RetrogeneDB ID: retro_rnor_2720

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 9:13826236..13826762(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mrpl13
• Ensembl ID: ENSRNOG00000004401
• Aliases: None
• Description: 39S ribosomal protein L13, mitochondrial [Source:RefSeq peptide;Acc:NP_001006986]

Sequence

>retro_rnor_2720
GTGTCTGGTTTCTCTAAGGCGCCCCAGCAGTGGGCCACTTTTGCTTGAATGTGGTATCTCTTGAATGGCAAAATGCAGCC
CCCCTGGCAAACTTGCGGCCGTAGCATCCAATAAATGGAAAGGGTTACACAAACCAGTGTGCCATCAGCTGGGTGATTGT
GGGGACCACATTGTCATAATAAGCACAAGACACATTGCGTTTTCTGGAAACAAATGGGAAGGAAAAGTGTGCTCTTCACA
TCCTGGCTACCCAGGGGGCTTCAGACAGGCGGCAGCTGCCCAGCGTCACCTGAAGGACCCAGTGGCGATGGTGAAGTTAG
CGACTTGTGACACGCTGCCTGAAATCCTGCACAGAAGGACAAGGATGCAAAGGCTGCATCTTTTTCCAGATGAGGATATC
CCAGAAGAGATTCTGAAAGATCTAGTGGAAGAGCTCCCTCAACCACGGAGAGTGCCTAAGGGCTGGACAAGTACACTCAA
GAAGAAACAGAGGTTTTCCCCGAGAGTGTGGGCTCCACCTGAGAAT

Alignment

ORF - retro_rnor_2720 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.34 %
• Parental protein coverage: 98.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSSFSKAPQQWATFARMWYLLDGKMQPP-GKLAAIASNKLQGLHKPVYHQLSDCGDHVVIINTRHIAFSG
          .S.FSKAPQQWATFA.MWYLL.GKMQPP.GKLAA.ASNK..GLHKPV.HQL.DCGDH.VII.TRHIAFSG
Retrocopy VSGFSKAPQQWATFA*MWYLLNGKMQPP>GKLAAVASNKWKGLHKPVCHQLGDCGDHIVIISTRHIAFSG

Parental  NKWEQKVYSSHTGYPGGFRQVTAAQLHLKDPVAIVKLATYGMLPKNLHRRTMMQRLHLFPDEDIPEDILK
          NKWE.KV.SSH.GYPGGFRQ..AAQ.HLKDPVA.VKLAT...LP..LHRRT.MQRLHLFPDEDIPE.ILK
Retrocopy NKWEGKVCSSHPGYPGGFRQAAAAQRHLKDPVAMVKLATCDTLPEILHRRTRMQRLHLFPDEDIPEEILK

Parental  NLVEELPQPRRVPK-RLDEYTQEEIEAF-PRVWAPPDD
          .LVEELPQPRRVPK..LD.YTQEE.E.F.PRVWAPP..
Retrocopy DLVEELPQPRRVPK<GLDKYTQEETEVF>PRVWAPPEN

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	17.18 RPM
SRP017611_kidney	0.00 RPM	21.84 RPM
SRP017611_liver	0.00 RPM	10.49 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2720 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2720 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2720 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006926	1 retrocopy	retro_chof_648,
Callithrix jacchus	ENSCJAG00000005359	1 retrocopy	retro_cjac_162,
Dipodomys ordii	ENSDORG00000016654	1 retrocopy	retro_dord_480,
Equus caballus	ENSECAG00000021161	1 retrocopy	retro_ecab_952,
Mustela putorius furo	ENSMPUG00000001080	2 retrocopies	retro_mputfur_1585, retro_mputfur_623,
Oryctolagus cuniculus	ENSOCUG00000016189	1 retrocopy	retro_ocun_675,
Ochotona princeps	ENSOPRG00000015721	2 retrocopies	retro_opri_274, retro_opri_454,
Pteropus vampyrus	ENSPVAG00000003719	1 retrocopy	retro_pvam_627,
Rattus norvegicus	ENSRNOG00000004401	1 retrocopy	retro_rnor_2720 ,
Sus scrofa	ENSSSCG00000005996	1 retrocopy	retro_sscr_1183,
Tupaia belangeri	ENSTBEG00000004571	5 retrocopies	retro_tbel_1026, retro_tbel_1596, retro_tbel_2517, retro_tbel_3095, retro_tbel_456,