RetrogeneDB ID: retro_pcap_299

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_284376:314..1009(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATG4C
• Ensembl ID: ENSPCAG00000003461
• Aliases: None
• Description: autophagy related 4C, cysteine peptidase [Source:HGNC Symbol;Acc:16040]

Sequence

>retro_pcap_299
TGGGTGTTGAAAACAAAGACCTATTTTAGTAGAAACTCCCCTGTACTAGTACTTGGAGAATACCATTTTAAATATGAAGA
TGAAAATAAAGTGTTACCTGCAAGATCAGGATGTGCAATGGAAGATTGTGTAATTTCAGGAAATGCGGAAGACTTTCGTA
AAGATTTTATTTCTAGAATATGGCTCATCTATAGCGAAGAGTTTCCTCAAATAGAAGGCTCAGTTTTGACAACAGACTGT
GGTTGGGGCTGTACGTTGAGAACTGGCCAGGTGCTGTTGGCTCAAGGACTCCTACTGCACTTTCTTGCTAGAGCTTGGAC
CTGGCCTGATGCTTTGAACATTGAAAATTCAGACTCTGAATCATGGACTTCTCACACTGTTAAAAAATTTACTGTGTCAT
TTGAAGCATCACTGTCAGGGGAAAGTGAACTCAAAACTCCATCAATTTCTTTGATAAAAAAACAATTGAGAGATACTGTG
ATGATCATGAAACACGAAATGAAATTTATCACAGGAAAATCATCTCTTGGTTTGATAATTTCCCTTTGGCCCTCTTTGGT
TTACATCAACTAACAGAGTATGGAAGGAAGTTGTGGGAAAAAGCTGGACATTGGTATGGACCAGCTGTGGTTGCTCACGT
ATTAAGAAAAGCAGGTGAAGAAGCAAGACACCCTGATTTACAAAGGCTAACTATG

Alignment

ORF - retro_pcap_299 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.61 %
• Parental protein coverage: 50.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  WVLKTKTYFSRNSPVLLLGKCYHFKYEDENKVLPARSGCAIEDCVISGNVEEFRKDFISRIWLTYREEFP
          WVLKTKTYFSRNSPVL.LG..YHFKYEDENKVLPARSGCA.EDCVISGN.E.FRKDFISRIWL.Y.EEFP
Retrocopy WVLKTKTYFSRNSPVLVLGE-YHFKYEDENKVLPARSGCAMEDCVISGNAEDFRKDFISRIWLIYSEEFP

Parental  QIEGSTLTTDCGWGCTLRTGQMLLAQGLLLHFLGRAWTWPDALNIENSDSESWTSHTVKKFTASFEASLS
          QIEGS.LTTDCGWGCTLRTGQ.LLAQGLLLHFL.RAWTWPDALNIENSDSESWTSHTVKKFT.SFEASLS
Retrocopy QIEGSVLTTDCGWGCTLRTGQVLLAQGLLLHFLARAWTWPDALNIENSDSESWTSHTVKKFTVSFEASLS

Parental  GESELKTPSVSL-KK-TIERYCDDRETRNEIYHRKIISWFGDSPLALFGLHQLIEYGKKSGKKAGDWYGP
          GESELKTPS.SL.KK.TIERYCDD.ETRNEIYHRKIISWF...PLALFGLHQL.EYG.K...KAG.WYGP
Retrocopy GESELKTPSISLIKK<TIERYCDDHETRNEIYHRKIISWFDNFPLALFGLHQLTEYGRKLWEKAGHWYGP

Parental  AVVAHILRKAVEEARHPDLQGLTI
          AVVAH.LRKA.EEARHPDLQ.LT.
Retrocopy AVVAHVLRKAGEEARHPDLQRLTM

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_299 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000004020	1 retrocopy	retro_ogar_1034,
Procavia capensis	ENSPCAG00000003461	1 retrocopy	retro_pcap_299 ,