RetrogeneDB ID: retro_mmus_662

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:86550854..86552597(-)
• 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_662
TTTTCTAATTTTCCCATATCTGAAGAACATGTCAAGCTTCTCAGGGCTCACACGGTAAACTTCGTCTTTCCTACACAAGC
CAAAATTTTCCACCATGTAGAGAGAGGGAAAGACTTAAATGCTCAAGCATGGTCAGGACCCAGAAAGTCCTTCTCCTTTG
CTATCCCTTTGACTGAGAAACTTCAATGTGGGCTACAAGAGAAGAAGAGAGGCCAAGCCTGTCAGGTACTAGTCCAGCAC
CTACAAGAGAATTAGCAAATCAAATGAGGAAAGATGTCAGGGATTTAAACAAAATGCTATCACTAGCTTGTTTTTATGGT
GGAACTCCCTACAGAGGTCAAATTGAATGAAGGCAGAGTAGGATCGATTTCCTGGTTGGGGCCCCAGGTCATTATAAAGA
AAACTTGAAGAATGGCAAGCTAGACCTTACCAAACTTAAACATGTTTTCCTGCATAAAGAGGACCAGATGTTGGATACGG
GTTTTGCTGATCAGGTGGAAGAAATTTTATGTGTGGCATACAAGAAAGATTCTGAAGACAACCCCCAAACATTACTTTTC
TCTGCAACTTGCCCTATTTTGGGTATTTATTGTTCTAAAAACTCCATGAGATCTACATACGAACAGGTGGACCTGATTGG
TAAAAAGACTCAGAAATCATCTATAACTGCGGAGCACCTGACAATTAAGTGTCTCTGGACAGACAGCACAGCAGGGATTG
GGACGTGATCCTAGTGTACAGTGGTCATCAGGGCACACAACCATCTTCTGTGGAACCAAGAAGGATGCCCAGGAGCTGGT
GCAGAACACATGCATGAAGCAGAATGTCTGGTCCTGACTTGGAAACATTCCGCAGAAGCAAAGGGAAGTCACACTGGAAA
GATTTCCAAAATGGCAATTTTGGAATTTTGGTGGCAACCAATGTTGCTGCCTCTGGGTTAGACAACCCTGAGGTTGACTT
GGATGTTCAGAGCTGTCCACTAAATGATGTGGGGTCTTCCATTCATGATTCAGGGTCAACAGACAGAGATGGAAGGATAG
AAATATGCACCTGCTTTTAACAGCACAAAGAAGAGTACCAGTTAGTTCAAGTGGAGCAGAAAGCAGGAATTACATTGAAA
TTGATGGGTGTTCCTTCTGCAACAGAAATCATAAAAGCCTCCAGCAAAGATGCCATCAGACTTTGGACTCTGTGTTTCCC
ACTCTCACTGGACATTTCAATAGTCAATTGAGAAGCCGATTAAGGAGAAAGGAACTAGAGAGGCCCTGGCAGCAGCTCTG
GTCCACATCTCAAGGGCCACATCAGTCATCTTGTGCTCCCTGATCAACTCAGAAACATGTTTTGTGACCATGATCCTGCA
GGGCTCTATTGAGATGCCCAGTATCGGTTATGCTTGGCAAAAACTTAAGGAGCAGCTTGACTGAGAGCATCGATGACAAA
CTGAAGGGCATGGCCCCCCTTAAATGAAAACTGGGAGTTGGTTTTGATGTCTGCACTGAAGAAATACAGGAGGAGTGGCA
TGACTTGAGATGCTGGCAGCTCACCATGGCCACTGAGCAGCCAGAGCAGGAGGGGGCCCCTGAAGGATATGGAGGCAGCA
GGAGGCAGCAGGATGCCAGCTGTGAGTCTTTCAGAGGAGAACAGAGTGGAAGCAGTCATGTGCAGGGACAGGGGCAGTGA
TAGCAAGGAGAAAGTAAAAACTTCAGAGAACAGTGACCAGGAGGTGGCAACAAAAGTAACAAA

Alignment

ORF - retro_mmus_662 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.2 %
• Parental protein coverage: 68.51 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 9

Retrocopy - Parental Gene Alignment:

Parental  FSNFPISEETVKLLKARGVNFLFPIQAKTFHHVYSGKDLIAQARTGTGKTFSFAIPLIEKLQGGLQERKR
          FSNFPISEE.VKLL.A..VNF.FP.QAK.FHHV..GKDL.AQA..G..K.FSFAIPL.EKLQ.GLQE.KR
Retrocopy FSNFPISEEHVKLLRAHTVNFVFPTQAKIFHHVERGKDLNAQAWSGPRKSFSFAIPLTEKLQCGLQEKKR

Parental  GRAPQVLVL-APTRELANQVSKDFSDITKKLSVACFYGGTPYGGQIERMRSGIDILVGTPGRIKDHLQNG
          G.A.QVLV..APTRELANQ..KD..D..K.LS.ACFYGGTPY.GQIE...S.ID.LVG.PG..K..L.NG
Retrocopy GQACQVLVQ<APTRELANQMRKDVRDLNKMLSLACFYGGTPYRGQIE*RQSRIDFLVGAPGHYKENLKNG

Parental  KLDLTKLKHVVLDEVDQMLDMGFADQVEEILCVAYKKDSEDNPQTLLFSATCP-HWVFNV-AKKYMKSTY
          KLDLTKLKHV.L...DQMLD.GFADQVEEILCVAYKKDSEDNPQTLLFSATCP..WVF.V..K..M.STY
Retrocopy KLDLTKLKHVFLHKEDQMLDTGFADQVEEILCVAYKKDSEDNPQTLLFSATCP>FWVFIV<SKNSMRSTY

Parental  EQVDLIGKKTQKAAITVEHLAIKCHWTERAAVIG-DVIRVYSGHQ-GRTIIFCETKKDAQELSQNTCIKQ
          EQVDLIGKKTQK..IT.EHL.IKC.WT...A.IG.DVI.VYSGHQ.G.T.IFC.TKKDAQEL.QNTC.KQ
Retrocopy EQVDLIGKKTQKSSITAEHLTIKCLWTDSTAGIG<DVILVYSGHQ<GHTTIFCGTKKDAQELVQNTCMKQ

Parental  DAQSLHGDIPQKQREITL-KGFRNGNFGVLVATNVAARGLDIPEVDLVVQSCPPKDVESYIHRSGRTGRA
          ...S..G.IPQKQRE.TL.K.F.NGNFG.LVATNVAA.GLD.PEVDL.VQSCP..DV.S.IH.SG.T.R.
Retrocopy NVWS*LGNIPQKQREVTL>KDFQNGNFGILVATNVAASGLDNPEVDLDVQSCPLNDVGSSIHDSGSTDRD

Parental  GRTGVCICFYQNKEEYQLAQVEQKAGIKFKRIGVPSATEIIKASSKDAIRL-LDSVPPTAISHFKQ-SAE
          GR...C.CF.Q.KEEYQL.QVEQKAGI..K..GVPSATEIIKASSKDAIRL.LDSV.PT...HF...S.E
Retrocopy GRIEICTCF*QHKEEYQLVQVEQKAGITLKLMGVPSATEIIKASSKDAIRL<LDSVFPTLTGHFNS<SIE

Parental  KLIEEKGAVEALAAALAHISGATSVDQRSLINSQAGFVTMILRCSIEMPNISYAWKELKEQLG-ESIDAK
          K.I.EKG..EALAAAL.HIS.ATSV...SLINS...FVTMIL..SIEMP.I.YAW..LKEQL..ESID.K
Retrocopy KPIKEKGTREALAAALVHISRATSVILCSLINSETCFVTMILQGSIEMPSIGYAWQKLKEQLD>ESIDDK

Parental  VKGMVFLKGKLGVCFDVRTEAVTEIQEKWHDSRRWQLTVATEQPELEGPPDGYRGRMGQRDGSRGAFRGQ
          .KGM..LK.KLGV.FDV.TE...EIQE.WHD.R.WQLT.ATEQPE.EG.P.GY.G...Q.D.S...FRG.
Retrocopy LKGMAPLK*KLGVGFDVCTE---EIQEEWHDLRCWQLTMATEQPEQEGAPEGYGGSRRQQDASCESFRGE

Parental  RGGSRNFRGQGQ--RGGSRNFRGQRPGGGNRGQK
          ..GS....GQGQ...G.S.NFR.Q.PGGGN...K
Retrocopy QSGSSHVQGQGQ**QGESKNFREQ*PGGGNKSNK

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	25.79 RPM
SRP007412_cerebellum	0.04 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 actvity near the 5' end of retro_mmus_662 was not detected

EST

No EST(s) were mapped for retro_mmus_662 retrocopy.

TSS

No TSS is located nearby retro_mmus_662 retrocopy 5' end.

Lab

retro_mmus_662 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_662 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,