RetrogeneDB ID: retro_pcap_104

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: GeneScaffold_6415:373..783(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDKN3
• Ensembl ID: ENSPCAG00000015559
• Aliases: None
• Description: cyclin-dependent kinase inhibitor 3 [Source:HGNC Symbol;Acc:1791]

Sequence

>retro_pcap_104
ATGAAGCCACCTAGTTCATTGGAAGCAAGTGAGCTTGACTCACCAGATAAAGAGTTTGTTGAAGATAAACAGACTCCAAT
CCAGATATCATGGCTGCCTCCGTTTCAAGTGAATTTATGTATATGTGCTCTTCCAGGTTATAAATTTAAAGATGTTAGAA
GAAATATCCAAAAAAAGATGCAAGAAAACTATGGTATACAAGATGTATTTGTTTTCTGTATCAGGGGAGAGTTATCAAAA
TATTGAGTCTAAAAACTTTTGGACTTCTACCAGCAGTATAAAAATATCACTCATCATCCTCTAATCCCAGATGGTGGACT
CCTGACATAGCCAACTGCTGTGAAATGATGATGGAGCTTGTAATCTGCCTTAAAAATAACTGAAAAAGCTTAGTACACTG
CTATGGAGGG

Alignment

ORF - retro_pcap_104 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 67.45 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKPPSSLQASEFDSSDEEPIEDEPTPVQISWLPLSRVNCSQFLGLCALPGCKFKDVRRNIQKDTEELRNC
          MKPPSSL.ASE.DS.D.E..ED..TP.QISWLP...VN....L..CALPG.KFKDVRRNIQK...E..N.
Retrocopy MKPPSSLEASELDSPDKEFVEDKQTPIQISWLPPFQVN----LCICALPGYKFKDVRRNIQKKMQE--NY

Parental  GIQDIFVLCTRGELSKYRVPNLLDIYRQCGIIPHHHPIPDGG-TPDIASCCEIMEELAVCLKNNRKTLIH
          GIQD.FV.C.RGELSKY.V..LLD.Y.Q...I.HH..IPDGG.TPDIA.CCE.M.EL..CLKNN.K.L.H
Retrocopy GIQDVFVFCIRGELSKY*V*KLLDFYQQYKNITHHPLIPDGG<TPDIANCCEMMMELVICLKNN*KSLVH

Parental  CYGG
          CYGG
Retrocopy CYGG

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_104 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 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012823	1 retrocopy	retro_chof_1806,
Echinops telfairi	ENSETEG00000018617	1 retrocopy	retro_etel_1763,
Felis catus	ENSFCAG00000015089	2 retrocopies	retro_fcat_135, retro_fcat_626,
Loxodonta africana	ENSLAFG00000014833	1 retrocopy	retro_lafr_637,
Macropus eugenii	ENSMEUG00000002497	3 retrocopies	retro_meug_1255, retro_meug_1768, retro_meug_1849,
Procavia capensis	ENSPCAG00000015559	1 retrocopy	retro_pcap_104 ,
Sarcophilus harrisii	ENSSHAG00000008977	1 retrocopy	retro_shar_502,
Tupaia belangeri	ENSTBEG00000010203	2 retrocopies	retro_tbel_1809, retro_tbel_4700,