RetrogeneDB ID: retro_mmur_1118

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: scaffold_23644:284..977(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HAX1
• Ensembl ID: ENSMICG00000010414
• Aliases: None
• Description: HCLS1 associated protein X-1 [Source:HGNC Symbol;Acc:16915]

Sequence

>retro_mmur_1118
CCAAGGTTTGATGGTTCCCATTCCCCTGAAGAATCTGGCTTCAGCTTCAGTTTCAGCCCAGGAGGAGGGATGCATTTCCA
TGGTAACTTTGGCTTTGAGGACCTAGTATGGGATTTCAATAGCATCTTCAACCAGATGGGGGCCTGGACCTTACCTTCCC
ATACTCCTGAACTGCCAGGTCCTGAGTCAGATACACCTGGTGAGAGACTGCGGGAGGGATGAACACTTTGGGACTCAATG
CTTAAGTATCCAGATTGTCACCAGCCCAGGATCTTTAGGGGGCGGGTCTTAGAGAGTGACGCAAGAACTGAATCCCCTAA
ACCAGCACCAGACTGGGGTTCTCAGAGACCTTTTCATAGGTTTCATGATATATGGCCTGTGACCCCCCATCCTAGAGCCA
GAGAGGACAATGATGTTGATTTCCAGGTCTCCCAGGAGGGTCTTGGCCTAGTTTTACAGCCCCAGCCCAAATCCTATTTC
AAGAGCATCTCTGTGACCAAGATCACTGGGCCAGATGGGATAGTGGAGGAGCACCGGACTGTGGTAGACAGTGAGGGCCA
GACAGAGACCACAGTAACCTGACAAGAGGCAGACAGCAGTTGTAGAAGTGATCTAGAATCACCAAGACCTCCGACCATGG
ATGATGCTTTTTCCATCCTGGATTTATTCCTAGGACTTTGGTTCCAGTCTCGG

Alignment

ORF - retro_mmur_1118 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.58 %
• Parental protein coverage: 83.64 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PRFDGPQPPEEFGFSFSFSPGGGMHFHDNFGFDDLVRDFNSIFSEMGAWTLPSHPPELPGPASETPGERL
          PRFDG...PEE.GFSFSFSPGGGMHFH.NFGF.DLV.DFNSIF..MGAWTLPSH.PELPGP.S.TPGERL
Retrocopy PRFDGSHSPEESGFSFSFSPGGGMHFHGNFGFEDLVWDFNSIFNQMGAWTLPSHTPELPGPESDTPGERL

Parental  REGQTLRDSMLKYPDSHQPRIFGG-VLESDARPESPKPAPDWGSQRPFHRFDDIWPVTPHPRAREDNDLD
          REG.TL.DSMLKYPD.HQPRIF.G.VLESDAR.ESPKPAPDWGSQRPFHRF.DIWPVTPHPRAREDND.D
Retrocopy REG*TLWDSMLKYPDCHQPRIFRGRVLESDARTESPKPAPDWGSQRPFHRFHDIWPVTPHPRAREDNDVD

Parental  SQVSQEGLGPVLQPQPKSYFKSISVTKITRPDGIVEEHRTVVDSEGRKETTVTRQEADSSPRSDPESPRP
          .QVSQEGLG.VLQPQPKSYFKSISVTKIT.PDGIVEEHRTVVDSEG..ETTVT.QEADSS.RSD.ESPRP
Retrocopy FQVSQEGLGLVLQPQPKSYFKSISVTKITGPDGIVEEHRTVVDSEGQTETTVT*QEADSSCRSDLESPRP

Parental  PAMDDAFSILDLFLGRWFRSR
          P.MDDAFSILDLFLG.WF.SR
Retrocopy PTMDDAFSILDLFLGLWFQSR

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Microcebus murinus was not studied using RNA-Seq expression data.

ChIP-Seq

Microcebus murinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmur_1118 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_1118 was not experimentally validated.

Homology

Retrocopy orthology:

Microcebus murinus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009660	1 retrocopy	retro_cjac_1888,
Dasypus novemcinctus	ENSDNOG00000016727	1 retrocopy	retro_dnov_1537,
Dipodomys ordii	ENSDORG00000012587	1 retrocopy	retro_dord_769,
Homo sapiens	ENSG00000143575	1 retrocopy	retro_hsap_4912,
Microcebus murinus	ENSMICG00000010414	2 retrocopies	retro_mmur_1118 , retro_mmur_1284,
Monodelphis domestica	ENSMODG00000017215	1 retrocopy	retro_mdom_433,
Mus musculus	ENSMUSG00000027944	3 retrocopies	retro_mmus_1306, retro_mmus_2000, retro_mmus_353,
Nomascus leucogenys	ENSNLEG00000011290	1 retrocopy	retro_nleu_2286,
Pan troglodytes	ENSPTRG00000001380	1 retrocopy	retro_ptro_3275,
Rattus norvegicus	ENSRNOG00000045647	1 retrocopy	retro_rnor_736,
Tupaia belangeri	ENSTBEG00000014445	1 retrocopy	retro_tbel_930,