RetrogeneDB ID: retro_mmus_3376

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:105545435..105545762(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mnf1
• Ensembl ID: ENSMUSG00000024208
• Aliases: Uqcc2, 2900010M23Rik, M19, Mnf1
• Description: mitochondrial nucleoid factor 1 [Source:MGI Symbol;Acc:MGI:1914517]

Sequence

>retro_mmus_3376
GGCCGGGACTTGGGCGCTTACCTGCGGCAGCGGGTAGTGCAGGCCTTCCGGGAGGGAGAGAACACCCAGATTACAGAACC
CGAGGCCTGTGATCAGATGTACGTGACCTTAGCACGACTGCATTCAAACTACTACAAGCACAAGTACCCTCGCCCCAGAG
CCACCAGCTTCAGTGGCCTGTCCGTGGAAGAGTACCAGCTGATCCTGTCCACAGGTACTTTGGAAGAGTTCCAAGAGATG
AATAAGAAACTGCAGGAGAAGTTTGCACCCACCAGGCCCGAGGAGAAGTACAAGGCCTGGACTCGGGTCCTGTCCCGCCC
ACGGACC

Alignment

ORF - retro_mmus_3376 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.38 %
• Parental protein coverage: 83.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GRDLGAYLRQRVAQAFREGENTQIAEPEACDQMYESLARLHSNYYKHKYPRPRDTSFSGLSVEEYKLILS
          GRDLGAYLRQRV.QAFREGENTQI.EPEACDQMY..LARLHSNYYKHKYPRPR.TSFSGLSVEEY.LILS
Retrocopy GRDLGAYLRQRVVQAFREGENTQITEPEACDQMYVTLARLHSNYYKHKYPRPRATSFSGLSVEEYQLILS

Parental  TDTLEEFQEMNKSMWKKLQEKFAPTRPEEKHKAWTRVLSRPRT
          T.TLEEFQEMNK....KLQEKFAPTRPEEK.KAWTRVLSRPRT
Retrocopy TGTLEEFQEMNK----KLQEKFAPTRPEEKYKAWTRVLSRPRT

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	30.63 RPM
SRP007412_cerebellum	0.00 RPM	25.71 RPM
SRP007412_heart	0.12 RPM	55.10 RPM
SRP007412_kidney	0.00 RPM	29.76 RPM
SRP007412_liver	0.00 RPM	14.42 RPM
SRP007412_testis	0.09 RPM	127.89 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3376 was not detected

EST

No EST(s) were mapped for retro_mmus_3376 retrocopy.

TSS

No TSS is located nearby retro_mmus_3376 retrocopy 5' end.

Lab

retro_mmus_3376 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3376 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000031270	1 retrocopy	retro_cfam_1168,
Dasypus novemcinctus	ENSDNOG00000002019	1 retrocopy	retro_dnov_674,
Echinops telfairi	ENSETEG00000006979	2 retrocopies	retro_etel_1912, retro_etel_2009,
Macropus eugenii	ENSMEUG00000005278	3 retrocopies	retro_meug_1335, retro_meug_2027, retro_meug_337,
Monodelphis domestica	ENSMODG00000013996	1 retrocopy	retro_mdom_515,
Mustela putorius furo	ENSMPUG00000003032	1 retrocopy	retro_mputfur_511,
Mus musculus	ENSMUSG00000024208	2 retrocopies	retro_mmus_2543, retro_mmus_3376 ,
Otolemur garnettii	ENSOGAG00000015604	2 retrocopies	retro_ogar_2127, retro_ogar_2204,
Tupaia belangeri	ENSTBEG00000001380	6 retrocopies	retro_tbel_1486, retro_tbel_1573, retro_tbel_1754, retro_tbel_3269, retro_tbel_361, retro_tbel_994,