RetrogeneDB ID: retro_mmus_1464

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 16:47075605..47076034(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081624
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Aprt
• Ensembl ID: ENSMUSG00000006589
• Aliases: Aprt, C85684
• Description: adenine phosphoribosyl transferase [Source:MGI Symbol;Acc:MGI:88061]

Sequence

>retro_mmus_1464
TCTGATCGTCCATCCATTCGCCTCCTGGCCAGTCACCTGAAGTCCACGCACAGTGGCAAGACCAACTACATCGCAGGTTT
AGACACTAGGGGCTTCCTGTTTGGCCCTTCCCTAGCTCAGGAGCTGGGCGTGGGCTATGTGCTCACCCAGAAGCACAGGA
AGTTGCTGGGCCCCACTGTGTCAGCCTCCTATGCTCTGGAGAATGGGAAGGCTGAGCTGGAATTCCAGAAATATGCCTTA
GAACCTGGGCGGAGAGTGGTCATTGTGGATGATCTCCTGGCCACTGGAGGAACCATGTGTAAGGCCTGTGAGCTGCTGTA
CCAGCTACAGGCTGAGGTGGGGGTGTGTGTGAGCCTGGTGGAGCTGATTTCCCTGAAGGGCAGGGAGAAGCTATGACCTA
TACCTTTCTTCTCTCTCCTGCAGTATGAC

Alignment

ORF - retro_mmus_1464 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.82 %
• Parental protein coverage: 79.44 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SFRASIRLLASHLKSTHSGKIDYIAGLDSRGFLFGPSLAQELGVGCVLIRKQGKLPGPTVSASYSLEYGK
          S.R.SIRLLASHLKSTHSGK..YIAGLD.RGFLFGPSLAQELGVG.VL..K..KL.GPTVSASY.LE.GK
Retrocopy SDRPSIRLLASHLKSTHSGKTNYIAGLDTRGFLFGPSLAQELGVGYVLTQKHRKLLGPTVSASYALENGK

Parental  AELEIQKDALEPGQRVVIVDDLLATGGTMFAACDLLHQLRAEVVECVSLVELTSLKGRERLGPIPFFSLL
          AELE.QK.ALEPG.RVVIVDDLLATGGTM..AC.LL.QL.AEV..CVSLVEL.SLKGRE.L.PIPFFSLL
Retrocopy AELEFQKYALEPGRRVVIVDDLLATGGTMCKACELLYQLQAEVGVCVSLVELISLKGREKL*PIPFFSLL

Parental  QYD
          QYD
Retrocopy QYD

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	10.35 RPM
SRP007412_cerebellum	0.00 RPM	7.16 RPM
SRP007412_heart	0.00 RPM	8.78 RPM
SRP007412_kidney	0.00 RPM	16.92 RPM
SRP007412_liver	0.00 RPM	18.00 RPM
SRP007412_testis	0.00 RPM	54.38 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1464 was not detected

EST

No EST(s) were mapped for retro_mmus_1464 retrocopy.

TSS

No TSS is located nearby retro_mmus_1464 retrocopy 5' end.

Lab

retro_mmus_1464 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1464 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000639	1 retrocopy	retro_btau_511,
Macropus eugenii	ENSMEUG00000010375	1 retrocopy	retro_meug_1277,
Mus musculus	ENSMUSG00000006589	3 retrocopies	retro_mmus_1464 , retro_mmus_3143, retro_mmus_440,