RetrogeneDB ID: retro_rnor_162

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: AABR06111698.1:39..1056(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000049528
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Marc2
• Ensembl ID: ENSRNOG00000037850
• Aliases: Marc2, Mg87, Mosc2, mARC1
• Description: MOSC domain-containing protein 2, mitochondrial precursor [Source:RefSeq peptide;Acc:NP_599237]

Sequence

>retro_rnor_162
ATGGGTTCCTCCAGCTCTACGGCTCTGGCTCGCCTCGGCCTCCCTGGGCAGCCGCGGTCCACCTGGCTCGGCGTCGCCGC
GCTGGGGCTGGCTGCGGTGGCGCTGGGGACCGTAGCTTGGCGTCGCACGCGTCCCCGGCGGCGCCGGCAGCTGCAGCAGG
TGGGCACGGTGTCGAAGGTTTGGATCTACCCGATCAAGTCCTGCAAGGGGGTGTCGGTGTGTGAGACCGAGTGCACGGAC
ATGGGGCTGCGCTGTGGCAAAGTGCGCGACAGGTTCTGGATGGTGGTGAAGGAGGACGGACACATGGTCACTGCCCACCA
GGAGCCTCGCCTTGTGCTGGTCTCCATCACCCTGGAGAACAATTACCTGACGCTGGAAGCTCCAGGCATGGAGCAGATAG
TTCTGCCAATCAAGCTCCCTTCTTCGAATAAGATCCACAACTGCAGGCTGTTTGGTCTCGACATCAAAGGCAGAGATTGT
GGCGATGAGGTAGCTCAGTGGTTCACCAACTACCTGAAGACGCAAGCCTACAGGTTGGTTCAGTTTGATACCAGCATGAA
AGGAAGAACAACGAAGAAACTTTACCCTTCTGAAAGTTACCTTCAGAACTATGAGGTAGCCTACCCGGACTGCAGCCCTG
TCCACCTGATTTCTGAAGCCTCCTTAGTCGATCTCAACACCAGGCTGAAGAAGAAAGTGAAGATGGAATATTTCAGGCCA
AACATCGTGGTGTCAGGCTGTGAGGCTTTCGAGGAGGATACTTGGGATGAACTCCTGATTGGTGACGTGGAGATGAAAAG
GGTGTTGAGCTGTCCCAGGTGCGTTTTGACTACAGTGGACCCAGACACCGGCATCATAGACAGGAAGGAGCCACTGGAGA
CCCTGAAGAGCTATCGCCTGTGTGATCCTTCTGTGAAGAGTATATACCAGTCATCTCCACTTTTTGGGATGTATTTCTCG
GTGGAGAAGCTTGGGAGCCTGAGAGTGGGTGACCCTGTGTACCGGATGGTGGATTAG

Alignment

ORF - retro_rnor_162 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.56 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGSSSSTALARLGLPGQPRSTWLGVAALGLAAVALGTVAWRRARPRRRRQLQQVGTVSKVWIYPIKSCKG
          MGSSSSTALARLGLPGQPRSTWLGVAALGLAAVALGTVAWRR.RPRRRRQLQQVGTVSKVWIYPIKSCKG
Retrocopy MGSSSSTALARLGLPGQPRSTWLGVAALGLAAVALGTVAWRRTRPRRRRQLQQVGTVSKVWIYPIKSCKG

Parental  VSVCETECTDMGLRCGKVRDRFWMVVKEDGHMITARQEPRLVLVTITLENNYLMLEAPGMEPIVLPIKLP
          VSVCETECTDMGLRCGKVRDRFWMVVKEDGHM.TA.QEPRLVLV.ITLENNYL.LEAPGME.IVLPIKLP
Retrocopy VSVCETECTDMGLRCGKVRDRFWMVVKEDGHMVTAHQEPRLVLVSITLENNYLTLEAPGMEQIVLPIKLP

Parental  SSNKIQDCRLFGLDIKGRDCGDEVARWFTSYLKTQAYRLVQFDTKMKGRTTKKLYPSESYLQNYEVAYPD
          SSNKI..CRLFGLDIKGRDCGDEVA.WFT.YLKTQAYRLVQFDT.MKGRTTKKLYPSESYLQNYEVAYPD
Retrocopy SSNKIHNCRLFGLDIKGRDCGDEVAQWFTNYLKTQAYRLVQFDTSMKGRTTKKLYPSESYLQNYEVAYPD

Parental  CSPIHLISEASLVDLNTRLQKKVKMEYFRPNIVVSGCEAFEEDTWDELLIGDVEMKRVLSCPRCVLTTVD
          CSP.HLISEASLVDLNTRL.KKVKMEYFRPNIVVSGCEAFEEDTWDELLIGDVEMKRVLSCPRCVLTTVD
Retrocopy CSPVHLISEASLVDLNTRLKKKVKMEYFRPNIVVSGCEAFEEDTWDELLIGDVEMKRVLSCPRCVLTTVD

Parental  PDTGIIDRKEPLETLKSYRLCDPSVKSLYQSSPLFGMYFSVEKIGSLRVGDPVYRMVD
          PDTGIIDRKEPLETLKSYRLCDPSVKS.YQSSPLFGMYFSVEK.GSLRVGDPVYRMVD
Retrocopy PDTGIIDRKEPLETLKSYRLCDPSVKSIYQSSPLFGMYFSVEKLGSLRVGDPVYRMVD

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	21.71 RPM
SRP017611_kidney	0.00 RPM	75.36 RPM
SRP017611_liver	0.00 RPM	110.13 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_162 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_162 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_162 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011332	1 retrocopy	retro_cfam_469,
Oryctolagus cuniculus	ENSOCUG00000013162	1 retrocopy	retro_ocun_1466,
Rattus norvegicus	ENSRNOG00000037850	1 retrocopy	retro_rnor_162 ,
Ictidomys tridecemlineatus	ENSSTOG00000006676	1 retrocopy	retro_itri_1413,