RetrogeneDB ID: retro_mmus_3373

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:99946561..99947324(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: March5
• Ensembl ID: ENSMUSG00000023307
• Aliases: March5, 1810015H18Rik, 2310008I22Rik, 2700055A20Rik, 5730499H23Rik, E130202O05Rik, MARCH-V, MITOL, Marchv, Rnf153
• Description: membrane-associated ring finger (C3HC4) 5 [Source:MGI Symbol;Acc:MGI:1915207]

Sequence

>retro_mmus_3373
AGAACAGCTGAGTGGGTGAGACCATGCAGGTGCAGAGGATGTACTAAGTGGGTTCACCAGGCTTGTCTCCAGCGCTGGGT
AGATGAAAAGCAAAGAGGAAACAGCACAGCCAGAGTGGCCTGTCCTCAGTGCAACACCGAGTACTTAATAGTGTTTCCAA
AGCTGGGTCCAGTTGTTTTATGTCTTGGATCTTGCAGATAGACTGATCTCAAAAGCTTGCCCTTTTGCTGCAGCAGGAAT
AATGGTTGGATCTATCTATTGGACAGCGGTGACTTACGGAGCAGTGACAGTGATGCAGGTTGTAGGCCACAAAGAAGGGC
TGGATGTTATGGAGCGAGCTGACCCTTTATTTCTTTTGATTGGACTTCTTACTATTCCTGTCATGCTGATACTAGGCAAA
ATGATTCGCTAGGAGGACTATGTGCTTAGACTATGGCACAAATACTCAAATAAACTACAAATCTTTAACAGTATATGTCC
AGGGACTGGTTGTCCTGTTCCTGGAATTCCAGCTGAAGCTAATCCTTTAGCAGATCATGTCTCTGCTACTAGAATTTTGT
GTGGAGCCCTTGTCTTTCCTACTATTGTGACAATAGTTGGTAAACTGATGTTCAGTAGTGTTAACTCAAATTTACAAAGG
ACAATCTTGGGTGGAAATGCTTTTGTTGCCATAAAAGGAGCATTTAAGGTTTACTTCAAACAGCAGCAATATTTGCGTCA
GGCACACCACAAAATCCTAAATTATCCAGAGCAAGAAGAAGCA

Alignment

ORF - retro_mmus_3373 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.9 %
• Parental protein coverage: 91.37 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RTAEWVRPCRCRGSTKWVHQACLQRWVDEKQRGNSTARVACPQCNAEYLIVFPKLGPVV-YVLDLADRLI
          RTAEWVRPCRCRG.TKWVHQACLQRWVDEKQRGNSTARVACPQCN.EYLIVFPKLGPVV.YVLDLADRLI
Retrocopy RTAEWVRPCRCRGCTKWVHQACLQRWVDEKQRGNSTARVACPQCNTEYLIVFPKLGPVV>YVLDLADRLI

Parental  SKACPFAAAGIMVGSIYWTAVTYGAVTVMQVVGHKEGLDVMERADPLFLLIGLPTIPVMLILGKMIRWED
          SKACPFAAAGIMVGSIYWTAVTYGAVTVMQVVGHKEGLDVMERADPLFLLIGL.TIPVMLILGKMIR.ED
Retrocopy SKACPFAAAGIMVGSIYWTAVTYGAVTVMQVVGHKEGLDVMERADPLFLLIGLLTIPVMLILGKMIR*ED

Parental  YVLRLWRKYSNKLQILNSIFPGIGCPVPRIPAEANPLADHVSATRILCGALVFPTIATIVGKLMFSSVNS
          YVLRLW.KYSNKLQI.NSI.PG.GCPVP.IPAEANPLADHVSATRILCGALVFPTI.TIVGKLMFSSVNS
Retrocopy YVLRLWHKYSNKLQIFNSICPGTGCPVPGIPAEANPLADHVSATRILCGALVFPTIVTIVGKLMFSSVNS

Parental  NLQRTILGGIAFVAIKGAFKVYFKQQQYLRQAHRKILNYPEQEEA
          NLQRTILGG.AFVAIKGAFKVYFKQQQYLRQAH.KILNYPEQEEA
Retrocopy NLQRTILGGNAFVAIKGAFKVYFKQQQYLRQAHHKILNYPEQEEA

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	43.95 RPM
SRP007412_cerebellum	0.00 RPM	30.74 RPM
SRP007412_heart	0.06 RPM	42.59 RPM
SRP007412_kidney	0.04 RPM	53.34 RPM
SRP007412_liver	0.11 RPM	62.13 RPM
SRP007412_testis	0.00 RPM	25.66 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3373 was not detected

EST

No EST(s) were mapped for retro_mmus_3373 retrocopy.

TSS

No TSS is located nearby retro_mmus_3373 retrocopy 5' end.

Lab

retro_mmus_3373 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3373 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020981	1 retrocopy	retro_btau_1749,
Macropus eugenii	ENSMEUG00000011031	1 retrocopy	retro_meug_1192,
Mus musculus	ENSMUSG00000023307	3 retrocopies	retro_mmus_1559, retro_mmus_3211, retro_mmus_3373 ,
Sarcophilus harrisii	ENSSHAG00000018432	1 retrocopy	retro_shar_459,
Xiphophorus maculatus	ENSXMAG00000007675	1 retrocopy	retro_xmac_25,