RetrogeneDB ID: retro_mmus_348

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:101385986..101386587(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Psmb6
• Ensembl ID: ENSMUSG00000018286
• Aliases: Psmb6, Lmp19, Mpnd
• Description: proteasome (prosome, macropain) subunit, beta type 6 [Source:MGI Symbol;Acc:MGI:104880]

Sequence

>retro_mmus_348
GTGCAGTTTAATGGGGGCATGGTTCTAGGAGCAGACTCTAGAACAACCACTGGGTCCTACATCGCCAATCGAGTGACGGA
CAAGCTGACCCCTATTCACGATTACATCTTCTGCTGCCGCTCAGGCTCAGCCGCTGATACCCAAGCAGTGGCGGATGCTG
TCACTTACCAGCTTGGTTTCCACAGTATTGAACTGAACGTGCCTCCACTAGTCCACACAGCCGCCAGTCTCTTTAAGGCG
ATGTGATACAGATACAGAGAAGATCTGATGGCAGGAATCATCATTGCAGGCTGGGACCCTCAAGAAGGAGGGCAGGTGTA
CACTGTTCCCATGGGGGGATATGATGGTAAGACAGTCCTTTGCCATCTGAGGCTCCATGCGCTCATACATCTATGGCTAT
GTTGATGCTGTCTATTGGGAAGGCATGACCAAGGACGAATGTCTGCAGTTCACTGCCAATGCTCTGGCTTTGGCCTTGGA
ATGTGACGGCTCCAGTGGAGGAGTGATCCGCTTGGCAGCCATTCAGGAGTCAGGGGTACAGCGGCAGGTGCTTTTGGGAG
ACCAGATCCCCATGTTCACCATTGCCACGTTGCCTCCTCCC

Alignment

ORF - retro_mmus_348 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.04 %
• Parental protein coverage: 84.03 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VQFNGGVVLGADSRTTTGSYIANRVTDKLTPIHDHIFCCRSGSAADTQAVADAVTYQLGFHSIELNEPPL
          VQFNGG.VLGADSRTTTGSYIANRVTDKLTPIHD.IFCCRSGSAADTQAVADAVTYQLGFHSIELN.PPL
Retrocopy VQFNGGMVLGADSRTTTGSYIANRVTDKLTPIHDYIFCCRSGSAADTQAVADAVTYQLGFHSIELNVPPL

Parental  VHTAASLFKEMCYRYREDLMAGIIIAGWDPQEGGQVYSVPMGG-MMVRQSFAIGGSGSSYIYGYVDATYR
          VHTAASLFK.M.YRYREDLMAGIIIAGWDPQEGGQVY.VPMGG.MMVRQSFAI.GS..SYIYGYVDA.Y.
Retrocopy VHTAASLFKAM*YRYREDLMAGIIIAGWDPQEGGQVYTVPMGG>MMVRQSFAI*GSMRSYIYGYVDAVYW

Parental  EGMTKDECLQFTANALALAMERDGSSGGVIRLAAIQESGVERQVLLGDQIPKFTIATLPPP
          EGMTKDECLQFTANALALA.E.DGSSGGVIRLAAIQESGV.RQVLLGDQIP.FTIATLPPP
Retrocopy EGMTKDECLQFTANALALALECDGSSGGVIRLAAIQESGVQRQVLLGDQIPMFTIATLPPP

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	0.02 RPM	44.13 RPM
SRP007412_cerebellum	0.00 RPM	56.01 RPM
SRP007412_heart	0.09 RPM	85.73 RPM
SRP007412_kidney	0.08 RPM	73.48 RPM
SRP007412_liver	0.00 RPM	78.89 RPM
SRP007412_testis	0.05 RPM	103.05 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_348 was not detected

EST

No EST(s) were mapped for retro_mmus_348 retrocopy.

TSS

No TSS is located nearby retro_mmus_348 retrocopy 5' end.

Lab

retro_mmus_348 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_348 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016075	1 retrocopy	retro_amel_1834,
Canis familiaris	ENSCAFG00000015855	1 retrocopy	retro_cfam_2173,
Callithrix jacchus	ENSCJAG00000012010	1 retrocopy	retro_cjac_775,
Loxodonta africana	ENSLAFG00000012859	1 retrocopy	retro_lafr_874,
Macropus eugenii	ENSMEUG00000010676	1 retrocopy	retro_meug_621,
Microcebus murinus	ENSMICG00000014854	2 retrocopies	retro_mmur_140, retro_mmur_718,
Monodelphis domestica	ENSMODG00000005554	1 retrocopy	retro_mdom_799,
Mus musculus	ENSMUSG00000018286	2 retrocopies	retro_mmus_348 , retro_mmus_3569,
Rattus norvegicus	ENSRNOG00000019551	1 retrocopy	retro_rnor_56,
Sorex araneus	ENSSARG00000006615	1 retrocopy	retro_sara_689,
Tursiops truncatus	ENSTTRG00000000566	1 retrocopy	retro_ttru_405,