RetrogeneDB ID: retro_mmus_3143

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:71224038..71224451(+)
• Located in intron of: None

Retrocopy information

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

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_3143
CCGTACTTCTTCTGAGCCTCCATCAGTCTCCTGGCCAGTCAGTTGAAGTCCACGCACAATGCAAGAACGACTACATCGCA
GGTCTAGACTCCAGGGGCTTCCTTTTTGGCCCTTCCCTAGCTCAAGAGCTTGGCTTGGGCTGTGTCCTCATCTGGAAGCA
CAGGAAGCTGTGGGGCCCCACTGCGTCAGCCTCCTATGCTCTGGAGTATGGGAAGACTGAGCTGGAAATCCAGAAAGATG
CCTTAGAACCCGAGCAGAAAGTGGTCGTTGTGGATGATCTCCCGGCCACTGGAGGAACCATGTGTGCGGCCTGTGAGCTG
CTGAACTAGCTACCGGCTGAGGTGGTAGAATGTGTGAGCTTGGTGGAGCGAACCTCCCTGAAAGGCAGGGAGAAGCTAGG
ACCCATACCGTTT

Alignment

ORF - retro_mmus_3143 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.86 %
• Parental protein coverage: 76.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PDSFRASIRLLASHLKSTHSG-KIDYIAGLDSRGFLFGPSLAQELGVGCVLIRKQGKLPGPTVSASYSLE
          P..F.ASI.LLAS.LKSTH...K.DYIAGLDSRGFLFGPSLAQELG.GCVLI.K..KL.GPT.SASY.LE
Retrocopy PYFF*ASISLLASQLKSTHNA<KNDYIAGLDSRGFLFGPSLAQELGLGCVLIWKHRKLWGPTASASYALE

Parental  YGKAELEIQKDALEPGQRVVIVDDLLATGGTMFAACDLLHQLRAEVVECVSLVELTSLKGRERLGPIPF
          YGK.ELEIQKDALEP.Q.VV.VDDL.ATGGTM.AAC.LL..L.AEVVECVSLVE.TSLKGRE.LGPIPF
Retrocopy YGKTELEIQKDALEPEQKVVVVDDLPATGGTMCAACELLN*LPAEVVECVSLVERTSLKGREKLGPIPF

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	0.14 RPM	10.35 RPM
SRP007412_cerebellum	0.13 RPM	7.16 RPM
SRP007412_heart	0.03 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_3143 was not detected

EST

No EST(s) were mapped for retro_mmus_3143 retrocopy.

TSS

No TSS is located nearby retro_mmus_3143 retrocopy 5' end.

Lab

retro_mmus_3143 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3143 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,