RetrogeneDB ID: retro_mmus_3560

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:167776248..167777298(+)
• Located in intron of: ENSMUSG00000049176

Retrocopy information

• Ensembl ID: ENSMUSG00000084378
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Btbd10
• Ensembl ID: ENSMUSG00000038187
• Aliases: Btbd10, 1110056N09Rik, Gmrp1
• Description: BTB (POZ) domain containing 10 [Source:MGI Symbol;Acc:MGI:1916065]

Sequence

>retro_mmus_3560
ACAATAGGGTGCTCTGCCTCACCTGTTGCTAAGGGAAGAGTCAACCACACCAAAATGAGTCTGCATGGTGCTCGTGGGGG
CCATGAGAGATCAAGAAATAGACGAAGGTCAAGTGACAGATCACAAGATTCATCTCATGAGAGAGCAGAGTCTCAGCTCA
CTCCTTGTATTAGAAATGTGACAACAAGGCAGCATCATATTGAACGAGAAAAAGATCATAGTTCTTCTCGTCCAAGCAGT
CCTCGTCCTCAAAGAGCATCCCCAAATGGCTCCATGAGCAGTGCTGGGAACAGTAGCAGGAACAGCAGTCAGTCAAGCTC
AGATGGTAGCTGTAAAACATCTGGGGAGATGGTGTTTGTGTATGGGAATGCAGAAGAAGGGCCTGGGAATGGGAAGACAT
CTGAGCGAGTGACCCTGATAGTGGATAACACCAGATCTGTTGTGGACCTGTCCATTTTTACTGCACAGCCAAATACAATG
TTGGGCAGGATGGTTGGATCTGGCCAGAAACATAATTTCACATGTCCCAACGAGAAAGGAGAATATGAGGTGGCAGAGGG
AATTGGTTCTACTGTGTTTCGAGCTATTTTGGATTACTATAAGAGAGGAATCATCCCCTGTCCTAATGGCATATCTATTC
CTGAACTGAGAGACACATGTGATTACCTTTGTATCTCTTTTGAATACAGTAGAATTAAATGTCGAGATCTCTGTGCCCTT
AAGCATGAGTTATCAAATGATGGGACTCATAGACAATTTGAATTTTATCTGGAAGAAATGATTCTCCCTCTCGTGGTAGC
AAGCATCCAGAGTGGGGAATGAGAGTGCCATATTGTAGTGCTTCCAGATGATGATGTAGTTGATTGGGATGAGGAGTATC
CACCACAGATGGGAGAGGAATATTCACAGATTATTTATAGCACACAATTACGTAGATTTTTCAAGTATATTGAAAACAGA
GATGTGGTCAAATCAGTTTTGAAGGAGAGGGGTCTTAAGAAGATTAGGATGGGAATAGAAGGCTATCCTACCTACAAAGA
AAAGGCCAGG

Alignment

ORF - retro_mmus_3560 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.07 %
• Parental protein coverage: 72.88 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TKGSSASRVAKGGVDHTKMSLHGASGGHERSRDRRRSSDRSRDSSHERAESQLTPCIRNVTSPTRQHHIE
          T.G.SAS.VAKG.V.HTKMSLHGA.GGHERSR.RRRSSDRS.DSSHERAESQLTPCIRNVT..TRQHHIE
Retrocopy TIGCSASPVAKGRVNHTKMSLHGARGGHERSRNRRRSSDRSQDSSHERAESQLTPCIRNVT--TRQHHIE

Parental  REKDHSSSRPSSPRPQRASPNGSMSSAGNSSRNSSQSSSDGSCKTSGEMVFVYENAKEGARNVRTSERVT
          REKDHSSSRPSSPRPQRASPNGSMSSAGNSSRNSSQSSSDGSCKTSGEMVFVY.NA.EG..N..TSERVT
Retrocopy REKDHSSSRPSSPRPQRASPNGSMSSAGNSSRNSSQSSSDGSCKTSGEMVFVYGNAEEGPGNGKTSERVT

Parental  LIVDNTRFVVDPSIFTAQPNTMLGRMFGSGREHNFTRPNEKGEYEVAEGIGSTVFRAILDYYKTGIIRCP
          LIVDNTR.VVD.SIFTAQPNTMLGRM.GSG..HNFT.PNEKGEYEVAEGIGSTVFRAILDYYK.GII.CP
Retrocopy LIVDNTRSVVDLSIFTAQPNTMLGRMVGSGQKHNFTCPNEKGEYEVAEGIGSTVFRAILDYYKRGIIPCP

Parental  DGISIPELREACDYLCISFEYSTIKCRDLSALMHELSNDGARRQFEFYLEEMILPLMVASAQSGERECHI
          .GISIPELR..CDYLCISFEYS.IKCRDL.AL.HELSNDG..RQFEFYLEEMILPL.VAS.QSGE.ECHI
Retrocopy NGISIPELRDTCDYLCISFEYSRIKCRDLCALKHELSNDGTHRQFEFYLEEMILPLVVASIQSGE*ECHI

Parental  VVLTDDDVVDWDEEYPPQMGEEYSQIIYSTKLYRFFKYIENRDVAKSVLKERGLKKIRLGIEGYPTYKEK
          VVL.DDDVVDWDEEYPPQMGEEYSQIIYST.L.RFFKYIENRDV.KSVLKERGLKKIR.GIEGYPTYKEK
Retrocopy VVLPDDDVVDWDEEYPPQMGEEYSQIIYSTQLRRFFKYIENRDVVKSVLKERGLKKIRMGIEGYPTYKEK

Parental  VK
          ..
Retrocopy AR

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
SRP007412_brain	0.00 RPM	72.21 RPM
SRP007412_cerebellum	0.00 RPM	46.29 RPM
SRP007412_heart	0.00 RPM	11.08 RPM
SRP007412_kidney	0.00 RPM	11.01 RPM
SRP007412_liver	0.00 RPM	3.85 RPM
SRP007412_testis	0.05 RPM	155.42 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3560 was not detected

EST

No EST(s) were mapped for retro_mmus_3560 retrocopy.

TSS

No TSS is located nearby retro_mmus_3560 retrocopy 5' end.

Lab

retro_mmus_3560 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3560 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,