RetrogeneDB ID: retro_mmus_111

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:89404277..89406521(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000035395
• Aliases: Pet2, PC231, PC326, Pex3
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Dcaf8
• Ensembl ID: ENSMUSG00000026554
• Aliases: Dcaf8, AA408877, AA433120, AA792214, AU018973, C76055, D1Dau35e, D1Ucla4, H326, Wdr42a
• Description: DDB1 and CUL4 associated factor 8 [Source:MGI Symbol;Acc:MGI:91860]

Sequence

>retro_mmus_111
ATGTCATCTCATGAGAGCTACACAAATGCTGCAGAGACCCCTGAGAATATAAGCATACTCAGCTGCTTGGGTGAGACTTC
TGGTGCCCTGGTGGACACAAAGACAATTTCTGACATTAAAACTATGGATCCAGAAGTGAGTCTGACACCAAGCAGTGATG
TTACTGGCACTGAAGACAGCAGTGTTTTAAGCCCTCAAAGTACTGATGTAAATTCTGTTGATAGTTACCAGGGTTATGAG
GGTGACGATGACGACGAAGAAGATGATGAAGATGACAAAGATGGCGATTCCAATCTTCCCAGCTTGGAGGACTCTGACAA
TTTTATCAGCTGTTTGGAAAACTCATATATCCCTCAAAATGTAGAGAAGCGTGAGGTTGTGGAAGAGCAGAGTCTGGGAA
GGCGTTTTCATCCATACGAGTTGGAGGCTGGTGAGGTTGTGGAAGGGCAGGGAGGGGGAAGCCTGTTCTATCCATATGAG
CTGGAGGCTGGAGAAGTTGTGGAAGCACAGAATGTTCAAAACCTGTTCCACCGTTATGAGTTGGAAGAAGGTGAGGTTGT
AGAAGCACAGGTAGTACAAAGCATGTTTCCCTACTATGAGTTGGAGGCAGGAGAAGTTGTGGAAGCTGAGGAAGTGCAAG
GTTTTTTCCAACGTTATGAATTGGAGGCTAGAGAGGTTATAGGAGCACAGGGAGGACAAGGTCTTTCCCGCCATTATGGA
TTGGAGGGAGGTGAGGTTGTGGAAGCAACAGCAGTGCGCAGACTGATTCAGCACCATGAGTTGGAGGAAGGTGAGGATGT
AGATGATCAGGAAGAGAGCTCTGAGATGCATGAAGAGACCAGTGAGGACAGCAGTGAGCAATATGACATTGAAGATGATA
GCTTGATAGATGAATGGATAGCTTTAGAGACATCTCCTCTCCCAAGACCTCGATGGAATGTCCTTAGTGCTCTTCGTGAT
AGGCAGCTGGGTTCAAGTGGTCGCTTTGTGTATGAAGCCTGTGGTGCAAGATTATTTGTGCAGCGTTTCTCACTAGAGCA
TGTTTTTGAAGGCCATTCTGGATGTGTCAACACTGTTCATTTTAACCAACATGGCACCCTGCTGGCTAGTGGCAGTGATG
ATCTAAAAGTGATTGTATGGGACTGGCTTAAAAAACGATCAGTACTGAACTTTGACAGTGGCCACAAAAATAATATCTTG
CAGGCTAAATTCCTTCCCAACTGTAATGATGCCATCTTGGCTATGTGTGGCCGTGATGGGCAGGTACGAGTTGCACAGCT
ATCTGCTGTGGCAGGCACCCACATGACTAAGCGTTTGGTGAAGCATGGGGGAGCATCTCATAGACTGGGTTTGGAACCAG
ATTCCCCCTTTAGGTTCTTAACTTCAGGTGAAGATGCAGTTGTCTTCAATATTGACCTCAGACAAGCCCACCCAGCTTCA
AAGTTGCTTGTAATCAAAGATGGTGATAAGAAAGTGGGACTGTATACAGTCTTTGTGAATCCTGCCAATGTCTACCAGTT
TGCTGTAGGTGGGCAAGATCAGTTTATGAGGATTTATGACCAAAGGAAAATTGATGAGAATGTCAACAATGGAGTTCTCA
AAAAATTCTGCCCTCATCACCTTCTTAGCTCTGATTACCCAGCACACATCACATCTCTGATGTACAGCTATGATGGCACA
GAGATCCTGGCTAGCTACAATGATGAAGATATTTATATCTTCAACTCTTCTGATAGTGATGGAGCTCAATATGCTAAGAG
ATATAAAGGACACAGAAATAATTCTACAGTGAAAGGTGTATATTTCTATGGCCCAAGAAGTGAATTCGTGATGAGTGGTA
GCGATTGTGGGCATATCTTCATCTGGGAAAAATCATCCTGCCAGATCGTTCAGTTCTTAGAGGCAGATGAAGGAGGAACA
ATAAACTGTATTGATTCACATCCTTACCTACCTGTGTTGGCATCCAGTGGGCTAGACCATGAAGTCAAAATCTGGTCACC
CATAGCTGAACCTTCCAAGAAGCTTGCCGGCTTAAAGAATGTGATTAAAATTAATAAGCTGAAACGAGATAATTTTACCT
TGCGCCACACTTCCCTGTTTAACAACAGCATGCTTTGTTTCCTCATGAGTCATGTGACACAGTCAAATTATGGACGCAGT
TGGAGAGGTATTAGAATTAATGCTGGAGGTGGAGATTTCAGTGACTCTTCCAGCAGCTCTGAGGAAACAAACCAAGAATC
ATAG

Alignment

ORF - retro_mmus_111 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65. %
• Parental protein coverage: 81.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DEEDEEQPRHRGQRKRASRDQDSSDDERALEDWVSSETTALPRPRWQALPALRERELGSSARFVYEACGA
          D...E....H.......S...D..DD......W...ET..LPRPRW..L.ALR.R.LGSS.RFVYEACGA
Retrocopy DDQEESSEMHEETSEDSSEQYDIEDDS-LIDEWIALETSPLPRPRWNVLSALRDRQLGSSGRFVYEACGA

Parental  RVFVQRFRLQHGLEGHTGCVNTLHFNQRGTWLASGSDDLKVVVWDWVRRQPVLDFESGHKSNVFQAKFLP
          R.FVQRF.L.H..EGH.GCVNT.HFNQ.GT.LASGSDDLKV.VWDW.....VL.F.SGHK.N..QAKFLP
Retrocopy RLFVQRFSLEHVFEGHSGCVNTVHFNQHGTLLASGSDDLKVIVWDWLKKRSVLNFDSGHKNNILQAKFLP

Parental  NSGDSTLAMCARDGQVRVAELSATQCCKNTKRVAQHKGASHKLALEPDSPCTFLSAGEDAVVFTIDLRQD
          N..D..LAMC.RDGQVRVA.LSA......TKR...H.GASH.L.LEPDSP..FL..GEDAVVF.IDLRQ.
Retrocopy NCNDAILAMCGRDGQVRVAQLSAVAGTHMTKRLVKHGGASHRLGLEPDSPFRFLTSGEDAVVFNIDLRQA

Parental  RPASKLVVTKEKEKKVGLYTIYVNPANTHQFAVGGRDQYVRIYDQRKIDENENNGVLKKFCPHHLVNSES
          .PASKL.V.K...KKVGLYT..VNPAN..QFAVGG.DQ..RIYDQRKIDEN.NNGVLKKFCPHHL..S..
Retrocopy HPASKLLVIKDGDKKVGLYTVFVNPANVYQFAVGGQDQFMRIYDQRKIDENVNNGVLKKFCPHHLLSSDY

Parental  KANITCLVYSHDGTELLASYNDEDIYLFNSSHSDGAQYIKRYKGHRNNATVKGVNFYGPKSEFVVSGSDC
          .A.IT.L.YS.DGTE.LASYNDEDIY.FNSS.SDGAQY.KRYKGHRNN.TVKGV.FYGP.SEFV.SGSDC
Retrocopy PAHITSLMYSYDGTEILASYNDEDIYIFNSSDSDGAQYAKRYKGHRNNSTVKGVYFYGPRSEFVMSGSDC

Parental  GHIFLWEKSSCQIIQFMEGDKGGVVNCLEPHPHLPVLATSGLDHDVKIWAPTAEASTELTGLKEVIKKNK
          GHIF.WEKSSCQI.QF.E.D.GG..NC...HP.LPVLA.SGLDH.VKIW.P.AE.S..L.GLK.VIK.NK
Retrocopy GHIFIWEKSSCQIVQFLEADEGGTINCIDSHPYLPVLASSGLDHEVKIWSPIAEPSKKLAGLKNVIKINK

Parental  RERDEDSLHHTDLFDSHMLWFLMHHLRQRRHHRRWREPGVGATDADSDESPSSSDTSDEE
          ..RD...L.HT.LF...ML.FLM.H..Q....R.WR.....A...D...S.SSS.....E
Retrocopy LKRDNFTLRHTSLFNNSMLCFLMSHVTQSNYGRSWRGIRINAGGGDFSDSSSSSEETNQE

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	124.10 RPM
SRP007412_cerebellum	0.00 RPM	151.11 RPM
SRP007412_heart	0.03 RPM	170.19 RPM
SRP007412_kidney	0.00 RPM	211.05 RPM
SRP007412_liver	0.03 RPM	142.30 RPM
SRP007412_testis	5.08 RPM	130.40 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_111 was not detected

EST

No EST(s) were mapped for retro_mmus_111 retrocopy.

TSS

No TSS is located nearby retro_mmus_111 retrocopy 5' end.

Lab

retro_mmus_111 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_111 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Bos taurus	retro_btau_1853
Canis familiaris	retro_cfam_223

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014293	1 retrocopy	retro_amel_47,
Bos taurus	ENSBTAG00000005796	1 retrocopy	retro_btau_1853,
Canis familiaris	ENSCAFG00000031010	1 retrocopy	retro_cfam_223,
Callithrix jacchus	ENSCJAG00000005913	1 retrocopy	retro_cjac_1322,
Echinops telfairi	ENSETEG00000012876	1 retrocopy	retro_etel_654,
Felis catus	ENSFCAG00000003925	1 retrocopy	retro_fcat_14,
Mustela putorius furo	ENSMPUG00000013949	1 retrocopy	retro_mputfur_173,
Mus musculus	ENSMUSG00000026554	1 retrocopy	retro_mmus_111 ,
Otolemur garnettii	ENSOGAG00000011349	1 retrocopy	retro_ogar_2113,
Pteropus vampyrus	ENSPVAG00000007982	1 retrocopy	retro_pvam_1356,
Sus scrofa	ENSSSCG00000006388	1 retrocopy	retro_sscr_88,
Tupaia belangeri	ENSTBEG00000001566	1 retrocopy	retro_tbel_3644,