RetrogeneDB ID: retro_meug_1645

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold50592:14535..14958(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TAF10
• Ensembl ID: ENSMEUG00000008216
• Aliases: None
• Description: TAF10 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 30kDa [Source:HGNC Symbol;Acc:11543]

Sequence

>retro_meug_1645
CCAGGGTCTGCAGTTGGGGATACTGCCCCCCTTGAAGGAGCCATGTCTAGTGGGGTGTATGTGTTATCTGATGCTGCCAA
TGGAGAAGTCAAGCCCATTGTGTCTAGTACACCCCTGGTGGACTTCCTTATGCAACTGGAAGACTACACACCCACAGTTT
CAGATGCTGTTACTGGCTACTACCTGAACCAGGCTGGTTTAGAAGCCTTTGATCCCGGAATTCTCTGGCTTATCTCCCTG
GCAGCCTAGAAGTTCATCTCTGACATTGCCAATGATGCTTTACCACACTACAAGTTGAAGGGCACTGCCTCTGGCAGTTC
CAGGAGGAAGAGCAAAGACCAAAAGTATAGCTTGACTATGGAAGACCGGACCCCCGCACTCAGGGAGTATGGCATCAATA
CCAAGAAGCCACATCACCTAAGC

Alignment

ORF - retro_meug_1645 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.72 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PVSAAGGTAPPEGAMSNGVYVLPGAANGEVKPVVSSTPLVDFLVQLEDYTPTIPDAVTGYYLNRAGFEAS
          P.SA.G.TAP.EGAMS.GVYVL..AANGEVKP.VSSTPLVDFL.QLEDYTPT..DAVTGYYLN.AG.EA.
Retrocopy PGSAVGDTAPLEGAMSSGVYVLSDAANGEVKPIVSSTPLVDFLMQLEDYTPTVSDAVTGYYLNQAGLEAF

Parental  DPRIVRLISLAAQKFISDIANDALQHCKMKGTASGSSRSKSKDRKYTLTMEDLTPALSEYGINVKKPHYF
          DP.I..LISLAA.KFISDIANDAL.H.K.KGTASGSSR.KSKD.KY.LTMED.TPAL.EYGIN.KKPH..
Retrocopy DPGILWLISLAA*KFISDIANDALPHYKLKGTASGSSRRKSKDQKYSLTMEDRTPALREYGINTKKPHHL

Parental  T
          .
Retrocopy S

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_1645 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1645 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 13 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016278	2 retrocopies	retro_amel_1088, retro_amel_297,
Canis familiaris	ENSCAFG00000006498	2 retrocopies	retro_cfam_1041, retro_cfam_992,
Dasypus novemcinctus	ENSDNOG00000000814	1 retrocopy	retro_dnov_592,
Equus caballus	ENSECAG00000007794	1 retrocopy	retro_ecab_525,
Erinaceus europaeus	ENSEEUG00000008412	3 retrocopies	retro_eeur_542, retro_eeur_692, retro_eeur_709,
Echinops telfairi	ENSETEG00000008886	1 retrocopy	retro_etel_2090,
Felis catus	ENSFCAG00000015390	1 retrocopy	retro_fcat_1458,
Loxodonta africana	ENSLAFG00000029330	1 retrocopy	retro_lafr_750,
Macropus eugenii	ENSMEUG00000008216	2 retrocopies	retro_meug_1645 , retro_meug_992,
Myotis lucifugus	ENSMLUG00000024459	1 retrocopy	retro_mluc_1960,
Macaca mulatta	ENSMMUG00000007743	1 retrocopy	retro_mmul_1144,
Mus musculus	ENSMUSG00000043866	1 retrocopy	retro_mmus_35,
Tursiops truncatus	ENSTTRG00000004894	1 retrocopy	retro_ttru_1113,