RetrogeneDB ID: retro_mmus_582

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:85790252..85791570(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ddx21
• Ensembl ID: ENSMUSG00000020075
• Aliases: Ddx21, AI255159, AL022742, D10Ertd645e, D10Wsu42e
• Description: DEAD (Asp-Glu-Ala-Asp) box polypeptide 21 [Source:MGI Symbol;Acc:MGI:1860494]

Sequence

>retro_mmus_582
AGTGAGACAGAAAAGTAAATACCCATAGAGCAGAAAGAAGAAGAATTTTCTAATTTTCCCATATCTGAAGAGAATGTCAA
GCTTCTCAGAGCTCCCAGGGTGAACCTCGTCTTTCCTGCACAAGTCAAGATTTTCCACCATGTAGACAGAGGGAAAGACT
TAATTGCTCAAGCATGGTCAGGACCCAGAAAGGCCTTCTCCTTTGCTATCCCTTTGACTGAGAAACTTCAATGTGGGCTA
CAAGAGAAGAAGAGAGGCCAAACCTGTCAGGTACTAGTCCAGGACCTACAAGAGAATTAGCAAACCAAGTGAGAAAAGAT
TTCAGGGACTCAAACAAAATGCTATCACTAGCTTGTTTTTATGGTGGAACTCCCTACAGAGGTCAAATTTAATGAAGACA
GAGTAGGATCGATATCCTGGTTGGGACCCCAGGTCATAATAAAGAAAACTTGCAGAATGGCAAGCTAGATATTACCAAAC
TTAAACATGTTTTCCAGCATAAAGAGGACCAGATGTTGGATACGGGTTTTGCTGATCAGGTGGAAGAAATTTTATGTGTG
GCATACAAGAAAGATACTGAAGACAACCCCCAAACATTACTTTTCTCTGCAACTTGCCCTATTTTGGGTATTTATTGTTC
TAAAAACTCCATGAGATCTACATACAAACAGGTTGACCTGATTGGTAAAAAGACTCAGAAATCATCTATAACTGCGGAGC
ACATGACAATTAAGTGTCTCTGGACAGACAGCACAGCAGGGATTGGGACGTGATCCTAGTGTACAGTGGTCATCAGGGCA
CACAACCATCTTCTCTGGAACCAAGAAGGATGCCCAGGAGCTGGTGCAAAACACATGCATGAAGCAGAATGTCTGGTCCT
GGCTTGGAAACATTCCGCAGAAGCAAAGGGAAATCACACTGGAAAGATTTCCAAAATGGCAATTTTGGTGTTTTCGTGGC
AACCAATGTTGCTGCCCCTGGGTTAGACATCCCTGAAATTGACTTGGTTGTTCAAAGCTGTCCACAAAAGGATATGCAGT
CTTCCGTTCATTATTCAGGGTGAACAGACAGAGATGGAAGGATAGAAGTATGCACCTGCTTTTATCAGCACAAAGAAGAG
TACCAGTTAGCTCAAGTGAAGCAGAAAGCAGGAACTACATTGAAATTGATGGGTGTTCCTTTTGCAACAGAAATCATAAA
AGCCTCCAGCAAAGATGCCATCAGGCTTTGGACTCTGTGTTCCCACTGTCGTTGGACAGTTCAATAGTCAACTGAGAAGC
CGATTGAGGAGAAAGGACCCAGAGAGGCCCTGGCAGCT

Alignment

ORF - retro_mmus_582 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.78 %
• Parental protein coverage: 51.82 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 9

Retrocopy - Parental Gene Alignment:

Parental  SETEKEIPVEQKEGAFSNFPISEETVKLLKARGVNFLFPIQAKTFHHVYSGKDLIAQARTGTGKTFSFAI
          SETEK.IP.EQKE..FSNFPISEE.VKLL.A..VN..FP.Q.K.FHHV..GKDLIAQA..G..K.FSFAI
Retrocopy SETEK*IPIEQKEEEFSNFPISEENVKLLRAPRVNLVFPAQVKIFHHVDRGKDLIAQAWSGPRKAFSFAI

Parental  PLIEKLQGGLQERKRGRAPQVLVL-APTRELANQVSKDFSDITKKLSVACFYGGTPYGGQIERMRSGIDI
          PL.EKLQ.GLQE.KRG...QVLV...PTRELANQV.KDF.D..K.LS.ACFYGGTPY.GQI....S.IDI
Retrocopy PLTEKLQCGLQEKKRGQTCQVLVQ<GPTRELANQVRKDFRDSNKMLSLACFYGGTPYRGQI**RQSRIDI

Parental  LVGTPGRIKDHLQNGKLDLTKLKHVVLDEVDQMLDMGFADQVEEILCVAYKKDSEDNPQTLLFSATCP-H
          LVGTPG..K..LQNGKLD.TKLKHV.....DQMLD.GFADQVEEILCVAYKKD.EDNPQTLLFSATCP..
Retrocopy LVGTPGHNKENLQNGKLDITKLKHVFQHKEDQMLDTGFADQVEEILCVAYKKDTEDNPQTLLFSATCP>F

Parental  WVFNV-AKKYMKSTYEQVDLIGKKTQKAAITVEHLAIKCHWTERAAVIG-DVIRVYSGHQ-GRTIIFCET
          WVF.V..K..M.STY.QVDLIGKKTQK..IT.EH..IKC.WT...A.IG.DVI.VYSGHQ.G.T.IF..T
Retrocopy WVFIV<SKNSMRSTYKQVDLIGKKTQKSSITAEHMTIKCLWTDSTAGIG<DVILVYSGHQ<GHTTIFSGT

Parental  KKDAQELSQNTCIKQDAQSLHGDIPQKQREITL-KGFRNGNFGVLVATNVAARGLDIPEVDLVVQSCPPK
          KKDAQEL.QNTC.KQ...S..G.IPQKQREITL.K.F.NGNFGV.VATNVAA.GLDIPE.DLVVQSCP.K
Retrocopy KKDAQELVQNTCMKQNVWSWLGNIPQKQREITL>KDFQNGNFGVFVATNVAAPGLDIPEIDLVVQSCPQK

Parental  DVESYIHRSGRTGRAGRTGVCICFYQNKEEYQLAQVEQKAGIKFKRIGVPSATEIIKASSKDAIRL-LDS
          D..S..H.SG.T.R.GR..VC.CFYQ.KEEYQLAQV.QKAG...K..GVP.ATEIIKASSKDAIRL.LDS
Retrocopy DMQSSVHYSG*TDRDGRIEVCTCFYQHKEEYQLAQVKQKAGTTLKLMGVPFATEIIKASSKDAIRL<LDS

Parental  V-PPTAISHFKQ-SAEKLIEEKGAVEALAA
          V..PT....F...S.EK.IEEKG..EALAA
Retrocopy V<VPTVVGQFNS<STEKPIEEKGPREALAA

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	25.79 RPM
SRP007412_cerebellum	0.00 RPM	28.18 RPM
SRP007412_heart	0.00 RPM	48.69 RPM
SRP007412_kidney	0.02 RPM	57.17 RPM
SRP007412_liver	0.00 RPM	54.86 RPM
SRP007412_testis	0.14 RPM	79.68 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_582 was not detected

EST

No EST(s) were mapped for retro_mmus_582 retrocopy.

TSS

No TSS is located nearby retro_mmus_582 retrocopy 5' end.

Lab

retro_mmus_582 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_582 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013791	2 retrocopies	retro_cfam_1024, retro_cfam_1925,
Callithrix jacchus	ENSCJAG00000012876	1 retrocopy	retro_cjac_1912,
Macropus eugenii	ENSMEUG00000010586	1 retrocopy	retro_meug_1383,
Microcebus murinus	ENSMICG00000015112	1 retrocopy	retro_mmur_95,
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,
Procavia capensis	ENSPCAG00000016697	1 retrocopy	retro_pcap_346,
Pongo abelii	ENSPPYG00000002389	1 retrocopy	retro_pabe_3816,
Tupaia belangeri	ENSTBEG00000002310	2 retrocopies	retro_tbel_1590, retro_tbel_4454,