RetrogeneDB ID: retro_mmus_1007

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:40778039..40778804(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000090475
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ubxn2a
• Ensembl ID: ENSMUSG00000020634
• Aliases: Ubxn2a, 6330407P03Rik, Ubxd4
• Description: UBX domain protein 2A [Source:MGI Symbol;Acc:MGI:2442310]

Sequence

>retro_mmus_1007
ATGAAAGAAGTAGACAATATAAGAGAAGAATGGGTTTGTGAAACAGGCCCTCCTGACAGTCAACCCCTCAATGATAATCA
ACAAAAGGACTGTGAATATTATGTTGACAGCCTTTTTGAGGAAGCAGGGAAGGCTGGTGCCAAATGCTTGTCCCCCACTG
AACAGAAGAAACAGGTAGATGTAAATATAAAATTGTGGAAAAACGGATTCACTGTCAACGATGATTTTAGAAGTTACTCT
GATGGTGCAAGTCAGCACTTTCTGAACTCCATCAAAAAGGGGGAATTACCTTCAGAATTACGGGGAATTTTTGATAAAGA
GGAGGTGGATGTTAAAGTAGAAAATAAGAAAAATGAAGTATGTATGTCTACAAAGCCTGTGTTCCATCCCTTCTCAGGAC
AGGGCCACAGACTAGCTAGTGCTACACCAAGAATCGTTTCTAAAGCAAAGAGTGTTGAAGTTGACAATAAAAGTACTTTG
TCTGCTGTTTCACTGAACATCTTGGAGCCCATTACCAGGATCCAGATCTGGTTAGCCAATGGGGAAAGAACTGTCCAAAG
ATTTAATGTTTCTCATAGGGTGAGCCACATCAAAGACTTCAATGAAAAATACCAAGGATCTCAGAGAAGCCCTCCTTTTG
CCCTGTCAACAGCTCTTCCTTTCCTCAGGTTTCTGGATGAAACGCTCACATTGGAAGAAGCAGATTTGAAGAATGCTGTA
ATCATTCAGAGACTCCAAAAAACTGCCAAGCCTTTTAGAAAACTT

Alignment

ORF - retro_mmus_1007 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.19 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKEVDNLDSIKEEWACETGPPDSQPLNDNQQKDCEYFVDSLFEEAGKAGAKCLSPTEQKKQVDVNIKLWK
          MKEVDN...I.EEW.CETGPPDSQPLNDNQQKDCEY.VDSLFEEAGKAGAKCLSPTEQKKQVDVNIKLWK
Retrocopy MKEVDN---IREEWVCETGPPDSQPLNDNQQKDCEYYVDSLFEEAGKAGAKCLSPTEQKKQVDVNIKLWK

Parental  NGFTVNDDFRSYSDGASQQFLNSIKKGELPSELWGIFDKEEVDVKVEDKKNEVCMSTKPVFQPFSGQGHR
          NGFTVNDDFRSYSDGASQ.FLNSIKKGELPSEL.GIFDKEEVDVKVE.KKNEVCMSTKPVF.PFSGQGHR
Retrocopy NGFTVNDDFRSYSDGASQHFLNSIKKGELPSELRGIFDKEEVDVKVENKKNEVCMSTKPVFHPFSGQGHR

Parental  LGSATPRIVSKAKSVEVDNKSTLSAVSLNNLEPITRIQIWLANGERTVQRFNVSHRVSHIKDFIEKYQGS
          L.SATPRIVSKAKSVEVDNKSTLSAVSLN.LEPITRIQIWLANGERTVQRFNVSHRVSHIKDF.EKYQGS
Retrocopy LASATPRIVSKAKSVEVDNKSTLSAVSLNILEPITRIQIWLANGERTVQRFNVSHRVSHIKDFNEKYQGS

Parental  QRSPPFALATALPFLRFLDETLTLEEADLKNAVIIQRLQKTAEPFRKL
          QRSPPFAL.TALPFLRFLDETLTLEEADLKNAVIIQRLQKTA.PFRKL
Retrocopy QRSPPFALSTALPFLRFLDETLTLEEADLKNAVIIQRLQKTAKPFRKL

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	32.71 RPM
SRP007412_cerebellum	0.00 RPM	42.25 RPM
SRP007412_heart	0.03 RPM	46.66 RPM
SRP007412_kidney	0.15 RPM	60.98 RPM
SRP007412_liver	0.00 RPM	20.37 RPM
SRP007412_testis	0.00 RPM	5.26 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1007 was not detected

EST

1 EST(s) were mapped to retro_mmus_1007 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BY013573	40778090	40778234	98.6	133	1	129

TSS

No TSS is located nearby retro_mmus_1007 retrocopy 5' end.

Lab

retro_mmus_1007 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1007 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001640	5 retrocopies	retro_chof_1096, retro_chof_1171, retro_chof_2641, retro_chof_961, retro_chof_964,
Callithrix jacchus	ENSCJAG00000007665	1 retrocopy	retro_cjac_2085,
Equus caballus	ENSECAG00000020144	1 retrocopy	retro_ecab_569,
Echinops telfairi	ENSETEG00000002623	1 retrocopy	retro_etel_1116,
Homo sapiens	ENSG00000173960	1 retrocopy	retro_hsap_2025,
Gorilla gorilla	ENSGGOG00000002445	1 retrocopy	retro_ggor_1463,
Myotis lucifugus	ENSMLUG00000015640	1 retrocopy	retro_mluc_1195,
Macaca mulatta	ENSMMUG00000006487	1 retrocopy	retro_mmul_2068,
Mus musculus	ENSMUSG00000020634	1 retrocopy	retro_mmus_1007 ,
Mus musculus	ENSMUSG00000027455	1 retrocopy	retro_mmus_2565,
Nomascus leucogenys	ENSNLEG00000000751	1 retrocopy	retro_nleu_2612,
Oryctolagus cuniculus	ENSOCUG00000008783	1 retrocopy	retro_ocun_207,
Otolemur garnettii	ENSOGAG00000000025	1 retrocopy	retro_ogar_1909,
Procavia capensis	ENSPCAG00000011502	4 retrocopies	retro_pcap_169, retro_pcap_255, retro_pcap_271, retro_pcap_323,
Pan troglodytes	ENSPTRG00000011705	1 retrocopy	retro_ptro_1347,
Rattus norvegicus	ENSRNOG00000004950	2 retrocopies	retro_rnor_1746, retro_rnor_2966,
Sorex araneus	ENSSARG00000010108	1 retrocopy	retro_sara_272,
Sus scrofa	ENSSSCG00000026283	1 retrocopy	retro_sscr_537,
Tupaia belangeri	ENSTBEG00000012158	1 retrocopy	retro_tbel_3887,