RetrogeneDB ID: retro_mmus_1938

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:77335358..77335961(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082006
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Psmb3
• Ensembl ID: ENSMUSG00000069744
• Aliases: Psmb3, AL033320, C10-II
• Description: proteasome (prosome, macropain) subunit, beta type 3 [Source:MGI Symbol;Acc:MGI:1347014]

Sequence

>retro_mmus_1938
ATGTCTATTATGTCCTACAATGGAGGGGCCGTCATGACCATGAAGGGAAAGAACTGTGTGGCCATCGCTGCAGACAGGCG
TTTTGGGATCCAGGCCCAGATGGTGACCACGGACTTCCAGAAGATATTTCCCATGGGTGACAGGCTCTACATAGGCTGGC
CAGTCTGGCCACTGACGTCCAGACAGTTGCCCAGCCTCTCAAGTTCCAACTGAACCTGTATGAGCTGAAAGAAGGTCGGC
AGATCAAGCCTTACACCCTCATGAGCATGGGTAGCCAACCTCCTGTATGAGAAGCGGTTTGGTACCTACTACACAGAGCC
TGTCACTGCTGGCCTGGACCCAAAGACTTTTAAGCCCTTCATTTGCTCTCTGGACCTCATTGACTGTCCCATGGTGACTG
ATGACTTCGTAGTCAGTGGTACCTGCTCTGAACAAATGTATGGGATGTGTTAGTCTCTCTGGGAGCCCAACATGGATCCA
GAACACCTATCTGAAACCATTTTTCAGGCCATGCTGAATGCAGTGGACCGGGATGCTGTGTCAGGCATGGGTATCATTGA
GAAAGACAAGATTACCACCAGGACGCTGAATGCCTGGATGGAC

Alignment

ORF - retro_mmus_1938 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.82 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSIMSYNGGAVMAMKGKNCVAIAADRRFGIQAQMVTTDFQKIFPMGDRLYIG-LAGLATDVQTVAQRLKF
          MSIMSYNGGAVM.MKGKNCVAIAADRRFGIQAQMVTTDFQKIFPMGDRLYIG.LA.LATDVQTVAQ.LKF
Retrocopy MSIMSYNGGAVMTMKGKNCVAIAADRRFGIQAQMVTTDFQKIFPMGDRLYIG<LASLATDVQTVAQPLKF

Parental  RLNLYELKEGRQIKPYTLMSM-VANLLYEKRFGPYYTEPVIAGLDPKTFKPFICSLDLIGCPMVTDDFVV
          .LNLYELKEGRQIKPYTLMSM.VANLLYEKRFG.YYTEPV.AGLDPKTFKPFICSLDLI.CPMVTDDFVV
Retrocopy QLNLYELKEGRQIKPYTLMSM>VANLLYEKRFGTYYTEPVTAGLDPKTFKPFICSLDLIDCPMVTDDFVV

Parental  SGTCSEQMYGMCESLWEPNMDPEHLFETISQAMLNAVDRDAVSGMGVIVHVIEKDKITTRTLKARMD
          SGTCSEQMYGMC.SLWEPNMDPEHL.ETI.QAMLNAVDRDAVSGMG.I....EKDKITTRTL.A.MD
Retrocopy SGTCSEQMYGMC*SLWEPNMDPEHLSETIFQAMLNAVDRDAVSGMGII----EKDKITTRTLNAWMD

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	22.12 RPM
SRP007412_cerebellum	0.04 RPM	17.19 RPM
SRP007412_heart	0.06 RPM	26.43 RPM
SRP007412_kidney	0.02 RPM	22.37 RPM
SRP007412_liver	0.00 RPM	25.83 RPM
SRP007412_testis	0.00 RPM	9.65 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1938 was not detected

EST

No EST(s) were mapped for retro_mmus_1938 retrocopy.

TSS

No TSS is located nearby retro_mmus_1938 retrocopy 5' end.

Lab

retro_mmus_1938 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1938 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004363	1 retrocopy	retro_amel_619,
Canis familiaris	ENSCAFG00000016587	2 retrocopies	retro_cfam_135, retro_cfam_532,
Callithrix jacchus	ENSCJAG00000008246	1 retrocopy	retro_cjac_2852,
Equus caballus	ENSECAG00000000987	1 retrocopy	retro_ecab_476,
Erinaceus europaeus	ENSEEUG00000015275	1 retrocopy	retro_eeur_10,
Felis catus	ENSFCAG00000014497	3 retrocopies	retro_fcat_1270, retro_fcat_1442, retro_fcat_784,
Homo sapiens	ENSG00000108294	2 retrocopies	retro_hsap_1121, retro_hsap_2387,
Gorilla gorilla	ENSGGOG00000007067	2 retrocopies	retro_ggor_103, retro_ggor_876,
Loxodonta africana	ENSLAFG00000002233	1 retrocopy	retro_lafr_70,
Macropus eugenii	ENSMEUG00000004131	2 retrocopies	retro_meug_1804, retro_meug_551,
Microcebus murinus	ENSMICG00000002997	1 retrocopy	retro_mmur_397,
Macaca mulatta	ENSMMUG00000012363	1 retrocopy	retro_mmul_868,
Monodelphis domestica	ENSMODG00000012614	2 retrocopies	retro_mdom_1722, retro_mdom_1812,
Mus musculus	ENSMUSG00000069744	8 retrocopies	retro_mmus_1449, retro_mmus_1551, retro_mmus_1790, retro_mmus_1938 , retro_mmus_2110, retro_mmus_41, retro_mmus_46, retro_mmus_536,
Nomascus leucogenys	ENSNLEG00000000594	3 retrocopies	retro_nleu_1511, retro_nleu_188, retro_nleu_371,
Oryctolagus cuniculus	ENSOCUG00000002598	1 retrocopy	retro_ocun_561,
Pongo abelii	ENSPPYG00000008505	2 retrocopies	retro_pabe_2153, retro_pabe_927,
Pteropus vampyrus	ENSPVAG00000002270	1 retrocopy	retro_pvam_822,
Rattus norvegicus	ENSRNOG00000012938	7 retrocopies	retro_rnor_1016, retro_rnor_2094, retro_rnor_2448, retro_rnor_2537, retro_rnor_2804, retro_rnor_743, retro_rnor_8,
Ictidomys tridecemlineatus	ENSSTOG00000014258	3 retrocopies	retro_itri_527, retro_itri_935, retro_itri_936,
Tupaia belangeri	ENSTBEG00000013010	2 retrocopies	retro_tbel_1387, retro_tbel_2693,