RetrogeneDB ID: retro_mmus_3033

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:63736978..63737412(-)
• Located in intron of: ENSMUSG00000033510

Retrocopy information

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

Parental gene information

• Parental gene symbol: Nop16
• Ensembl ID: ENSMUSG00000025869
• Aliases: Nop16, AA409471, D13Wsu177e
• Description: NOP16 nucleolar protein [Source:MGI Symbol;Acc:MGI:107862]

Sequence

>retro_mmus_3033
GTGGAATGCTCGTTGGAGGGCAGTACCGTGGACCACACCAAATCTGTGCGGCAAAACCTGGCAGAGATGGGGTTGGTCAT
AGACCCCCAACAGGGCGGATTCCCTCTGTAAGAGGAAGGTAAAGTCCATGGAAGTAGACGCAGAGGAGGGACCCAATCTT
GTATGGAAGCCCTACGTGGTAAATGACCTGAAGGCAGAAGCCAGCCTCCCAGAGAAGAAAGGAAATACTTTGTCTCGGGA
CCTCATCGACTATGTTCAGTACGTGGTGGAGAATCACGGGGAAGACTATAAGGCCATGGCCGGGGAAGAGGAGAATTACT
ATCAAGACACCCCCGAAACAGATTCAGAATAAGATCAATGTCTATAAGCGCTTTTACCCAACAGAATGGCAAGCCTTCAT
CAATTCTTTGCAGAGTAAGAAGATGGAGGTAGAC

Alignment

ORF - retro_mmus_3033 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.59 %
• Parental protein coverage: 81.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IECSHIRHAWDHTKSVRQNLAEMGLAMDP-NKAVPLRKKKVKAMEVDTEERPRDLVRKPYVVNDLEAEAS
          .ECS......DHTKSVRQNLAEMGL..DP.N.A..L.K.KVK.MEVD.EE.P..LV.KPYVVNDL.AEAS
Retrocopy VECSLEGSTVDHTKSVRQNLAEMGLVIDP>NRADSLCKRKVKSMEVDAEEGP-NLVWKPYVVNDLKAEAS

Parental  LPEKKGNTLSRDLIDYVRYMVENHGEDYKAMARDEKNYYQDT-PKQIRNKINVYKRFYPTEWQAFIDSLQ
          LPEKKGNTLSRDLIDYV.Y.VENHGEDYKAMA..E.NYYQDT.PKQI.NKINVYKRFYPTEWQAFI.SLQ
Retrocopy LPEKKGNTLSRDLIDYVQYVVENHGEDYKAMAGEEENYYQDT>PKQIQNKINVYKRFYPTEWQAFINSLQ

Parental  SKKMEVD
          SKKMEVD
Retrocopy SKKMEVD

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	12.52 RPM
SRP007412_cerebellum	0.30 RPM	10.42 RPM
SRP007412_heart	0.00 RPM	9.99 RPM
SRP007412_kidney	0.00 RPM	19.10 RPM
SRP007412_liver	0.00 RPM	18.30 RPM
SRP007412_testis	0.23 RPM	10.20 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3033 was not detected

EST

No EST(s) were mapped for retro_mmus_3033 retrocopy.

TSS

No TSS is located nearby retro_mmus_3033 retrocopy 5' end.

Lab

retro_mmus_3033 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3033 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012315	1 retrocopy	retro_cjac_2208,
Cavia porcellus	ENSCPOG00000026072	1 retrocopy	retro_cpor_129,
Echinops telfairi	ENSETEG00000010391	1 retrocopy	retro_etel_1329,
Myotis lucifugus	ENSMLUG00000003504	1 retrocopy	retro_mluc_2425,
Mustela putorius furo	ENSMPUG00000012552	1 retrocopy	retro_mputfur_381,
Mus musculus	ENSMUSG00000025869	2 retrocopies	retro_mmus_3033 , retro_mmus_3258,
Rattus norvegicus	ENSRNOG00000017284	1 retrocopy	retro_rnor_2739,
Sus scrofa	ENSSSCG00000029577	1 retrocopy	retro_sscr_510,