RetrogeneDB ID: retro_mmus_1982

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:146305546..146306386(+)
• Located in intron of: ENSMUSG00000037110

Retrocopy information

• Ensembl ID: ENSMUSG00000042938
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Atpaf1
• Ensembl ID: ENSMUSG00000028710
• Aliases: Atpaf1, 6330547J17Rik, AI593252, ATP11, ATP11p
• Description: ATP synthase mitochondrial F1 complex assembly factor 1 [Source:MGI Symbol;Acc:MGI:2180560]

Sequence

>retro_mmus_1982
GTGTTCCCGGTGCGCCGGGGCTCGGGCCTGCCCCCCGAGGGAGCAGACGGCAGTGGGGTCAGCGAGCTGGAAGCGAACCC
CTTCTACGACCGCTACCGGGACAAGATCCAGCAGCTGCGCAGGTCTGACCCAGCGGCCTTTGAGTCCCGCCTGGAGAAGC
GCAGTGAGTTCCGAAAGCAGCCAGTGGGGCACTCCAAACAAAGTGATTTTATCAAGTGTATGGAGCAGAAGACAGATGCC
TTGGGGAAACAGCCTGTGAGCAAAGGATTCACTAAGGACAAGACTCTCAGTTCAGTCTTCAACGTTGAGATGGTGAAAGA
CAAAACTGCGGAGGAAATAAAACAGATTTGGCAGCAGTATTTTTCAGCAAAAGACACAGTCTACGCAGTTATTCCTAAAG
AGAAGTTTGATTTGATCTGGAACAGGGCTCAGTCCTGCCCAACATTTCTTTGTGCACTACCAAGAAGGGATGGTTATGAG
TTCTTTGTAGGACAATGGACAGGTACAGAGCTCCACTTCACTGCACTTATAAATATTCAGACCCGAGGGGATGCAGCAGC
CAGCCAGCTGATTTTATATCACTATCCTGAACTTAAGGAAGAAAAGGGCATAGTGCTGATGACAGCAGAAATGGACTCCA
CATTTCTGAATGTTGTGGAGGCACAGTGCATCGCCAATCAGGTTCAGCTCTTCTACGCCACCGATCGGAAGGAGATCTAT
GGGCTAGTAGAGACCTTTAACTTCAGACCAAATGAGTTCAAATATATGTCTGTCATCGCTGAGTTGGAGCAAAGTGGACT
TGGAGCCGAACTGAAACGTGCCCAGAACCAAGATAAGACT

Alignment

ORF - retro_mmus_1982 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 80.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VFPVRRGSGLPPEGADGSGVSELEANPFYDRYRDKIQQLRRSDPAAFESRLEKRSEFRKQPVGHSKQSDF
          VFPVRRGSGLPPEGADGSGVSELEANPFYDRYRDKIQQLRRSDPAAFESRLEKRSEFRKQPVGHSKQSDF
Retrocopy VFPVRRGSGLPPEGADGSGVSELEANPFYDRYRDKIQQLRRSDPAAFESRLEKRSEFRKQPVGHSKQSDF

Parental  IKCMEQKTDALGKQPVSKGFTKDKTLSSVFNVEMVKDKTAEEIKQIWQQYFSAKDTVYAVIPKEKFDLIW
          IKCMEQKTDALGKQPVSKGFTKDKTLSSVFNVEMVKDKTAEEIKQIWQQYFSAKDTVYAVIPKEKFDLIW
Retrocopy IKCMEQKTDALGKQPVSKGFTKDKTLSSVFNVEMVKDKTAEEIKQIWQQYFSAKDTVYAVIPKEKFDLIW

Parental  NRAQSCPTFLCALPRRDGYEFFVGQWTGTELHFTALINIQTRGDAAASQLILYHYPELKEEKGIVLMTAE
          NRAQSCPTFLCALPRRDGYEFFVGQWTGTELHFTALINIQTRGDAAASQLILYHYPELKEEKGIVLMTAE
Retrocopy NRAQSCPTFLCALPRRDGYEFFVGQWTGTELHFTALINIQTRGDAAASQLILYHYPELKEEKGIVLMTAE

Parental  MDSTFLNVVEAQCIANQVQLFYATDRKEIYGLVETFNFRPNEFKYMSVIAELEQSGLGAELKRAQNQDKT
          MDSTFLNVVEAQCIANQVQLFYATDRKEIYGLVETFNFRPNEFKYMSVIAELEQSGLGAELKRAQNQDKT
Retrocopy MDSTFLNVVEAQCIANQVQLFYATDRKEIYGLVETFNFRPNEFKYMSVIAELEQSGLGAELKRAQNQDKT

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	0.09 RPM	12.41 RPM
SRP007412_cerebellum	0.04 RPM	9.03 RPM
SRP007412_heart	0.03 RPM	15.69 RPM
SRP007412_kidney	0.12 RPM	8.43 RPM
SRP007412_liver	0.03 RPM	2.59 RPM
SRP007412_testis	0.14 RPM	5.49 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1982 was not detected

EST

1 EST(s) were mapped to retro_mmus_1982 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AA110292	146305997	146306112	95.7	110	5	105

TSS

No TSS is located nearby retro_mmus_1982 retrocopy 5' end.

Lab

retro_mmus_1982 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1982 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000094	1 retrocopy	retro_btau_1192,
Cavia porcellus	ENSCPOG00000003349	1 retrocopy	retro_cpor_965,
Mustela putorius furo	ENSMPUG00000012737	1 retrocopy	retro_mputfur_1060,
Mus musculus	ENSMUSG00000028710	1 retrocopy	retro_mmus_1982 ,