RetrogeneDB ID: retro_pcap_66

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: GeneScaffold_3704:309511..309974(+)
• Located in intron of: ENSPCAG00000000744

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLMO1
• Ensembl ID: ENSPCAG00000001084
• Aliases: None
• Description: slowmo homolog 1 (Drosophila) [Source:HGNC Symbol;Acc:24639]

Sequence

>retro_pcap_66
ATGAAGATCTGGACCTCTGAGCACGTCTTTGACCACCTGTGGGAAACGGTCACAACAGCTGCCATGCAGAAGTACCCCAA
CCCCATGAACCCCAGCGTGGTCGGGGTCGACGTCCCGCACAGACACGGGGATCCCTCTGGGAAGCTGCACAGCCACCGGC
TTCTCAGCACCGAGTGGGGCCTGCCCTCCATCGTGAAGTCGATCATTGGTGCAGCCATAACCAAGACGTACATGCAGGAG
CATTCTGTGGTGGATCCTGTGGGAAGGACGATGGAGTTGAAATCCACTAATATTTCATTTACAAACATGGTTTCAGTAGA
TGAGAGACTGATGCACAAACCACATCCTCAGGGCCCAGAAAAAACATTCTAACTCAACAAGCCCTCATCACTGTGAAGGG
GTCAGCCTCAGCAGCTACCTGGAAGGCCACATGGCTAGTGCCATCTCATCCAACGCCAGCAAG

Alignment

ORF - retro_pcap_66 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.24 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MKTWSSEHVFSYPWDTVIKAAMRKYPNPMNPSVVGVDVLERTVDCRGRLHSYRLLSTEWGLPTIVKAILG
          MK.W.SEHVF...W.TV..AAM.KYPNPMNPSVVGVDV..R..D..G.LHS.RLLSTEWGLP.IVK.I.G
Retrocopy MKIWTSEHVFDHLWETVTTAAMQKYPNPMNPSVVGVDVPHRHGDPSGKLHSHRLLSTEWGLPSIVKSIIG

Parental  TRRTLTYITEHSVVDPVEKKMELCSTNITLTNLVSVDERLVYTPHLENSEMT-VLTQEAIITVK-GISLG
          ...T.TY..EHSVVDPV...MEL.STNI..TN.VSVDERL...PH....E.T..LTQ.A.ITVK.G.SL.
Retrocopy AAITKTYMQEHSVVDPVGRTMELKSTNISFTNMVSVDERLMHKPHPQGPEKT<ILTQQALITVK<GVSLS

Parental  SYLESLMANTISSNAKK
          SYLE..MA..ISSNA.K
Retrocopy SYLEGHMASAISSNASK

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_66 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012800	2 retrocopies	retro_amel_1395, retro_amel_330,
Mus musculus	ENSMUSG00000024530	1 retrocopy	retro_mmus_1332,
Oryctolagus cuniculus	ENSOCUG00000022237	1 retrocopy	retro_ocun_723,
Procavia capensis	ENSPCAG00000001084	1 retrocopy	retro_pcap_66 ,