RetrogeneDB ID: retro_mmus_1752

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:16951282..16951811(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rnaseh2b
• Ensembl ID: ENSMUSG00000021932
• Aliases: Rnaseh2b, 1110019N06Rik, 2610207P08Rik, Dleu8
• Description: ribonuclease H2, subunit B [Source:MGI Symbol;Acc:MGI:1914403]

Sequence

>retro_mmus_1752
CTAGTGTATGTAAAATGGGTTAACCTGCATTCACAGGAAGGAACATTTCCTTGTTCAAGATGTTTCTACAGCAGCTGTGT
GAAATCAATATTTTCAAGGAAAAACACCATTCTTGGTTGATAAATCAATCAATTCAATTGGAGGGTTTTTCCACTATACA
GCATCCATGGACACACCATTTCTTTTCCTTCCCTACCTCAGGAAGTCTGGCAAAGTAGGAAACTTTCAACCCGTGGATCA
GAGGACAGTAGATGACATACTTCCAAATTGCATCTTACTGATGAAATTTCCTGGGCTTGGGAAGTCCCTTCACCATGTGA
TGGAGGGAAAAGAAACAATGAGCAAGAAATATTGCAGCACAGAGAAGACGTTGAAGTGACTAGAGAAAAAGGTCAACTAA
ACTATGCCAGCACTGAAGGTCAATAATGACTACGCGAGTGCCCGGGTACATCTAGCTGCTGGGCTGCAGTTTTCCACGGG
TGATCAGGTTCCCAGGGACAGGGAAGGCATTTATGTTTGCTATACCCAC

Alignment

ORF - retro_mmus_1752 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.8 %
• Parental protein coverage: 57.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LLFVKLANPHSGEGA-TYLIDMCLQQLFEIKVFKEKHHSWFINQSVQ-SGGLLHFATPMDPLFLLLHYLL
          L..VK..N.HS.EG....L..M.LQQL.EI..FKEKHHSW.INQS.Q..GG..H....MD..FL.L.YL.
Retrocopy LVYVKWVNLHSQEGT<ISLFKMFLQQLCEINIFKEKHHSWLINQSIQ<IGGFFHYTASMDTPFLFLPYLR

Parental  KAGKEGKYQPLDQVVVDDTFPDCTLLLRFPELEKSLRHVTEEKEVNSKKYYKYSSEKTLKWLEKKVNQTV
          K.GK.G..QP.DQ..VDD..P.C.LL..FP.L.KSL.HV.E.KE..SKKY...S.EKTLK.LEKKVN.T.
Retrocopy KSGKVGNFQPVDQRTVDDILPNCILLMKFPGLGKSLHHVMEGKETMSKKY--CSTEKTLK*LEKKVN*TM

Parental  VALKANNVNVGARVQSSA---YFSGGQVSRDKEEDYVRYAH
          .ALK.NN....ARV...A......G.QV.RD.E..YV.Y.H
Retrocopy PALKVNNDYASARVHLAAGLQFSTGDQVPRDREGIYVCYTH

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	5.05 RPM
SRP007412_cerebellum	0.00 RPM	5.38 RPM
SRP007412_heart	0.00 RPM	5.45 RPM
SRP007412_kidney	0.00 RPM	12.30 RPM
SRP007412_liver	0.00 RPM	5.35 RPM
SRP007412_testis	0.00 RPM	2.42 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1752 was not detected

EST

No EST(s) were mapped for retro_mmus_1752 retrocopy.

TSS

No TSS is located nearby retro_mmus_1752 retrocopy 5' end.

Lab

retro_mmus_1752 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1752 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020149	1 retrocopy	retro_btau_407,
Callithrix jacchus	ENSCJAG00000008585	1 retrocopy	retro_cjac_2249,
Dasypus novemcinctus	ENSDNOG00000010489	1 retrocopy	retro_dnov_2225,
Mus musculus	ENSMUSG00000021932	1 retrocopy	retro_mmus_1752 ,