RetrogeneDB ID: retro_mmus_3648

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:79902613..79903566(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082372
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rnf41
• Ensembl ID: ENSMUSG00000025373
• Aliases: Rnf41, 2210404G21Rik, 4930511A05Rik, 4933415P08Rik, D10Ertd722e, FLRF, Nrdp1
• Description: ring finger protein 41 [Source:MGI Symbol;Acc:MGI:1914838]

Sequence

>retro_mmus_3648
ATGGGGTATGATGTAACCCGTTTCCAGGGGTTCATTGATGAGGACCTTATCTGCCCTATTTGCAATGGAGTCTTGGAGGA
TCCAGTACAGGCGCCTCATTGTGAGCATGCCTTCTGCAATGCCTGCATCATCCAATGGTTTTCTCAGCAGCAAACATGTC
CGGTAGACCATAGCTTTGTCACGGTTGCCCACCTGCGCCCAGTACCTCGGATCATGCGAAACATATTGTCAAAGCTAAAG
ATTGCCTGTGACAACACTGTGTTTGGCTGCAGTGCTCGTGTCAGACTTGACAACCTAATGTCACACCTCAGTGTCTGTGA
GTACAACCTGAAGCAGCCAGTGACCTGTGAGCAGGGCTGTGGTCTGGAGATACCCAAAAATGAACTGCCAAACCATAATT
GCATCAAGCACCTGCGCTCCGTGTTCCAGCAGCAGCAGACACTCATCTCAGAGCTGGAGAAAACATCTGCTGAACACAAG
CACCAACTGGCAGAACAGAAGCACGAAATTAAGCTGATGAAGGCATATATGCGAAAGATCCACAGGGTCAACCCCAACCT
TCAGAACCTAGAGGAGATAATCGAGTACAATGAGATCCTCGAGTGGCTCAACTCCCCACAACCACCAGCAACTGAGACCA
ACTGGGGAGGGATGATCTCCTCTCCTGACACTGTGCTCCAGACTGTAATCAACCACTCCACTGTGGAAAGTGGCAGCCCA
ACCTCTCCTGGCAATGAGCTGAGCGAAAATGCCCATGAATACAGCGAGTCCCAGGGTGTGGCCACATTAGAGACAAGACA
GATGAACCAGCACTACTATGAAAACTACATGACAAGGACACTCCTGACAATCAGGCTGTAGTCGTGATGGCCTTCGAGAA
CTAGCACATGATTGACAACATGGTGCAGGAACCAGAGCTCATCATGATATTTGCTCATGGTTCAGATGAGATA

Alignment

ORF - retro_mmus_3648 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.68 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGYDVTRFQGDVDEDLICPICSGVLEEPVQAPHCEHAFCNACITQWFSQQQTCPVDRSVVTVAHLRPVPR
          MGYDVTRFQG..DEDLICPIC.GVLE.PVQAPHCEHAFCNACI.QWFSQQQTCPVD.S.VTVAHLRPVPR
Retrocopy MGYDVTRFQGFIDEDLICPICNGVLEDPVQAPHCEHAFCNACIIQWFSQQQTCPVDHSFVTVAHLRPVPR

Parental  IMRNMLSKLQIACDNAVFGCSAVVRLDNLMSHLSDCEHNPKRPVTCEQGCGLEMPKDELPNHNCIKHLRS
          IMRN.LSKL.IACDN.VFGCSA.VRLDNLMSHLS.CE.N.K.PVTCEQGCGLE.PK.ELPNHNCIKHLRS
Retrocopy IMRNILSKLKIACDNTVFGCSARVRLDNLMSHLSVCEYNLKQPVTCEQGCGLEIPKNELPNHNCIKHLRS

Parental  VVQQQQSRIAELEKTSAEHKHQLAEQKRDIQLLKAYMRAIRSVNPNLQNLEETIEYNEILEWVNSLQ-PA
          V.QQQQ..I.ELEKTSAEHKHQLAEQK..I.L.KAYMR.I..VNPNLQNLEE.IEYNEILEW.NS.Q.PA
Retrocopy VFQQQQTLISELEKTSAEHKHQLAEQKHEIKLMKAYMRKIHRVNPNLQNLEEIIEYNEILEWLNSPQPPA

Parental  RVTRWGGMISTPDAVLQAVIKRSLVESGCPASIVNELIENAHERSWPQGLATLETRQMNRRYYENYVAKR
          ..T.WGGMIS.PD.VLQ.VI..S.VESG.P.S..NEL.ENAHE.S..QG.ATLETRQMN..YYENY....
Retrocopy TETNWGGMISSPDTVLQTVINHSTVESGSPTSPGNELSENAHEYSESQGVATLETRQMNQHYYENYMTRT

Parental  I-PGKQAVVVMACENQHMGDDMVQEPGLVMIFAHGVEEI
          ..P..QAVVVMA.EN.HM.D.MVQEP.L.MIFAHG..EI
Retrocopy L<PDNQAVVVMAFEN*HMIDNMVQEPELIMIFAHGSDEI

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	62.85 RPM
SRP007412_cerebellum	0.00 RPM	66.65 RPM
SRP007412_heart	0.03 RPM	16.28 RPM
SRP007412_kidney	0.00 RPM	19.21 RPM
SRP007412_liver	0.00 RPM	7.18 RPM
SRP007412_testis	8.64 RPM	75.88 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3648 was not detected

EST

No EST(s) were mapped for retro_mmus_3648 retrocopy.

TSS

No TSS is located nearby retro_mmus_3648 retrocopy 5' end.

Lab

retro_mmus_3648 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3648 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000001320	1 retrocopy	retro_meug_901,
Meleagris gallopavo	ENSMGAG00000006916	1 retrocopy	retro_mgal_15,
Myotis lucifugus	ENSMLUG00000006057	1 retrocopy	retro_mluc_300,
Mus musculus	ENSMUSG00000025373	2 retrocopies	retro_mmus_3645, retro_mmus_3648 ,
Ochotona princeps	ENSOPRG00000001348	1 retrocopy	retro_opri_528,
Sarcophilus harrisii	ENSSHAG00000002679	1 retrocopy	retro_shar_38,