RetrogeneDB ID: retro_mmus_493

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:139928241..139929609(-)
• Located in intron of: ENSMUSG00000089991

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ruvbl1
• Ensembl ID: ENSMUSG00000030079
• Aliases: Ruvbl1, 2510009G06Rik, Pontin52, Tip49a
• Description: RuvB-like protein 1 [Source:MGI Symbol;Acc:MGI:1928760]

Sequence

>retro_mmus_493
ATGAAGATTGAGGAGGTGAAGAGCACCACGAAGACGCAGCGCATCGCCTCCCACAGCCACGTGAAGGGTCTGGGGCTGGA
CGAGAGCGGCCTAGCCAAGCAGGCGGCTTCGGGTCTCGTGGGCCAGGAGAACGCGAGAGAGGCATGTGGCGTCATTGTAG
AATTAATCAAAAGCAAGAAAATGGCTGGAAGAGCTGTCTTGTTGGCGGGGCCTCCTGGAACTGGCAAGACAGCCTTGGCC
CTTGCTATTGCTCAGGAGCTGGGCAGTAAAGTCCCTTTCTGCCCGATGGTGGGTAGCGAGGTATACTCAACTGAGATCAA
AAAGACAGAGGTGCTGATGGAGAACTTCCGCAGGGCTATTGGGTTGCGGATAAAGGAGACTAAGGAGGTTTATGAAGGGG
AGGTGACAGAGCTCACTCCCTGTGAGACAGAGAACCCCATGGGTGGGTACGGCAAAACTATCAGCCATGTGATCATAGGG
CTCAAGACTGCCAAAGGAACCAAACAGCTGAAGCTGGACCCCAGTATTTTTGAAAGTTTGCAGAAAGAACGAGTAGAGGC
TGGAGATGTGATTTACATTGAAGCAAATAGTGGAGCTGTGAAGAGGCAAGGCAGGTGTGACACCTGTGCCACAGAGTTTG
ACCTTGAAGCTGAAGAGTATGTCCCTTTGCCAAAGGGAGATGTGCACAAGAAGAAGGAAATCATATAGGATGTGACCTTG
CATGACCTGGATGTGGCTAATGCGCGGCCTCAGGGTGGGCAAGATATTCTGTCTATGATGGGCCAGTTGATGAAGCCAAA
AAAGACAGAGATCACAGATAAACTTCGAGGGGAGATCAACAAAGTGGTGAACAAATACATTGACCAGGGCGTGGCCGAGC
TAGTCCCTGGAGTGCTCTTTGTCGATGAGGTCCACATGCTGGATATCGAGTGCTTTACCTACCTGCACCGAGCCCTGGAG
TCCTCCATCGCCCCCATTGTCATCTTTGCATCCAACCGAGGCAACTGTGTCATCAGGGGCACTGAGGACATCACTTCTCC
ACACGGCATCCCGTTGGATCTGCTAGACAGGGTGATGATCATCAGGACCATGCTGTACACGCCACAGGAGATGAAGCAGA
TCATTAAGATCCGAGCCCAGACGGAAGGCATCAACATCAGCGAGGAGGCGCTGAACCACCTCGGGGAGATTGGCACCAAG
ACCACTCTGAGGTATTCGGTGCAGCTGCTGACCCCAGCCAACCTGCTGGCAAAGATCAATGGCAAGGACAGCATTGAGAA
GGAGCACGTGGAATAGATCAGCGAGCTCTTCTATGACGCCAAGTCCTCTGCCAAGATTTTGGCTGACCAGCAGGACAAGT
ACATGAAG

Alignment

ORF - retro_mmus_493 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.34 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKIEEVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGLVGQENAREACGVIVELIKSKKMAGRAVLLAG
          MKIEEVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGLVGQENAREACGVIVELIKSKKMAGRAVLLAG
Retrocopy MKIEEVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGLVGQENAREACGVIVELIKSKKMAGRAVLLAG

Parental  PPGTGKTALALAIAQELGSKVPFCPMVGSEVYSTEIKKTEVLMENFRRAIGLRIKETKEVYEGEVTELTP
          PPGTGKTALALAIAQELGSKVPFCPMVGSEVYSTEIKKTEVLMENFRRAIGLRIKETKEVYEGEVTELTP
Retrocopy PPGTGKTALALAIAQELGSKVPFCPMVGSEVYSTEIKKTEVLMENFRRAIGLRIKETKEVYEGEVTELTP

Parental  CETENPMGGYGKTISHVIIGLKTAKGTKQLKLDPSIFESLQKERVEAGDVIYIEANSGAVKRQGRCDTYA
          CETENPMGGYGKTISHVIIGLKTAKGTKQLKLDPSIFESLQKERVEAGDVIYIEANSGAVKRQGRCDT.A
Retrocopy CETENPMGGYGKTISHVIIGLKTAKGTKQLKLDPSIFESLQKERVEAGDVIYIEANSGAVKRQGRCDTCA

Parental  TEFDLEAEEYVPLPKGDVHKKKEIIQDVTLHDLDVANARPQGGQDILSMMGQLMKPKKTEITDKLRGEIN
          TEFDLEAEEYVPLPKGDVHKKKEII.DVTLHDLDVANARPQGGQDILSMMGQLMKPKKTEITDKLRGEIN
Retrocopy TEFDLEAEEYVPLPKGDVHKKKEII*DVTLHDLDVANARPQGGQDILSMMGQLMKPKKTEITDKLRGEIN

Parental  KVVNKYIDQGVAELVPGVLFVDEVHMLDIECFTYLHRALESSIAPIVIFASNRGNCVIRGTEDITSPHGI
          KVVNKYIDQGVAELVPGVLFVDEVHMLDIECFTYLHRALESSIAPIVIFASNRGNCVIRGTEDITSPHGI
Retrocopy KVVNKYIDQGVAELVPGVLFVDEVHMLDIECFTYLHRALESSIAPIVIFASNRGNCVIRGTEDITSPHGI

Parental  PLDLLDRVMIIRTMLYTPQEMKQIIKIRAQTEGINISEEALNHLGEIGTKTTLRYSVQLLTPANLLAKIN
          PLDLLDRVMIIRTMLYTPQEMKQIIKIRAQTEGINISEEALNHLGEIGTKTTLRYSVQLLTPANLLAKIN
Retrocopy PLDLLDRVMIIRTMLYTPQEMKQIIKIRAQTEGINISEEALNHLGEIGTKTTLRYSVQLLTPANLLAKIN

Parental  GKDSIEKEHVEEISELFYDAKSSAKILADQQDKYMK
          GKDSIEKEHVE.ISELFYDAKSSAKILADQQDKYMK
Retrocopy GKDSIEKEHVE*ISELFYDAKSSAKILADQQDKYMK

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	0.12 RPM	13.85 RPM
SRP007412_cerebellum	0.13 RPM	16.15 RPM
SRP007412_heart	0.12 RPM	7.19 RPM
SRP007412_kidney	0.13 RPM	10.78 RPM
SRP007412_liver	0.14 RPM	10.46 RPM
SRP007412_testis	0.14 RPM	19.85 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_493 was not detected

EST

No EST(s) were mapped for retro_mmus_493 retrocopy.

TSS

No TSS is located nearby retro_mmus_493 retrocopy 5' end.

Lab

retro_mmus_493 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_493 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000004254	1 retrocopy	retro_mluc_1421,
Mus musculus	ENSMUSG00000030079	1 retrocopy	retro_mmus_493 ,
Ochotona princeps	ENSOPRG00000011261	1 retrocopy	retro_opri_1115,
Rattus norvegicus	ENSRNOG00000013195	2 retrocopies	retro_rnor_2883, retro_rnor_424,