RetrogeneDB ID: retro_mmus_831

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:102731300..102731757(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000084375
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Psma1
• Ensembl ID: ENSMUSG00000030751
• Aliases: Psma1, C2, HC2, Pros-30, alpha-type
• Description: proteasome (prosome, macropain) subunit, alpha type 1 [Source:MGI Symbol;Acc:MGI:1347005]

Sequence

>retro_mmus_831
CTCTGTGTTGACAACCGTATTGGCGTCTCAACTGTGAGACTTACTGTTGATACTGTTATGTAATCTTACACACCAATACG
TGTTTGGATTTCAGATCTACATTTGACAGACCATTTCCTGTGTTATGCCTTGCTTGTATCTCTAATTGGAAGCAAGACCC
AGACACCAACACAGGAGTGTGGCCGGAGACCATATGGTGTGGGGGGCTTCCTGCTGTTTAAGATGATATGAGTCCTCACA
TTTCCCAAACCTGTCCATCTGCTATTTCATCTGCAGTTATGTCCACTGGAACTATTCAACCAGCTTGCACTTACTTAGAA
AAACATATGTCTACATTTATGAAATGCAATTTAAAAGAACTGGTTAAACGTGGCCGTGAGCCTTGAAAGAGAAACTTTCC
ACAGAACAAAACCCAGCTATGAAGGAAGTCCTTACTGGGACTTCAGGGAAAGACTTG

Alignment

ORF - retro_mmus_831 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.27 %
• Parental protein coverage: 59.32 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LHVDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQRYGRRPYGVGLL
          L.VDN.IG.S...LT.D...................D..L....LVSLIGSKTQ.PTQ..GRRPYGVG..
Retrocopy LCVDNRIGVSTVRLTVDTVM*SYTPIRVWISDLHLTDHFLCYALLVSLIGSKTQTPTQECGRRPYGVGGF

Parental  I-AGYDDMGPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFMECNLDELVKHGLR-ALRETLPA
          ..A..DDM.PHI.QTCPSA.......MS.G...Q.A.TYLE.HMS.FM.CNL.ELVK.G...AL.E.L..
Retrocopy L<AV*DDMSPHISQTCPSA--ISSAVMSTGT-IQPACTYLEKHMSTFMKCNLKELVKRGRE<ALKEKLST

Parental  EQDLTTKNVSIGIVGKDL
          EQ....K.V..G..GKDL
Retrocopy EQNPAMKEVLTGTSGKDL

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	0.19 RPM	53.43 RPM
SRP007412_cerebellum	1.22 RPM	49.15 RPM
SRP007412_heart	0.00 RPM	62.26 RPM
SRP007412_kidney	0.02 RPM	69.16 RPM
SRP007412_liver	0.00 RPM	60.52 RPM
SRP007412_testis	0.00 RPM	20.13 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_831 was not detected

EST

No EST(s) were mapped for retro_mmus_831 retrocopy.

TSS

No TSS is located nearby retro_mmus_831 retrocopy 5' end.

Lab

retro_mmus_831 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_831 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002440	2 retrocopies	retro_amel_1733, retro_amel_1903,
Bos taurus	ENSBTAG00000006564	1 retrocopy	retro_btau_1833,
Choloepus hoffmanni	ENSCHOG00000005395	11 retrocopies	retro_chof_155, retro_chof_1844, retro_chof_1991, retro_chof_2376, retro_chof_2626, retro_chof_267, retro_chof_2712, retro_chof_459, retro_chof_519, retro_chof_719, retro_chof_77,
Equus caballus	ENSECAG00000024086	1 retrocopy	retro_ecab_1078,
Felis catus	ENSFCAG00000011381	1 retrocopy	retro_fcat_972,
Homo sapiens	ENSG00000129084	1 retrocopy	retro_hsap_4720,
Gorilla gorilla	ENSGGOG00000001416	1 retrocopy	retro_ggor_2933,
Macropus eugenii	ENSMEUG00000011112	1 retrocopy	retro_meug_71,
Myotis lucifugus	ENSMLUG00000009251	4 retrocopies	retro_mluc_2444, retro_mluc_2445, retro_mluc_2463, retro_mluc_2515,
Macaca mulatta	ENSMMUG00000016446	1 retrocopy	retro_mmul_2509,
Mustela putorius furo	ENSMPUG00000013199	4 retrocopies	retro_mputfur_1243, retro_mputfur_224, retro_mputfur_338, retro_mputfur_825,
Mus musculus	ENSMUSG00000030751	1 retrocopy	retro_mmus_831 ,
Nomascus leucogenys	ENSNLEG00000017705	1 retrocopy	retro_nleu_1990,
Oryctolagus cuniculus	ENSOCUG00000000439	2 retrocopies	retro_ocun_1461, retro_ocun_1490,
Otolemur garnettii	ENSOGAG00000011622	3 retrocopies	retro_ogar_2267, retro_ogar_2644, retro_ogar_992,
Ochotona princeps	ENSOPRG00000013677	1 retrocopy	retro_opri_370,
Pongo abelii	ENSPPYG00000003466	2 retrocopies	retro_pabe_1883, retro_pabe_3664,
Pan troglodytes	ENSPTRG00000003385	1 retrocopy	retro_ptro_3137,
Sarcophilus harrisii	ENSSHAG00000015626	1 retrocopy	retro_shar_217,
Ictidomys tridecemlineatus	ENSSTOG00000006270	2 retrocopies	retro_itri_1470, retro_itri_987,
Tupaia belangeri	ENSTBEG00000012037	3 retrocopies	retro_tbel_2629, retro_tbel_323, retro_tbel_982,
Tarsius syrichta	ENSTSYG00000003869	2 retrocopies	retro_tsyr_1723, retro_tsyr_374,
Vicugna pacos	ENSVPAG00000008820	3 retrocopies	retro_vpac_344, retro_vpac_648, retro_vpac_82,