RetrogeneDB ID: retro_mmus_2543

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:7923832..7924120(+)
• 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_2543
GAGGGAGAGAACACCCAGACTGCAGAGACTGAGGCCTGTGATCACATGTACAAGAGATTAGCATGGCTGCATTCAAACTA
CTACAAGCTCAAGTACCCTGGCTCCAGAGACACCAGCTTCAGTGGCCAATCCATGGAAGCATACAAGCTGATCCTGTCCT
CAGACGCTTTGGAAGAGTTTCAAGAGATGAGTAAGAGTATGTGGAAGAAACTGCAAGAGAAGTTTGCGGCCACAAGGCCT
GAGGAGAAGCATAAAGTCTAAGCTCAGGTCCTGTCCTGCCCATGTACC

Alignment

ORF - retro_mmus_2543 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.08 %
• Parental protein coverage: 70.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EGENTQIAEPEACDQMYESLARLHSNYYKHKYPRPRDTSFSGLSVEEYKLILSTDTLEEFQEMNKSMWKK
          EGENTQ.AE.EACD.MY..LA.LHSNYYK.KYP..RDTSFSG.S.E.YKLILS.D.LEEFQEM.KSMWKK
Retrocopy EGENTQTAETEACDHMYKRLAWLHSNYYKLKYPGSRDTSFSGQSMEAYKLILSSDALEEFQEMSKSMWKK

Parental  LQEKFAPTRPEEKHKAWTRVLSRPRT
          LQEKFA.TRPEEKHK....VLS.P.T
Retrocopy LQEKFAATRPEEKHKV*AQVLSCPCT

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

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2543 was not detected

EST

No EST(s) were mapped for retro_mmus_2543 retrocopy.

TSS

No TSS is located nearby retro_mmus_2543 retrocopy 5' end.

Lab

retro_mmus_2543 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2543 has 0 orthologous retrocopies within eutheria group .

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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,