RetrogeneDB ID: retro_mmus_2686

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:109528450..109529029(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000093688
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Actr1a
• Ensembl ID: ENSMUSG00000025228
• Aliases: Actr1a, Arp1, alpha-Arp1
• Description: ARP1 actin-related protein 1A, centractin alpha [Source:MGI Symbol;Acc:MGI:1858964]

Sequence

>retro_mmus_2686
CTGAAACACATCTGGCAATATGTCTATTCTAAAGACCAGATGCAGAGGTTCTCAGAGAAGCATCCTGTGCTCCTGACTGA
GGCACTTTTAAGCCCTCGGAGAAACCTGGAGCGAGCTGCAGATGCTTTCTTCGAGATCTTCAGTGTGCCAGCTCTCTTCA
TCTCCATGCAAGCTGTGCTTAGCCTTTATGCACAGGCAGAACCACAGGCCTGGTGTGGATTCTGGGAATGGAGTCATCGT
GCGGTCCTGATTCACTATGCCTCACTCCATCATGCATGTTGACATTGCTGGTTGAGATGTGTCACACTTCTTCTGCCTCT
ACCTATGGAAGGAGGGCTATGATTTCCACTCCTCCATTGAGTTTGAGATTGTCAAGACCATAAAGAAAAGAGCTTGCTAC
CTGTTCATAGCTCCCAGAAGGATGAGACACTGGAGACGGAGAAGGCTCAGTACTACCTGCCTGATGGCAGCAAAGTTGAA
ATAGGCCCTTCCAGGTTCCGGGTCCCCGAGCTGCTGTTCAGGCCAGACTTGATTGGCAAGAAGAGTGAAAGTATCCATGA
AGTGCTGTGCTGGTGTTTG

Alignment

ORF - retro_mmus_2686 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.63 %
• Parental protein coverage: 52.66 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MERIWQYVYSKDQLQTFSEEHPVLLTEAPLNPRKNRERAAEVFFETFNVPALFISMQAVLSLYA-TGRTT
          ...IWQYVYSKDQ.Q.FSE.HPVLLTEA.L.PR.N.ERAA..FFE.F.VPALFISMQAVLSLYA.TGRTT
Retrocopy LKHIWQYVYSKDQMQRFSEKHPVLLTEALLSPRRNLERAADAFFEIFSVPALFISMQAVLSLYA<TGRTT

Parental  GVV-LDSGDGVTHAVPIYEGFAMPHSIMRIDIAGRDVSRFLRLYLRKEGYDFHSSSEFEIVKAIKERACY
          G.V..DSG......V.....F.MPHSIM..DIAG.DVS.F..LYL.KEGYDFHSS.EFEIVK.IK.RACY
Retrocopy GLV<VDSG----NGVIVRS*FTMPHSIMHVDIAG*DVSHFFCLYLWKEGYDFHSSIEFEIVKTIKKRACY

Parental  LSINP-QKDETLETEKAQYYLPDGSTIEIGPSRFRAPELLFRPDLIGEESEGIHEVLVFAI
          L.I.P.QKDETLETEKAQYYLPDGS..EIGPSRFR.PELLFRPDLIG..SE.IHEVL....
Retrocopy LFIAP<QKDETLETEKAQYYLPDGSKVEIGPSRFRVPELLFRPDLIGKKSESIHEVLCWCL

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	0.07 RPM	173.40 RPM
SRP007412_cerebellum	0.00 RPM	174.16 RPM
SRP007412_heart	0.00 RPM	109.92 RPM
SRP007412_kidney	0.00 RPM	106.87 RPM
SRP007412_liver	0.00 RPM	67.48 RPM
SRP007412_testis	0.73 RPM	268.35 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2686 was not detected

EST

No EST(s) were mapped for retro_mmus_2686 retrocopy.

TSS

No TSS is located nearby retro_mmus_2686 retrocopy 5' end.

Lab

retro_mmus_2686 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2686 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000138107	1 retrocopy	retro_hsap_2141,
Mus musculus	ENSMUSG00000025228	1 retrocopy	retro_mmus_2686 ,
Mus musculus	ENSMUSG00000029580	7 retrocopies	retro_mmus_1613, retro_mmus_1677, retro_mmus_283, retro_mmus_2880, retro_mmus_3411, retro_mmus_3532, retro_mmus_761,
Mus musculus	ENSMUSG00000062825	7 retrocopies	retro_mmus_1043, retro_mmus_1524, retro_mmus_2383, retro_mmus_3128, retro_mmus_3265, retro_mmus_3607, retro_mmus_3705,
Nomascus leucogenys	ENSNLEG00000015157	1 retrocopy	retro_nleu_2751,
Pongo abelii	ENSPPYG00000002605	1 retrocopy	retro_pabe_1930,
Pan troglodytes	ENSPTRG00000002894	1 retrocopy	retro_ptro_1567,
Drosophila melanogaster	FBgn0011745	1 retrocopy	retro_dmel_80,