RetrogeneDB ID: retro_pcap_236

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_202994:684..954(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HMGA1
• Ensembl ID: ENSPCAG00000016076
• Aliases: None
• Description: high mobility group AT-hook 1 [Source:HGNC Symbol;Acc:5010]

Sequence

>retro_pcap_236
ATGAGCGAATCGAGCTCGAAGTCCAGCCAGCCCTTGGCCTCCAAGCAGGAAAAGGACGGCACTGAGAAGCGGGGGCGGGG
CAGGCCTCGCAAGCAGTCTCCGGTGAGTCCTGGTACAGCGCTGGTAGGGAGTCAGAAAGAGCCCAGCGAAGTGCCAACAC
CTAAGAGACCTCGGGGCCGACCAAAGGGGAGCAAAAACAGGGGTGCTGCCAAGACCCGGAAAACCATCACAGCTCCAGGA
AGGAAACCAAGGGGCAGACCCAAAAAGCTG

Alignment

ORF - retro_pcap_236 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80. %
• Parental protein coverage: 72.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSESSSKSSQPLASKQEKDGTEKRGRGRPRKQPPVSPGTALVGSQKEPSEVPTPKRPRGRPKGSKNKGRR
          MSESSSKSSQPLASKQEKDGTEKRGRGRPRKQ.PVSPGTALVGSQKEPSEVPTPKRPRGRPKGSKN.G..
Retrocopy MSESSSKSSQPLASKQEKDGTEKRGRGRPRKQSPVSPGTALVGSQKEPSEVPTPKRPRGRPKGSKNRGAA

Parental  RKKR---ASPRSPRRRSSDL
          .......A..R.PR.R...L
Retrocopy KTRKTITAPGRKPRGRPKKL

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_236 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015226	2 retrocopies	retro_cjac_1197, retro_cjac_3158,
Macaca mulatta	ENSMMUG00000019529	2 retrocopies	retro_mmul_1276, retro_mmul_2406,
Mus musculus	ENSMUSG00000046711	1 retrocopy	retro_mmus_188,
Procavia capensis	ENSPCAG00000016076	1 retrocopy	retro_pcap_236 ,
Pongo abelii	ENSPPYG00000029838	4 retrocopies	retro_pabe_1941, retro_pabe_2441, retro_pabe_3623, retro_pabe_960,
Pteropus vampyrus	ENSPVAG00000014283	1 retrocopy	retro_pvam_116,
Rattus norvegicus	ENSRNOG00000000488	1 retrocopy	retro_rnor_164,