RetrogeneDB ID: retro_mmur_1009

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: scaffold_159640:40..317(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPC3
• Ensembl ID: ENSMICG00000005485
• Aliases: None
• Description: actin related protein 2/3 complex, subunit 3, 21kDa [Source:HGNC Symbol;Acc:706]

Sequence

>retro_mmur_1009
CTCCAAAAGTGCAATTTCAAAAGCCAAGGCGATAAAGAAATCCATACACTGAGAATCATTAATTTTCCCACTCCTGGAGA
GCCTAGTATTAAGTTTTCTACTGAATACAATTCATGCCAAACCTGCAAACAGAGGAATATGAAGTGATGAGAGCCTGTTT
ACAACAGCTAAGGCAAGAGACTGGACTGAGATTTTTGTGAGAAGTTTTTGACCCTGAGAATGATAAACCCAACAAGTGGT
AACTTGCTTTGTGAAGAGACAGTTCGTGAACAAGAAC

Alignment

ORF - retro_mmur_1009 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.16 %
• Parental protein coverage: 51.12 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LQKCNSKSQGEKEMYTLGITNFPIPGEPGFPLNAIYAK-PANKQEDE--VMRAYLQQLRQETGLRLCEKV
          LQKCN.KSQG.KE..TL.I.NFP.PGEP.......Y.....N.Q..E..VMRA.LQQLRQETGLR....V
Retrocopy LQKCNFKSQGDKEIHTLRIINFPTPGEPSIKFSTEYNS<MPNLQTEEYEVMRACLQQLRQETGLRFL*EV

Parental  FDPQNDKPSKW-WTCFVKRQFMNKS
          FDP.NDKP.KW..TCFVKRQF.NK.
Retrocopy FDPENDKPNKW<VTCFVKRQFVNKN

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_1009 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_1009 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 13 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008456	1 retrocopy	retro_cfam_11,
Callithrix jacchus	ENSCJAG00000009360	1 retrocopy	retro_cjac_242,
Echinops telfairi	ENSETEG00000006992	2 retrocopies	retro_etel_116, retro_etel_1323,
Felis catus	ENSFCAG00000004132	2 retrocopies	retro_fcat_1048, retro_fcat_73,
Homo sapiens	ENSG00000111229	5 retrocopies	retro_hsap_2431, retro_hsap_303, retro_hsap_3425, retro_hsap_892, retro_hsap_918,
Microcebus murinus	ENSMICG00000005485	2 retrocopies	retro_mmur_1009 , retro_mmur_1507,
Macaca mulatta	ENSMMUG00000006492	3 retrocopies	retro_mmul_1105, retro_mmul_1174, retro_mmul_543,
Monodelphis domestica	ENSMODG00000011628	1 retrocopy	retro_mdom_71,
Mustela putorius furo	ENSMPUG00000002151	2 retrocopies	retro_mputfur_1346, retro_mputfur_1540,
Oryctolagus cuniculus	ENSOCUG00000011908	1 retrocopy	retro_ocun_1252,
Oreochromis niloticus	ENSONIG00000003785	1 retrocopy	retro_onil_18,
Sarcophilus harrisii	ENSSHAG00000014805	3 retrocopies	retro_shar_144, retro_shar_439, retro_shar_576,
Sus scrofa	ENSSSCG00000009821	1 retrocopy	retro_sscr_177,