RetrogeneDB ID: retro_mmus_2907

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:26072071..26072929(+)
• Located in intron of: ENSMUSG00000040583

Retrocopy information

• Ensembl ID: ENSMUSG00000045149
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rnf170
• Ensembl ID: ENSMUSG00000013878
• Aliases: Rnf170, 6720407G21Rik, AI481227
• Description: ring finger protein 170 [Source:MGI Symbol;Acc:MGI:1924983]

Sequence

>retro_mmus_2907
ATGCAAAGATATTGGCGTTTCCAAGACAACAAGATACAAGATATATGCTTTGGAGTCCTAGGAGAATCTTGGATTCAAAG
ACCTGTAATGGCCAGGTACTACAGTGAAGGTCAGAGTTTGCAGCAGGATGACTCATTTATAGAAGGAGTGAGCGACCAAG
TCCTTGTGGCTGTGGTGGTCAGCTTCGCGTTGATCGCTACTCTCCTGTATGCACTTCTCAGAAATGTACAGCAGAACATC
CATCCAGAAAACCAGGAGCTAGTCAGAGTGCTTCGAGAACAATTCCAAACAGAACAGGATGTCCCTGCTCCTGCCCGACA
GCAGTTCTACACTGAAATGTACTGTCCAATCTGCTTACATCAAGCCTCCTTTCCTGTTGAAACAAACTGTGGACATCTCT
TTTGTGGTTCCTGCATAATTGCATACTGGCGATACGGGTCCTGGCTTGGTGCAATCAGTTGTCCTATCTGTAGACAAACG
GTAACTCTCCTCCTAACAGTATTTGGTGAAGATGATCAATCTCAGGATGTTATAAGATTGCGTCAAGATGTTAATGATTA
TAACCGGAGATTCTCAGGGCAGCCTAGATCTATTATGGAAAGGATCATGGACCTCCCCACCTTGCTGAGACATGCGTTCA
GGGAAGTGTTTTCAGTTGGGGGCCTCTTCTGGATGTTCCGCATTAGGATAATGCTTTGTTTGATGGGAGCTTTTTTCTAT
TTAATATCACCTCTAGATTTTGTACCTGAAGCCTTGTTTGGAATTCTGGGCTTTCTAGATGATTTCTTTGTTATCTTTTT
GTTGCTTATTTACATCTCCATTATGTATCGAGAAGTGATAACCCAAAGACTAACTAGG

Alignment

ORF - retro_mmus_2907 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.3 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQRYWRFQDNKIQDICFGVLGESWIQRPVMARYYSEGQSLQQDDSFIEGVSDQVLVAVVVSLALTATLLY
          MQRYWRFQDNKIQDICFGVLGESWIQRPVMARYYSEGQSLQQDDSFIEGVSDQVLVAVVVS.AL.ATLLY
Retrocopy MQRYWRFQDNKIQDICFGVLGESWIQRPVMARYYSEGQSLQQDDSFIEGVSDQVLVAVVVSFALIATLLY

Parental  ALLRNVQQNIHPENQELVRVLREQFQTEQDVPAPARQQFYTEMYCPICLHQASFPVETNCGHLFCGSCII
          ALLRNVQQNIHPENQELVRVLREQFQTEQDVPAPARQQFYTEMYCPICLHQASFPVETNCGHLFCGSCII
Retrocopy ALLRNVQQNIHPENQELVRVLREQFQTEQDVPAPARQQFYTEMYCPICLHQASFPVETNCGHLFCGSCII

Parental  AYWRYGSWLGAISCPICRQTVTLLLTVFGEDDQSQDVIRLRQDVNDYNRRFSGQPRSIMERIMDLPTLLR
          AYWRYGSWLGAISCPICRQTVTLLLTVFGEDDQSQDVIRLRQDVNDYNRRFSGQPRSIMERIMDLPTLLR
Retrocopy AYWRYGSWLGAISCPICRQTVTLLLTVFGEDDQSQDVIRLRQDVNDYNRRFSGQPRSIMERIMDLPTLLR

Parental  HAFREVFSVGGLFWMFRIRIMLCLMGAFFYLISPLDFVPEALFGILGFLDDFFVIFLLLIYISIMYREVI
          HAFREVFSVGGLFWMFRIRIMLCLMGAFFYLISPLDFVPEALFGILGFLDDFFVIFLLLIYISIMYREVI
Retrocopy HAFREVFSVGGLFWMFRIRIMLCLMGAFFYLISPLDFVPEALFGILGFLDDFFVIFLLLIYISIMYREVI

Parental  TQRLTR
          TQRLTR
Retrocopy TQRLTR

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	0.07 RPM	15.98 RPM
SRP007412_cerebellum	0.04 RPM	13.42 RPM
SRP007412_heart	0.03 RPM	8.06 RPM
SRP007412_kidney	0.04 RPM	8.07 RPM
SRP007412_liver	0.14 RPM	10.13 RPM
SRP007412_testis	0.05 RPM	5.58 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2907 was not detected

EST

No EST(s) were mapped for retro_mmus_2907 retrocopy.

TSS

No TSS is located nearby retro_mmus_2907 retrocopy 5' end.

Lab

retro_mmus_2907 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2907 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000001127	1 retrocopy	retro_meug_862,
Monodelphis domestica	ENSMODG00000010090	1 retrocopy	retro_mdom_197,
Mus musculus	ENSMUSG00000013878	1 retrocopy	retro_mmus_2907 ,
Otolemur garnettii	ENSOGAG00000007925	1 retrocopy	retro_ogar_2905,
Pteropus vampyrus	ENSPVAG00000013497	1 retrocopy	retro_pvam_856,
Sorex araneus	ENSSARG00000006471	1 retrocopy	retro_sara_706,
Sarcophilus harrisii	ENSSHAG00000018446	1 retrocopy	retro_shar_118,