RetrogeneDB ID: retro_mmus_3296

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:90118936..90119809(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000096647
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Tmem41b
• Ensembl ID: ENSMUSG00000047554
• Aliases: Tmem41b, 1500015G02Rik, 1500031M19Rik, AU018901, D7Ertd70e, D7Ertd743e
• Description: transmembrane protein 41B [Source:MGI Symbol;Acc:MGI:1289225]

Sequence

>retro_mmus_3296
ATGGCGAAAGGCAGAGTCGCTGATCGATCGCCCACCGAAATGTTGCACTCGACCCCAGCCGGGGACCGGGCAGTGAGGAC
CCAGGGTTCCGCCGCGCCTGGCAGCAAAGATCATCTGAACGAAAAGCCTTGTGCAGAAGCTGGATCAGCAAGAACATCAC
TCCTTATACTGGTGTCCATTTTTTCATGTGCAGCTTTTGTTATGTTTTTGGTATATAAAAATTTTCCTCAGCTTAGTGAG
GAAGAGAGGGTGAATATGAAGGTTCCGAGAGATATGGATGACGCCAAGGCTCTAGGAAAAGTTCTCTCCAAATATAAGGA
TACCTTTTATGTACAAGTACTGGTTGCTTATTTTGCTACATATATTTTTTTGCAAACATTTGCTATCCCAGGTTCCATAT
TCCTCAGTATACTCTCCGGGTTCCTTTATCCCTTCCCACTTGCCTTATTCCTTGTTTGTTTGTGCTCCGGACTTGGTGCC
TCATTCTGCTACATGCTCTCCTACTTAGTTGGAAGACCCGTTGTATACAAATACCTAACAGAGAAGGCAGTGAAATGGTC
ACAGCAGGTAGAGCGTCACAGAGAACATCTTATTAACTACATTATATTTTTGAGAATCACACCGTTTCTTCCTAATTGGT
TTATTAATATTACATCTCCTGTGATAAATGTACCATTGAAAGTGTTTTTTATTGGCACTTTTCTAGGTGTTGCACCTCCT
TCTTTTGTAGCAATCAAGGCAGGAACAACTCTGTGTCAGCTTACAACAGCAGGGGAAGCTGTTTCCTGGAGCTCGGTATT
TATTCTGATGGTTTTGACTCTTCTTTCTATCCTGCCAGCCATCTTCCAAAAACAACTAAAGCAGAAGTTTGAG

Alignment

ORF - retro_mmus_3296 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.31 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAKGRVADRSPTEMLHSTPAGDRAVRTQGSAAPGSKDHLNEKPCAEAGSARTSLLILVSIFSCAAFVMFL
          MAKGRVADRSPTEMLHSTPAGDRAVRTQGSAAPGSKDHLNEKPCAEAGSARTSLLILVSIFSCAAFVMFL
Retrocopy MAKGRVADRSPTEMLHSTPAGDRAVRTQGSAAPGSKDHLNEKPCAEAGSARTSLLILVSIFSCAAFVMFL

Parental  VYKNFPQLSEEERVNMKVPRDMDDAKALGKVLSKYKDTFYVQVLVAYFATYIFLQTFAIPGSIFLSILSG
          VYKNFPQLSEEERVNMKVPRDMDDAKALGKVLSKYKDTFYVQVLVAYFATYIFLQTFAIPGSIFLSILSG
Retrocopy VYKNFPQLSEEERVNMKVPRDMDDAKALGKVLSKYKDTFYVQVLVAYFATYIFLQTFAIPGSIFLSILSG

Parental  FLYPFPLALFLVCLCSGLGASFCYMLSYLVGRPVVYKYLTEKAVKWSQQVERHREHLINYIIFLRITPFL
          FLYPFPLALFLVCLCSGLGASFCYMLSYLVGRPVVYKYLTEKAVKWSQQVERHREHLINYIIFLRITPFL
Retrocopy FLYPFPLALFLVCLCSGLGASFCYMLSYLVGRPVVYKYLTEKAVKWSQQVERHREHLINYIIFLRITPFL

Parental  PNWFINITSPVINVPLKVFFIGTFLGVAPPSFVAIKAGTTLHQLTTAGEAVSWSSVFILMVLALLSILPA
          PNWFINITSPVINVPLKVFFIGTFLGVAPPSFVAIKAGTTL.QLTTAGEAVSWSSVFILMVL.LLSILPA
Retrocopy PNWFINITSPVINVPLKVFFIGTFLGVAPPSFVAIKAGTTLCQLTTAGEAVSWSSVFILMVLTLLSILPA

Parental  IFQKQLKQKFE
          IFQKQLKQKFE
Retrocopy IFQKQLKQKFE

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	0.02 RPM	18.50 RPM
SRP007412_cerebellum	0.13 RPM	15.24 RPM
SRP007412_heart	0.06 RPM	11.08 RPM
SRP007412_kidney	0.23 RPM	12.57 RPM
SRP007412_liver	0.05 RPM	11.14 RPM
SRP007412_testis	0.96 RPM	14.27 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3296 was not detected

EST

2 EST(s) were mapped to retro_mmus_3296 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BY016258	90118884	90119260	99	372	3	367
BY237152	90118881	90119301	96.2	404	15	387

TSS

No TSS is located nearby retro_mmus_3296 retrocopy 5' end.

Lab

retro_mmus_3296 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3296 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000026871	1 retrocopy	retro_ecab_122,
Loxodonta africana	ENSLAFG00000006953	1 retrocopy	retro_lafr_1229,
Mus musculus	ENSMUSG00000047554	1 retrocopy	retro_mmus_3296 ,