RetrogeneDB ID: retro_mmus_344

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:91296408..91296876(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083064
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Zfp330
• Ensembl ID: ENSMUSG00000031711
• Aliases: Zfp330, BC008086, Noa36, Znf330
• Description: zinc finger protein 330 [Source:MGI Symbol;Acc:MGI:1353574]

Sequence

>retro_mmus_344
GAATGTGAGCAAGGGGTATGGGACCATGGAGGAAGAATATTCAGCTGTTCGTTTTGCCATAATTTTCTCTGTGAAGATGA
CCAGTTTGAGCATCAAGCCAGCTGCCAAGTTTTAGAAGCAGAAACATTTAAATGTGTTTCCTGCAGTCAACTTGGCCAGC
ATTCATGTCTCCGCTGTAAGGCTTGTTTCTGTGATGAACATACAAGGAGCAAAGTGTTTAAGCAAGAAAAAGGAAAACAA
CCTCCTTGCCCTAAATGTGGGCATGAAACACAGGAGACAAAGGATCTTAACATGTCAACACGCTCCTTGAAATTTGGCAG
GCAGACTGGAGGAGAAGAAGGGTATGATGCGTCGGACAAGTATGGAGATACTGGATACCATGATGAGGAGGAGGAGGATG
AAGCAGAGGATGAAGAGGAAGAAGATGGGAAGGACTCAAATGCTGAGTCATCAGATCTGTTCAGTAAC

Alignment

ORF - retro_mmus_344 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.16 %
• Parental protein coverage: 51.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ECERGVWDHGGRIFSCSFCHNFLCEDDQFEHQASCQVLEAETFKCVSCNRLGQHSCLRCKACFCDEHTRS
          ECE.GVWDHGGRIFSCSFCHNFLCEDDQFEHQASCQVLEAETFKCVSC..LGQHSCLRCKACFCDEHTRS
Retrocopy ECEQGVWDHGGRIFSCSFCHNFLCEDDQFEHQASCQVLEAETFKCVSCSQLGQHSCLRCKACFCDEHTRS

Parental  KVFKQEKGKQPPCPKCGHETQETKDLSMSTRSLKFGRQTGGEEDGASGYDAYWKNLSSDKYGDTGYHDDD
          KVFKQEKGKQPPCPKCGHETQETKDL.MSTRSLKFGRQTGGEE....GYDA..K......Y.D....D..
Retrocopy KVFKQEKGKQPPCPKCGHETQETKDLNMSTRSLKFGRQTGGEE----GYDASDK-YGDTGYHDEEEEDEA

Parental  EEEDEAEDEEEEDGKDSDAESS
          E.E.E.ED........SD..S.
Retrocopy EDEEE-EDGKDSNAESSDLFSN

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	0.19 RPM	17.73 RPM
SRP007412_cerebellum	0.13 RPM	20.06 RPM
SRP007412_heart	0.09 RPM	13.95 RPM
SRP007412_kidney	0.10 RPM	20.64 RPM
SRP007412_liver	0.25 RPM	13.41 RPM
SRP007412_testis	0.32 RPM	43.27 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_mmus_344 in 1 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001XVA	POLR2A	1:91295092..91295438

EST

No EST(s) were mapped for retro_mmus_344 retrocopy.

TSS

No TSS is located nearby retro_mmus_344 retrocopy 5' end.

Lab

retro_mmus_344 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_344 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000031711	1 retrocopy	retro_mmus_344 ,
Oryctolagus cuniculus	ENSOCUG00000014580	1 retrocopy	retro_ocun_1479,
Sus scrofa	ENSSSCG00000009052	1 retrocopy	retro_sscr_1043,