RetrogeneDB ID: retro_rnor_2872

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:134632805..134633791(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000021419
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Btbd10
• Ensembl ID: ENSRNOG00000014341
• Aliases: Btbd10, RGD1306301
• Description: BTB/POZ domain-containing protein 10 [Source:RefSeq peptide;Acc:NP_001014044]

Sequence

>retro_rnor_2872
TCTGTGGAGATGGTGTTTGTGTATGAGAATGCAAAAGAAGGGGCTCAGAATGTGAGGACATCTGAGCGAGTGACCCTGAT
AGTGGATAACACCAGATTTGTTGAGGACCTGTCCATTTTTCCTGCACATCCAAATACAATGTTGGGCAGAATGTTTGGAT
CTGACCGGGAATACAATTTCTCACCTCCCAATGAGAAGGGAGAATATGAGGTGGCAAGGGGAATTGGTTCTACTGTATTT
CAAGCTATTTTGGATTACTATAAGACAGGAATTATCAGTTGTCCTGATGGCATATCTATTCCTGAACTGAGAGAAGCATG
CAATTACCTTTGTATTTCTTTGGAATACAGCACAATTAAATGTAGAGATCTCGGTGCCCTTATGAATGAATTATCAAACG
ATGGTGCACGTAGAGAATTTGAATTTTATCTGGAGGAAATGATCCTCCCTCTCATGGTAGCAAGGGCCCAGGGTGGAGAA
CGAGAGTGCCATATAGTAGTGCTTACAGACGATGATGTGGTTGATTGGGATGAGGAGTATCCACCACAGATGGGAGAGGA
GTATTCACAGGTTATTCATAGCACAAAATTATATAGATTCTCAAAGTACATTGAAAACAGAAATGTGGCCAAAGCAGTTT
TGAAAGAGAGGGGTCTTAAGATTAGATTTGGAATAGAAGGCTACCCTAGCAACAAAGGAAAAGTTAAGAAAAGGCCAGGG
GGCCGTCCAGAAGTCATTTACAACTATGTCCAAAGACCCTTCATTCAGATGTCCTGGGAGAAGGAGGAAGGAAAGAGTCA
GCATGTCGACTCTCGGTGTGTAAAGAGTAAATCTATCACCAACCTGGCAGCACCTGCTGCAGACATTGCCCAGGACCAGC
TGGTAGTCATGCACCCTACTCCCCAGGAGGATGAGCTGGATAGCCTTCCCAGCCACCCCGCCTCAGCAACAATGACCTTG
ATCCTGGTGCACAGAAGTCAATGCTG

Alignment

ORF - retro_rnor_2872 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.01 %
• Parental protein coverage: 77.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SGEMVFVYENAKEGARSVRTSERVTLIVDNTRFVVDPSIFTAQPNTMLGRMFGSGREHNFTRPNEKGEYE
          S.EMVFVYENAKEGA..VRTSERVTLIVDNTRFV.D.SIF.A.PNTMLGRMFGS.RE.NF..PNEKGEYE
Retrocopy SVEMVFVYENAKEGAQNVRTSERVTLIVDNTRFVEDLSIFPAHPNTMLGRMFGSDREYNFSPPNEKGEYE

Parental  VAEGIGSTVFRAILDYYKTGIIRCPDGISIPELREACDYLCISFEYSTIKCRDLSALMHELSNDGARRQF
          VA.GIGSTVF.AILDYYKTGII.CPDGISIPELREAC.YLCIS.EYSTIKCRDL.ALM.ELSNDGARR.F
Retrocopy VARGIGSTVFQAILDYYKTGIISCPDGISIPELREACNYLCISLEYSTIKCRDLGALMNELSNDGARREF

Parental  EFYLEEMILPLMVASAQSGERECHIVVLTDDDVVDWDEEYPPQMGEEYSQIIYSTKLYRFFKYIENRDVA
          EFYLEEMILPLMVA.AQ.GERECHIVVLTDDDVVDWDEEYPPQMGEEYSQ.I.STKLYRF.KYIENR.VA
Retrocopy EFYLEEMILPLMVARAQGGERECHIVVLTDDDVVDWDEEYPPQMGEEYSQVIHSTKLYRFSKYIENRNVA

Parental  KSVLKERGLKKIRLGIEGYPTYKEKVKKRPGGRPEVIYNYVQRPFIRMSWEKEEGKSRHVDFQCVKSKSI
          K.VLKERGL.KIR.GIEGYP..K.KVKKRPGGRPEVIYNYVQRPFI.MSWEKEEGKS.HVD..CVKSKSI
Retrocopy KAVLKERGL-KIRFGIEGYPSNKGKVKKRPGGRPEVIYNYVQRPFIQMSWEKEEGKSQHVDSRCVKSKSI

Parental  TNLAAAAADIPQDQLVVMHPTPQVDELDSLPSHPAS-GNNDLDPDAQNPML
          TNLAA.AADI.QDQLVVMHPTPQ.DELDSLPSHPAS..NNDLDP.AQ..ML
Retrocopy TNLAAPAADIAQDQLVVMHPTPQEDELDSLPSHPAS<SNNDLDPGAQKSML

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	47.52 RPM
SRP017611_kidney	0.00 RPM	10.12 RPM
SRP017611_liver	0.00 RPM	3.29 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2872 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2872 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2872 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000024984	1 retrocopy	retro_cpor_137,
Monodelphis domestica	ENSMODG00000008728	1 retrocopy	retro_mdom_1020,
Mus musculus	ENSMUSG00000038187	1 retrocopy	retro_mmus_3560,
Nomascus leucogenys	ENSNLEG00000017691	1 retrocopy	retro_nleu_232,
Otolemur garnettii	ENSOGAG00000000739	1 retrocopy	retro_ogar_3201,
Pan troglodytes	ENSPTRG00000003377	1 retrocopy	retro_ptro_753,
Rattus norvegicus	ENSRNOG00000014341	2 retrocopies	retro_rnor_2220, retro_rnor_2872 ,
Sorex araneus	ENSSARG00000000266	1 retrocopy	retro_sara_405,
Sus scrofa	ENSSSCG00000013395	2 retrocopies	retro_sscr_639, retro_sscr_640,
Tarsius syrichta	ENSTSYG00000000445	2 retrocopies	retro_tsyr_196, retro_tsyr_367,
Tursiops truncatus	ENSTTRG00000013943	1 retrocopy	retro_ttru_897,