RetrogeneDB ID: retro_mmur_893

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: scaffold_12173:9939..10475(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK4
• Ensembl ID: ENSMICG00000003789
• Aliases: None
• Description: cyclin-dependent kinase 4 [Source:HGNC Symbol;Acc:1773]

Sequence

>retro_mmur_893
ATGACTACCTCTCAATATGAGCCAGTAGTTGAAATTGGTGTCAGCACTTACAAGACATATACAAGGCCCATAATCCCCAC
AGTGGCAACTTTGTGGCCTTCAAGAGTGTTATAGTCTCTAATGAAGGAGGAGCCGGAGAGGGCCTTTCCATCAACACAGT
TTATAATGTAGTCTAACTGAGGTGGCTTGAGGATTTTGAGCATCCCAGTGTTGTCTGGCTGATGGACACCTGTGCCATGA
CCCAAACTGACTTAGAGATCAAGGAAACCCTGGTGTTTGAGCATATATATACACCAAGACCTAAGTATGTGTCTGGACAA
AACACCCCACCAGGATTGCTATCAAAGTCAATCAAAGATAGGATGCACCAGTTTCTAAGAGGCCTAGATTTCCTTCATGC
CAAATGCATGATTTATCTAGATCTGAAGCCAGAGGACATTCTGGTGAGAAGTGGTGGAACATTCAAGCTGGCTGAAAGTC
AAGCAGGCCTGGCCAGAATCTATAGCTACCAGATGACACTTACACCTGTGGTTGTT

Alignment

ORF - retro_mmur_893 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.0 %
• Parental protein coverage: 59.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MATSRYEPVAEIGVGAYGT-VYKARDPHSGHFVALKSVRVPNGGGAGGGLPISTVREVALLRRLEAFEHP
          M.TS.YEPV.EIGV..Y.T..YKA..PHSG.FVA.KSV.V.N.GGAG.GL.I.TV..V..LR.LE.FEHP
Retrocopy MTTSQYEPVVEIGVSTYKT<IYKAHNPHSGNFVAFKSVIVSNEGGAGEGLSINTVYNVV*LRWLEDFEHP

Parental  NVVRLMDVCATSRTDREIKVTLVFEHIDQDLRTYLD-KAPPPGLPAETIKDLMRQFLRGLDFLHANCIVH
          .VV.LMD.CA...TD.EIK.TLVFEHI......Y......PPGL....IKD.M.QFLRGLDFLHA.C...
Retrocopy SVVWLMDTCAMTQTDLEIKETLVFEHIYTPRPKYVSGQNTPPGLLSKSIKDRMHQFLRGLDFLHAKCMIY

Parental  RDLKPENILVTSGGTVKLAD--FGLARIYSYQMALTPVVV
          .DLKPE.ILV.SGGT.KLA....GLARIYSYQM.LTPVVV
Retrocopy LDLKPEDILVRSGGTFKLAESQAGLARIYSYQMTLTPVVV

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_893 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_893 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 14 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007160	1 retrocopy	retro_btau_738,
Canis familiaris	ENSCAFG00000000280	1 retrocopy	retro_cfam_690,
Callithrix jacchus	ENSCJAG00000006697	3 retrocopies	retro_cjac_2163, retro_cjac_2891, retro_cjac_2951,
Felis catus	ENSFCAG00000029663	1 retrocopy	retro_fcat_516,
Gorilla gorilla	ENSGGOG00000001404	1 retrocopy	retro_ggor_275,
Macropus eugenii	ENSMEUG00000014609	1 retrocopy	retro_meug_23,
Microcebus murinus	ENSMICG00000003789	1 retrocopy	retro_mmur_893 ,
Microcebus murinus	ENSMICG00000005793	1 retrocopy	retro_mmur_43,
Myotis lucifugus	ENSMLUG00000023651	2 retrocopies	retro_mluc_1137, retro_mluc_354,
Macaca mulatta	ENSMMUG00000023694	1 retrocopy	retro_mmul_401,
Mus musculus	ENSMUSG00000006728	5 retrocopies	retro_mmus_1219, retro_mmus_1298, retro_mmus_2878, retro_mmus_3109, retro_mmus_636,
Nomascus leucogenys	ENSNLEG00000017205	1 retrocopy	retro_nleu_1847,
Pan troglodytes	ENSPTRG00000005147	1 retrocopy	retro_ptro_180,
Tarsius syrichta	ENSTSYG00000011937	3 retrocopies	retro_tsyr_1383, retro_tsyr_1701, retro_tsyr_544,