RetrogeneDB ID: retro_pcap_155

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_11862:14078..14795(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL28
• Ensembl ID: ENSPCAG00000011480
• Aliases: None
• Description: mitochondrial ribosomal protein L28 [Source:HGNC Symbol;Acc:14484]

Sequence

>retro_pcap_155
GAAGGCATCTGCTCGTGCCTGCCACAGCACTACCTGCACTCCCTGGAAGAAGTGCCCAAGCCCACTCCCCTCCAGTACAG
GCCCCATGGGGCCAAGTTCAAGATCAACCCCAAGAATAGGCAGTGAAAGTGTGTGGATGGCTTGCCGATACTCCTTTACT
ATCCCCCTGAGTTCCAGCTGGGGCTGTGGAGTGGTGAGGGCTGGACACTGGGCCACAGATAATGTCAGGAACCGCAAGGC
TCCAAGAGGGTGAAGAAGGTCTGGAAGCCATTGCTATTCTAGCACGAGCTGAACAGTGAGATCCTGGACAAGGCGTTCTC
TGTGACTGTGACCATGAGGACACTGGACCTAATGGATAAGGCCTATAGGTCTGACTTCTACATCCTCAAGACCCCAAAGG
AGGTCCCATGTTCCAAATTCGTGATGGACTTGAAGCTTGGCATGCTGCTGTACCTTGCCTGGTGGGACACACAGCTGCAC
CCGGACGACCCAGAGTGGAGGGCGGCCGTCCACAACAGGTACAAGGAGTTTGCCATCCCTGAGGCTGAGATGGAGTGGGG
GGGCCTGAGGCTGGATGAGGCTGCAGAGAAGCAGTGGATCCTGGAGGAGAAGTACCCTGTCCCTCTGTTTAAGGTCTACG
TGGCTAAGCTGGTGCAAGAGCTTCAGCAGCAGGCACTGTCCGAGCCGGTGGTATCGCAGAAGAGGGTGATTGGTAAG

Alignment

ORF - retro_pcap_155 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.9 %
• Parental protein coverage: 93.36 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EGIYSRLPQHYLRSLEEAPAPTPVHYRPHGAKFRINPKNGQRERVENVPIPLYYPPESQLGLWGGEGWIL
          EGI.S.LPQHYL.SLEE.P.PTP..YRPHGAKF.INPKN.Q...V...PI.LYYPPE.QLGLW.GEGW.L
Retrocopy EGICSCLPQHYLHSLEEVPKPTPLQYRPHGAKFKINPKNRQ*KCVDGLPILLYYPPEFQLGLWSGEGWTL

Parental  GHRYVRNRKRSKRVKKVWKPQLFQRELYSEILDKKFSVTVTMRTLDLIDEAYGFDFYILKTPKEDLCSKF
          GHR.......SKRVKKVWKP.LF..EL.SEILDK.FSVTVTMRTLDL.D.AY..DFYILKTPKE..CSKF
Retrocopy GHR*CQEPQGSKRVKKVWKPLLF*HELNSEILDKAFSVTVTMRTLDLMDKAYRSDFYILKTPKEVPCSKF

Parental  GMDLKRGMLLRLARQDPRLHPDDPERRAAIYDRYKEFAVPEAEAEWVGLTLDEAVEKQRLLEEKDPVPLF
          .MDLK.GMLL.LA..D..LHPDDPE.RAA...RYKEFA.PEAE.EW.GL.LDEA.EKQ..LEEK.PVPLF
Retrocopy VMDLKLGMLLYLAWWDTQLHPDDPEWRAAVHNRYKEFAIPEAEMEWGGLRLDEAAEKQWILEEKYPVPLF

Parental  KVYVAELVQQLQQQALSEPVVLPKRVIGK
          KVYVA.LVQ.LQQQALSEPVV..KRVIGK
Retrocopy KVYVAKLVQELQQQALSEPVVSQKRVIGK

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_155 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000000407	1 retrocopy	retro_meug_1004,
Mus musculus	ENSMUSG00000024181	1 retrocopy	retro_mmus_1956,
Procavia capensis	ENSPCAG00000011480	1 retrocopy	retro_pcap_155 ,