RetrogeneDB ID: retro_meug_154

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: GeneScaffold_450:62654..63036(-)
• Located in intron of: ENSMEUG00000003141

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP1S1
• Ensembl ID: ENSMEUG00000016245
• Aliases: None
• Description: adaptor-related protein complex 1, sigma 1 subunit [Source:HGNC Symbol;Acc:559]

Sequence

>retro_meug_154
GTCAGGAGAGAAAAAAAGATGGTTCTGGCCAGAAAGCCCAAGATGTGCAGCTTCCTGAAGTAGAGAGACTTCAAAGCTGT
CAATAAGAGATATGCCTGTCTCTACTTCTGCTGCGCCATTGAGGGCCAAAATAATAAGCTCATCACAGTGGAACTGATCC
ACTGATACGTGAAGCTCCTGGACAAATATTTTGGCAGCGTTATGTGAATTAGACATCATCTTCAACTTTGAGAAGGCCTA
CTTCATCTTGGATGAATTTCTGATGGGTGATGATGTCCAGGATACCTTTAAGAAAAGTATGTTAAAGGCCATAGAACAAG
CAGATCTACTACAGGAGGAAGATGAGTCACCTCAAAGTGCCCTGGAGGAAATGGGTTTGGCA

Alignment

ORF - retro_meug_154 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.81 %
• Parental protein coverage: 80.89 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VRELMQVVLARKPKMCSFLEWRDLKVVYKRYASLYFCCAIEGQDNELITLELIHRYVELLDKYFGSV-CE
          VR.....VLARKPKMCSFL..RD.K.V.KRYA.LYFCCAIEGQ.N.LIT.ELIH.YV.LLDKYFGSV.CE
Retrocopy VRREKKMVLARKPKMCSFLK*RDFKAVNKRYACLYFCCAIEGQNNKLITVELIH*YVKLLDKYFGSV>CE

Parental  LDIIFNFEKAYFILDEFLMGGDVQDTSKKSVLKAIEQADLLQEEDESPRSVLEEMGLA
          LDIIFNFEKAYFILDEFLMG.DVQDT.KKS.LKAIEQADLLQEEDESP.S.LEEMGLA
Retrocopy LDIIFNFEKAYFILDEFLMGDDVQDTFKKSMLKAIEQADLLQEEDESPQSALEEMGLA

Legend:

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

Expression

RNA-Seq

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq

Macropus eugenii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_meug_154 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_154 was not experimentally validated.

Homology

Retrocopy orthology:

Macropus eugenii 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 10 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002673	1 retrocopy	retro_amel_210,
Felis catus	ENSFCAG00000029169	1 retrocopy	retro_fcat_152,
Homo sapiens	ENSG00000106367	1 retrocopy	retro_hsap_3765,
Macropus eugenii	ENSMEUG00000001062	2 retrocopies	retro_meug_1156, retro_meug_1993,
Macropus eugenii	ENSMEUG00000016245	3 retrocopies	retro_meug_1011, retro_meug_154 , retro_meug_2051,
Macropus eugenii	ENSMEUG00000016580	11 retrocopies	retro_meug_1074, retro_meug_1342, retro_meug_1488, retro_meug_168, retro_meug_1864, retro_meug_289, retro_meug_318, retro_meug_361, retro_meug_816, retro_meug_909, retro_meug_938,
Microcebus murinus	ENSMICG00000005406	2 retrocopies	retro_mmur_1026, retro_mmur_1368,
Myotis lucifugus	ENSMLUG00000009898	2 retrocopies	retro_mluc_1493, retro_mluc_2061,
Mustela putorius furo	ENSMPUG00000015867	1 retrocopy	retro_mputfur_1184,
Pan troglodytes	ENSPTRG00000019520	3 retrocopies	retro_ptro_1234, retro_ptro_24, retro_ptro_2554,