RetrogeneDB ID: retro_rnor_2654

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 8:128143847..128144634(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000018786
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Mrrf
• Ensembl ID: ENSRNOG00000025997
• Aliases: None
• Description: Ribosome-recycling factor, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q5RKI9]

Sequence

>retro_rnor_2654
GTGGCCTTGGGAATAAGATGCTTTCGCCTACTGCACCCTGCCTTTCGCAGTTACCTGGCTGATTTGAGCAGACCTGTTTC
AGAAGTTCCCATGAAGACAGTGTGTGAAAGACAACATGATCATATACAGTACTCAGCCTACCCAGCAGAGCCAGTTCACC
ATTTTGCAACCAAGAAGGCCAAAGCCAAAGGGAAAGGACAGCCCCAGGCCAGAGTAAACATTAACACTGTCTTGGTTGAG
GACATAATCAGCTTGGAAGAGGTGGATGAAGACAATGAAATCTGTGGTGGAAGCACTTAAAGATAATTTCAATAAGACTC
TCAACATAAGGACTGCACCAGGATCCCTTGATCATATTACTGTGGTAACTGCTGATGGGAAGCTCCCTCTAAACCAGATT
GGCCAGATCTCCGTGAAGTCGCCGCAGCTGATTCTGGTGAATATGGCCAGCTTCCCAGAGTGTACAGCTACAGCTATCAA
GGCTATAAGAGAAAGTGGAATGAATCTGAACCCAGAAGTGGAAGGAACACTATTTCGGGTACCCATTCCTAAAGTAAGCA
GGGAACACAGAGAAATGCTGGTGAAACCGGCCAAACAGAACACCAACAAAGCCAAAGAAAGTTTACGGAAGGTTCGCACT
AATGCAATGAATAAACCGAAGAAGTCAAAGGACAAAACCTCGGAGGACACCATTAGGCTCATCGAGAAGCAGATCAGCCA
AATGGCGGACGACACTGTGGCAGAGCTGGACCAGCATCTGGCAGCAAAGACCAAAGAACTTCTTGGA

Alignment

ORF - retro_rnor_2654 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.02 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MALGIRCFRLLHPAFSSYLADLSRPVSEVPMKTVRGRQRDHIQYSAHPAVPVRQFATKKAKAKGKGQPQA
          .ALGIRCFRLLHPAF.SYLADLSRPVSEVPMKTV..RQ.DHIQYSA.PA.PV..FATKKAKAKGKGQPQA
Retrocopy VALGIRCFRLLHPAFRSYLADLSRPVSEVPMKTVCERQHDHIQYSAYPAEPVHHFATKKAKAKGKGQPQA

Parental  RVNINTALVEDIISLEEVDED-MKSVMEALKDNFNKTLNIRTAPGSLDHITVVTADGKLALNQIGQISMK
          RVNINT.LVEDIISLEEVDED.MKSV.EALKDNFNKTLNIRTAPGSLDHITVVTADGKL.LNQIGQIS.K
Retrocopy RVNINTVLVEDIISLEEVDED>MKSVVEALKDNFNKTLNIRTAPGSLDHITVVTADGKLPLNQIGQISVK

Parental  SPQLILVNMASFPECTAAAIKAIRESGMNLNPEVEGTLIRVPIPKVTREHREMLVKLAKQNTNKAKENLR
          SPQLILVNMASFPECTA.AIKAIRESGMNLNPEVEGTL.RVPIPKV.REHREMLVK.AKQNTNKAKE.LR
Retrocopy SPQLILVNMASFPECTATAIKAIRESGMNLNPEVEGTLFRVPIPKVSREHREMLVKPAKQNTNKAKESLR

Parental  KVRTNAMNKLKKSKDKTSEDTIRLIEKQISQMADDTVAELDRHLAAKTKELLG
          KVRTNAMNK.KKSKDKTSEDTIRLIEKQISQMADDTVAELD.HLAAKTKELLG
Retrocopy KVRTNAMNKPKKSKDKTSEDTIRLIEKQISQMADDTVAELDQHLAAKTKELLG

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	0.00 RPM	15.24 RPM
SRP017611_kidney	0.00 RPM	37.89 RPM
SRP017611_liver	0.00 RPM	17.68 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2654 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2654 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2654 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000007351	1 retrocopy	retro_cpor_877,
Homo sapiens	ENSG00000148187	1 retrocopy	retro_hsap_4897,
Gorilla gorilla	ENSGGOG00000023499	1 retrocopy	retro_ggor_98,
Mus musculus	ENSMUSG00000026887	1 retrocopy	retro_mmus_340,
Nomascus leucogenys	ENSNLEG00000017177	1 retrocopy	retro_nleu_1263,
Pongo abelii	ENSPPYG00000019570	1 retrocopy	retro_pabe_80,
Pan troglodytes	ENSPTRG00000021324	1 retrocopy	retro_ptro_3265,
Rattus norvegicus	ENSRNOG00000025997	2 retrocopies	retro_rnor_1477, retro_rnor_2654 ,
Sarcophilus harrisii	ENSSHAG00000012469	2 retrocopies	retro_shar_610, retro_shar_704,
Tupaia belangeri	ENSTBEG00000016569	1 retrocopy	retro_tbel_4411,