RetrogeneDB ID: retro_mmus_3362

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:84973046..84974881(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ddx50
• Ensembl ID: ENSMUSG00000020076
• Aliases: Ddx50, 4933429B04Rik, 8430408E17Rik, GU2, RH-II
• Description: DEAD (Asp-Glu-Ala-Asp) box polypeptide 50 [Source:MGI Symbol;Acc:MGI:2182303]

Sequence

>retro_mmus_3362
CAGAGGAGACTAACATGTGAACAAAAGGAAGAAGCCTTCTCTAATTTCTCCATTTCTGAGGAGACCATAAAGCTTCTGAA
AGGTCGAGGGATAACATATCTCTTTCCTATTCAAGTTAAAACCTTTGGTCCTGTATATGAAGGAAAAGATTTAATTTCTC
AAGCCTGGACAGGAACAGGAAAGACATTCTCTTTTGCCATACCCTTGATTGAAAGGCTCCAAAGAAATCAAGAAACAATT
AAAAAAAACCGCTCACCAAAGGTACTCGTTTTGGCTCCAACAAGGGAATTGGCAAATCAAGTAGCCAAAGATTTCAAAGA
TATAACTAGAAAACTCAATGTGGCATGTTTTTATGGTGGAACATCATATCAAAGCCAGATTAATCAAATTCGGAATGGTA
TTGACATCCTTGTTGGGACCCCAGGGCGTATCAAAGACCATCTGCAAAGTGGCTGTTTGGATCTTTCAAAGCTACGCCAT
GTTGTGCTTGATGAAGTAGATCAAATGTTAGATTTAGGTTTTGCTGAACAAGTTGAAGATATTATTCATGAATCCTACAA
AACTGATTCAGAAGACAATCTTCAGACCTTACATTTTTCTGCAACTTGCCCACAGTGGGTATACAAAGTTGCAAAAAAAA
TACATGAAATCCAGATATGAACAGGTTGACCTTTTTGGAAAAATGACTCAAAAAGCTGCAACCACTGTGGAACATTTGGC
TATCCAGTGTCATTGGTCTCAGAGACCAGCAGTTATTGGAGATGTCTTTCAGGTCTACAGTGGGTCTGAAGGGAGAGCTA
TTATCTTCTGTGAGATTAAGAAGAATGTTACTGAAATGGCCATGAATCCACACATAAAGCAGAATGCCCAGTGTTTGCAT
GGAGACATTGCACAGTCACAAAGAGAAATGACCTTGAAAGGCTTCAGAGAAGGTAGTTTTAAAGTTTTGGTGGCAACCAA
TGTGGCTGCTCGTGGCTTGGACATTCCTGAAGTTGACCTTGTGATTCAGAGTTCTCCTCCACAGGATGTTGAATCCTATA
TCCATCGCTCTGGACACACAGGTAGAGCTGGCCGGACAGGAATTTGTGTATGTTTTTATCAACCAAGGGAAAGAGTTCAA
CTGAGATATGTGGAGCAGAAAGCCGGAATTACTTTTAAACGTGTAGGTGTTCCATCTACAATGGATTTAGTTAAATCTAA
AAGCATGGATGCCATCAGGTCTCTGGCTTCTGTTTCTTATGCTGCTGTTGATTTTTTCCAACCATCAGCTCAAAGACTGA
TAGAAGAGAAGGGGGTAGTGGATGTGTTGGCTGCAGCCTTAGCTCACATTTCTGGTGCATCAAGCTTTGAACCACGGTCT
TTGATCACCTCTGATAAGAGGTTTGTGACCATAACTCTGGAAAGCCCAGAAGAAATACAGGATGTCAGCTGTGCTTAGAA
GGAACTTAACAGAAAGCTCAGTAGTAATGCTGTGTCTCACGTAACCAGAATGTGCCTCCTGAAAGGAAATATGGGTGTTT
GCTTTGATGTTCCTACAAGTGAGTCAGAAAGATTACAGGCAGGGTGGCATGATTCAGACTGGATACTCTCAGTGCCAGCC
AAATTACCTGAAATTGAAGAATATTATGATGGAAACGCATCATCTAATCCCAGACAGAGGAGCAGCTGGTCTGGAGGCAG
GTCAGGCCGTTCAGGCCGGTCTGGTGGTCGATCTGGTGGCAGATCAGGTAGACAGAGTCCACAGGGAAGTCGGTCAGGAA
GTCGGCAAGATGGTAGAAGACAAAGTGGGAACAGAAATCGATCAAGAAGTGGGGGGCCATAAACAGAATTTTGAC

Alignment

ORF - retro_mmus_3362 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.17 %
• Parental protein coverage: 83.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EETLTREQKEGAFSNFSISEETIKLLKGRGVTYLFPIQVKTFGPVYEGKDLIAQARTGTGKTFSFAIPLI
          ...LT.EQKE.AFSNFSISEETIKLLKGRG.TYLFPIQVKTFGPVYEGKDLI.QA.TGTGKTFSFAIPLI
Retrocopy QRRLTCEQKEEAFSNFSISEETIKLLKGRGITYLFPIQVKTFGPVYEGKDLISQAWTGTGKTFSFAIPLI

Parental  ERLQRNQETIKKSRSPKVLVLAPTRELANQVAKDFKDITRKLSVACFYGGTSYQSQINQIRNGIDILVGT
          ERLQRNQETI...RSPKVLVLAPTRELANQVAKDFKDITRKL.VACFYGGTSYQSQINQIRNGIDILVGT
Retrocopy ERLQRNQETIXXXRSPKVLVLAPTRELANQVAKDFKDITRKLNVACFYGGTSYQSQINQIRNGIDILVGT

Parental  PGRIKDHLQSGRLDLSKLRHVVLDEVDQMLDLGFAEQVEDIIHESYKTDSEDNPQTLLFSATCPQWVYKV
          PGRIKDHLQSG.LDLSKLRHVVLDEVDQMLDLGFAEQVEDIIHESYKTDSEDN.QTL.FSATCPQWVYKV
Retrocopy PGRIKDHLQSGCLDLSKLRHVVLDEVDQMLDLGFAEQVEDIIHESYKTDSEDNLQTLHFSATCPQWVYKV

Parental  AKK-YMKSRYEQVDLVGKMTQKAATTVEHLAIQCHWSQRPAVIGDVLQVYSGSEGRAIIFCETKKNVTEM
          ....YMKSRYEQVDL.GKMTQKAATTVEHLAIQCHWSQRPAVIGDV.QVYSGSEGRAIIFCE.KKNVTEM
Retrocopy XXX>YMKSRYEQVDLFGKMTQKAATTVEHLAIQCHWSQRPAVIGDVFQVYSGSEGRAIIFCEIKKNVTEM

Parental  AMNPHIKQNAQCLHGDIAQSQREITLKGFREGSFKVLVATNVAARGLDIPEVDLVIQSSPPQDVESYIHR
          AMNPHIKQNAQCLHGDIAQSQRE.TLKGFREGSFKVLVATNVAARGLDIPEVDLVIQSSPPQDVESYIHR
Retrocopy AMNPHIKQNAQCLHGDIAQSQREMTLKGFREGSFKVLVATNVAARGLDIPEVDLVIQSSPPQDVESYIHR

Parental  SGRTGRAGRTGICVCFYQPRERGQLRYVEQKAGITFKRVGVPSTMDLVKSKSMDAIRSLASVSYAAVDFF
          SG.TGRAGRTGICVCFYQPRER.QLRYVEQKAGITFKRVGVPSTMDLVKSKSMDAIRSLASVSYAAVDFF
Retrocopy SGHTGRAGRTGICVCFYQPRERVQLRYVEQKAGITFKRVGVPSTMDLVKSKSMDAIRSLASVSYAAVDFF

Parental  RPSAQRLIEEKGAVDALAAALAHISGASSFEPRSLITSDKGFVTMTLESPEEIQDVSCAWKELNRKLSSN
          .PSAQRLIEEKG.VD.LAAALAHISGASSFEPRSLITSDK.FVT.TLESPEEIQDVSCA.KELNRKLSSN
Retrocopy QPSAQRLIEEKGVVDVLAAALAHISGASSFEPRSLITSDKRFVTITLESPEEIQDVSCA*KELNRKLSSN

Parental  AVSHVTRMCLLKGNMGVCFDVPTSESERLQAEWHDSDWILSVPAKLPEIEEYYDGNTSSNPRQRSGWSGG
          AVSHVTRMCLLKGNMGVCFDVPTSESERLQA.WHDSDWILSVPAKLPEIEEYYDGN.SSNPRQRS.WS..
Retrocopy AVSHVTRMCLLKGNMGVCFDVPTSESERLQAGWHDSDWILSVPAKLPEIEEYYDGNASSNPRQRSSWSXX

Parental  RSGRSGRSGGRSGGRSGRQSRQGSRSGSRQDGRRRSGNRNRSRS-GGHKRNFD
          ........GGRSGGRSGRQS.QGSRSGSRQDGRR.SGNRNRSRS.GGHK.NFD
Retrocopy XXXXXXXXGGRSGGRSGRQSPQGSRSGSRQDGRRQSGNRNRSRS>GGHKQNFD

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	0.12 RPM	50.14 RPM
SRP007412_cerebellum	0.00 RPM	41.16 RPM
SRP007412_heart	0.09 RPM	32.06 RPM
SRP007412_kidney	0.08 RPM	46.33 RPM
SRP007412_liver	0.05 RPM	41.81 RPM
SRP007412_testis	0.09 RPM	54.43 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3362 was not detected

EST

No EST(s) were mapped for retro_mmus_3362 retrocopy.

TSS

No TSS is located nearby retro_mmus_3362 retrocopy 5' end.

Lab

retro_mmus_3362 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3362 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018844	1 retrocopy	retro_cjac_1298,
Homo sapiens	ENSG00000107625	2 retrocopies	retro_hsap_2089, retro_hsap_2866,
Macaca mulatta	ENSMMUG00000001006	1 retrocopy	retro_mmul_982,
Mus musculus	ENSMUSG00000020075	2 retrocopies	retro_mmus_582, retro_mmus_662,
Mus musculus	ENSMUSG00000020076	1 retrocopy	retro_mmus_3362 ,
Mus musculus	ENSMUSG00000020719	1 retrocopy	retro_mmus_788,
Nomascus leucogenys	ENSNLEG00000011631	2 retrocopies	retro_nleu_1300, retro_nleu_609,
Otolemur garnettii	ENSOGAG00000001844	2 retrocopies	retro_ogar_1492, retro_ogar_555,
Pongo abelii	ENSPPYG00000002390	3 retrocopies	retro_pabe_2007, retro_pabe_2369, retro_pabe_2418,
Pan troglodytes	ENSPTRG00000002562	2 retrocopies	retro_ptro_1536, retro_ptro_1938,