RetrogeneDB ID: retro_rnor_1804

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:89672366..89672993(+)
• Located in intron of: ENSRNOG00000009630

Retrocopy information

• Ensembl ID: ENSRNOG00000032900
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Timm23
• Ensembl ID: ENSRNOG00000019811
• Aliases: None
• Description: mitochondrial import inner membrane translocase subunit Tim23 [Source:RefSeq peptide;Acc:NP_062225]

Sequence

>retro_rnor_1804
ATGGAGGGTGGCGGAGGAAGTAGCAACAAATCCACCGGCGGGTTAGCGGGCTTCTTCGGAGCGGGAGGAGCGGGTTACTC
GAACGCTGATTTGGCCGGCGTCCCGCTGACTGGTATGAACCCCCTGTCTCCTTACTTAAATGTGGACCCACGCTATCTCG
TTCAGGATACAGATGAGTTTATTTTGCCAACTGGAGCTAATAAAACCCGAGGCAGGTTTGAACTGGCTTTCTTCACCATT
GGAGGATGCTGCATGACAGGGGCTGCATTCGGGGCACTGAACGGGCTTCGTTTAGGATTGAAGGAAACTCAGAGCATGCC
CTGGTCCAAACCAAGAAATGTACAGATTTTGAATATGGTGACTAGACAAGGGGCACTTTGGGCTAATACTCTAGGTTCCC
TGGCTTTGCTCTATAGTGCTTTTGGCGTTATCATTGAGAAAACACGGGGTGCAGAAGATGACCTCAACACAGTAGCAGCT
GGAACCATGACAGGAATGTTATATAAATGTACAGGTGGTCTTCGAGGAATAGCACGTGGTGGCCTGGCGGGACTGACACT
CACCAGTGTCTATGCACTGTATAACAACTGGGAGCACATGAAAGGTTCCCTGCTCCAACAGTCACTC

Alignment

ORF - retro_rnor_1804 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MEGGGGSSNKSTGGLAGFFGAGGAGYSNADLAGVPLTGMNPLSPYLNVDPRYLVQDTDEFILPTGANKTR
          MEGGGGSSNKSTGGLAGFFGAGGAGYSNADLAGVPLTGMNPLSPYLNVDPRYLVQDTDEFILPTGANKTR
Retrocopy MEGGGGSSNKSTGGLAGFFGAGGAGYSNADLAGVPLTGMNPLSPYLNVDPRYLVQDTDEFILPTGANKTR

Parental  GRFELAFFTIGGCCMTGAAFGALNGLRLGLKETQSMPWSKPRNVQILNMVTRQGALWANTLGSLALLYSA
          GRFELAFFTIGGCCMTGAAFGALNGLRLGLKETQSMPWSKPRNVQILNMVTRQGALWANTLGSLALLYSA
Retrocopy GRFELAFFTIGGCCMTGAAFGALNGLRLGLKETQSMPWSKPRNVQILNMVTRQGALWANTLGSLALLYSA

Parental  FGVIIEKTRGAEDDLNTVAAGTMTGMLYKCTGGLRGIARGGLAGLTLTSVYALYNNWEHMKGSLLQQSL
          FGVIIEKTRGAEDDLNTVAAGTMTGMLYKCTGGLRGIARGGLAGLTLTSVYALYNNWEHMKGSLLQQSL
Retrocopy FGVIIEKTRGAEDDLNTVAAGTMTGMLYKCTGGLRGIARGGLAGLTLTSVYALYNNWEHMKGSLLQQSL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.14 RPM	18.33 RPM
SRP017611_kidney	0.07 RPM	39.64 RPM
SRP017611_liver	0.34 RPM	28.64 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1804 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1804 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1804 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007501	1 retrocopy	retro_amel_1488,
Canis familiaris	ENSCAFG00000029477	1 retrocopy	retro_cfam_329,
Choloepus hoffmanni	ENSCHOG00000007073	1 retrocopy	retro_chof_797,
Callithrix jacchus	ENSCJAG00000013336	1 retrocopy	retro_cjac_2965,
Cavia porcellus	ENSCPOG00000019917	2 retrocopies	retro_cpor_1013, retro_cpor_321,
Monodelphis domestica	ENSMODG00000002661	2 retrocopies	retro_mdom_1202, retro_mdom_860,
Mus musculus	ENSMUSG00000013701	1 retrocopy	retro_mmus_2,
Oryctolagus cuniculus	ENSOCUG00000000525	1 retrocopy	retro_ocun_73,
Otolemur garnettii	ENSOGAG00000015393	1 retrocopy	retro_ogar_2627,
Ochotona princeps	ENSOPRG00000005255	2 retrocopies	retro_opri_520, retro_opri_920,
Procavia capensis	ENSPCAG00000015914	1 retrocopy	retro_pcap_181,
Rattus norvegicus	ENSRNOG00000019811	3 retrocopies	retro_rnor_1804 , retro_rnor_225, retro_rnor_661,
Sorex araneus	ENSSARG00000010335	1 retrocopy	retro_sara_86,
Sus scrofa	ENSSSCG00000025276	1 retrocopy	retro_sscr_404,
Ictidomys tridecemlineatus	ENSSTOG00000007041	1 retrocopy	retro_itri_1043,