RetrogeneDB ID: retro_pcap_238

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_204239:1241..1683(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL20
• Ensembl ID: ENSPCAG00000001425
• Aliases: None
• Description: mitochondrial ribosomal protein L20 [Source:HGNC Symbol;Acc:14478]

Sequence

>retro_pcap_238
ATCTTCCTTAGGATGCAAGTTTGGCTGCTGAACCAACTCACTGACCATTATTGGCAAATCTAAAAGGTGCTGAAGCATGC
CCAGACTTCAGGGGAAGGAAAAATACATGCCGCAGATTGGTCATCAGAGCTGTGACTAGAGCATTTGTGAAATGTACAAA
AAGCATGAAGAGTGAAGAAAAGGAACATGAGGACACCTTGGATCCATTGAATCACAGCTGCTTTTCAAGATCATGGCCTG
AAGCACCAAGCCTTTTTTGGCAATTTAATTAAGTGCCAGGTGGAGCTCAACAGGAAAGCGCTTGCAGACCTGGCCACCTA
CTAGTCAACGACTTTTAAATCTGTCAGCTTTGGCCGAAAGGAAGAGAGAGGAGGGATTTGCTGCTGTCTTAGAGGGTGGA
AAGGGGCCAGAAGGCATGTTCTCCCACGTGGTGCACTACCGC

Alignment

ORF - retro_pcap_238 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.23 %
• Parental protein coverage: 99.33 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VFLTTQLWLRNRVTDRYWRIQEVLKHAR-HFRGRKNRCYRLAVRAVIRAFVKCTK-ARRLKKRNMRTLWI
          .FL..Q.WL.N..TD.YW.I..VLKHA...FRGRKN.C.RL..RAV.RAFVKCTK.A.R.KKRNMRT.WI
Retrocopy IFLRMQVWLLNQLTDHYWQI*KVLKHAQ<DFRGRKNTCRRLVIRAVTRAFVKCTK>A*RVKKRNMRTPWI

Parental  SRITAASEEHGLKYPAFISNLIKCQVELNRKVLADLAIYEPKTFKSL-AALAKRRREEGFAAALGDGKEP
          ..ITAA...HGLK..AF..NLIKCQVELNRK.LADLA.Y...TFKS..A.....R.EEGFAA.L..GK.P
Retrocopy H*ITAAFQDHGLKHQAFFGNLIKCQVELNRKALADLATY*STTFKSV>ALAERKR-EEGFAAVLEGGKGP

Parental  EGVFSRVVHYR
          EG.FS.VVHYR
Retrocopy EGMFSHVVHYR

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_238 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013932	2 retrocopies	retro_amel_143, retro_amel_545,
Canis familiaris	ENSCAFG00000019259	2 retrocopies	retro_cfam_2112, retro_cfam_826,
Dasypus novemcinctus	ENSDNOG00000010105	1 retrocopy	retro_dnov_1620,
Homo sapiens	ENSG00000242485	1 retrocopy	retro_hsap_2508,
Gorilla gorilla	ENSGGOG00000027251	1 retrocopy	retro_ggor_1565,
Myotis lucifugus	ENSMLUG00000011857	1 retrocopy	retro_mluc_1423,
Monodelphis domestica	ENSMODG00000006562	2 retrocopies	retro_mdom_1424, retro_mdom_719,
Mus musculus	ENSMUSG00000029066	1 retrocopy	retro_mmus_1624,
Otolemur garnettii	ENSOGAG00000005968	1 retrocopy	retro_ogar_2263,
Procavia capensis	ENSPCAG00000001425	1 retrocopy	retro_pcap_238 ,
Tupaia belangeri	ENSTBEG00000008735	2 retrocopies	retro_tbel_2193, retro_tbel_892,