAGTTGTTCCGCTAGTACGCAAATTAAAGAAATTTTATGAATTTTCCCAGCGGTTAGAAGCAGCATTACGAGGTCT
TCTGGGAGCCTTGACAAGCACCCCATACTCTCTCACCCAGTACCTAGAGCGAGAGCATGCTCTTGCTAAACAGTTTGCAG
AAATTCTTCATTTCACACTCCGGTTTGCTGAACTCAAGATGACAAATCCTGCCATACAGAATGATTTCAGCTACTATAAA
AGAACAGTGAGTCGTACGAGGATTAACAATGTTCCAGCAGAAGGAGAAAATGAAATAAATAAC

Alignment

ORF - retro_pcap_40 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.37 %
• Parental protein coverage: 59.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGNLLKVLTCTDLEQGPNFFLDFENAQPTESEKEIYNQVNVVLKDAEGILEDLQSYRGAGHEIREAIQHP
          .GNLLKVLTCTDLE.GPNFFLDFENAQPTESEKEIYNQVNVVLKDAEGILEDLQSYRGAGHEIREAIQHP
Retrocopy IGNLLKVLTCTDLEHGPNFFLDFENAQPTESEKEIYNQVNVVLKDAEGILEDLQSYRGAGHEIREAIQHP

Parental  ADEKLQEKAWGAVVPLVGKLKKFYEFSQRLEAALRGLLGALTSTPYSPTQHLEREQALAKQFAEILHFTL
          A.EKLQEKAWGAVVPLV.KLKKFYEFSQRLEAALRGLLGALTSTPYS.TQ.LERE.ALAKQFAEILHFTL
Retrocopy AYEKLQEKAWGAVVPLVRKLKKFYEFSQRLEAALRGLLGALTSTPYSLTQYLEREHALAKQFAEILHFTL

Parental  RFDELKMTNPAIQNDFSYYRRTLSRMRINNVPAEGENEVNN
          RF.ELKMTNPAIQNDFSYY.RT.SR.RINNVPAEGENE.NN
Retrocopy RFAELKMTNPAIQNDFSYYKRTVSRTRINNVPAEGENEINN

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_40 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 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000009323	3 retrocopies	retro_dnov_1596, retro_dnov_1723, retro_dnov_896,
Dipodomys ordii	ENSDORG00000005160	1 retrocopy	retro_dord_381,
Echinops telfairi	ENSETEG00000015647	1 retrocopy	retro_etel_1299,
Felis catus	ENSFCAG00000015625	1 retrocopy	retro_fcat_1690,
Oryctolagus cuniculus	ENSOCUG00000013690	1 retrocopy	retro_ocun_953,
Procavia capensis	ENSPCAG00000002866	3 retrocopies	retro_pcap_293, retro_pcap_332, retro_pcap_40 ,
Sus scrofa	ENSSSCG00000005959	1 retrocopy	retro_sscr_978,