RetrogeneDB ID: retro_mmus_1035

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:75199434..75199944(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Psma4
• Ensembl ID: ENSMUSG00000032301
• Aliases: Psma4, C9
• Description: proteasome (prosome, macropain) subunit, alpha type 4 [Source:MGI Symbol;Acc:MGI:1347060]

Sequence

>retro_mmus_1035
GTTGAGCTCATTGCTCAAAGTATTTATTACAGTATAAGGAGCCAATTCCCTGTGAGAAGTTGGTTACAGCACTGTATGAT
ATCAAACAGGCATATACACAGTTTGGCAGCAAACATCCCTTTGGTGTTTCTTTGCTGGAATTTAGCTGGAATAAGCACTA
TGGCTTTTCAGCTCTATCAGAGTGACCCAAGTGAAAACTATGGGGGATGGAAAGCCAAGTGCCTTGGAAACAGCAGTGCT
GCAGCTGTGTCAATGTTGAAACAAGATTACAAAGGAGAAATGACTCTGAAGTCAGCCCTCACTCTGGTTGTCAGGTGATA
AAAAAGACAGTGGATGTTAGTAAACTGTCAGGTGGAAAAAGTGGAAATTACCACACTAGCAAGAGAGAGTGGAAAGACAG
TGATCAGAGTCCTCAAGCAAAAGGAAGTGGAACAGATCAAAAAACATGAAGAGGAAGAAGCTAAAGCTGAGCGAGAGAAG
AAAGAAAAAGAACAGAGAGAAAAGGATAAA

Alignment

ORF - retro_mmus_1035 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.39 %
• Parental protein coverage: 65.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LRLIAQ-RYLLQYQEPIPCEQLVTALCDIKQAYTQFGGKRPFGVSLLYIGWDKHYG-FQLYQSDPSGNYG
          ..LIAQ..YLLQY.EPIPCE.LVTAL.DIKQAYTQFG.K.PFGVSLL...W.KHYG.FQLYQSDPS.NYG
Retrocopy VELIAQ<KYLLQYKEPIPCEKLVTALYDIKQAYTQFGSKHPFGVSLLEFSWNKHYG>FQLYQSDPSENYG

Parental  GWKATCIGNNSAAAVSMLKQDYKEGEMTLKSALALAVK-VLNKTMDVSKLS-AEKVEIATLTRESGKTVI
          GWKA.C.GN.SAAAVSMLKQDYK.GEMTLKSAL.L.V..V..KT.DVSKLS..EKVEI.TL.RESGKTVI
Retrocopy GWKAKCLGNSSAAAVSMLKQDYK-GEMTLKSALTLVVR<VIKKTVDVSKLS>VEKVEITTLARESGKTVI

Parental  RVLKQKEVEQLIKKHEEEEAKAEREKKEKEQREKDK
          RVLKQKEVEQ.IKKHEEEEAKAEREKKEKEQREKDK
Retrocopy RVLKQKEVEQ-IKKHEEEEAKAEREKKEKEQREKDK

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	40.56 RPM
SRP007412_cerebellum	0.00 RPM	40.03 RPM
SRP007412_heart	0.00 RPM	55.57 RPM
SRP007412_kidney	0.00 RPM	82.39 RPM
SRP007412_liver	0.00 RPM	81.27 RPM
SRP007412_testis	0.00 RPM	43.77 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1035 was not detected

EST

No EST(s) were mapped for retro_mmus_1035 retrocopy.

TSS

No TSS is located nearby retro_mmus_1035 retrocopy 5' end.

Lab

retro_mmus_1035 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1035 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010369	1 retrocopy	retro_cjac_58,
Myotis lucifugus	ENSMLUG00000027860	1 retrocopy	retro_mluc_1404,
Mus musculus	ENSMUSG00000032301	2 retrocopies	retro_mmus_1035 , retro_mmus_1707,
Tupaia belangeri	ENSTBEG00000011678	5 retrocopies	retro_tbel_1746, retro_tbel_2953, retro_tbel_3324, retro_tbel_4164, retro_tbel_614,
Tarsius syrichta	ENSTSYG00000011745	1 retrocopy	retro_tsyr_21,