RetrogeneDB ID: retro_meug_1167

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold312523:889..1293(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PQLC3
• Ensembl ID: ENSMEUG00000009376
• Aliases: None
• Description: PQ loop repeat containing 3 [Source:HGNC Symbol;Acc:28503]

Sequence

>retro_meug_1167
GAGTACCCAATCTTCATAGCACAAGATGTCGTCCTCTTGCTATGTATTTTTCATTATAATGGAGGCATGAAGCTTGCCAT
CCCTCATATTGTCATATTGCTTGGTGGATGGTACATCTTGACTCTTCAAAAGTGGATAACAGACTTGGCAATGAATTTGT
GCACCTTTACTAGTGCTGCCAGCAAGTTTGCCCAGCTCCAGTACTTGTGGGAGGCAAGAGATTCTGGTGCAGTGAGTGCC
CTGACCTGGAGCATGTCTGCGTATACTTGTGCAACAAGAGTAGTAACAACTTTAATGACCTCACAGGATCTTATGGTTCT
TGTCCGTTCCTGATAATGCTGGCTTTAAATATATGGGTAACAGCTACAATACTTCTCTATAGGAAAACAACTACAAAGGA
TGAA

Alignment

ORF - retro_meug_1167 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.03 %
• Parental protein coverage: 66.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EYPILIAQDVVLLLCIFHYNGGMNLAIPHIVILLGGWYILTLQKWITDLAMNLCTFTSAASKFAQLQYLW
          EYPI.IAQDVVLLLCIFHYNGGM.LAIPHIVILLGGWYILTLQKWITDLAMNLCTFTSAASKFAQLQYLW
Retrocopy EYPIFIAQDVVLLLCIFHYNGGMKLAIPHIVILLGGWYILTLQKWITDLAMNLCTFTSAASKFAQLQYLW

Parental  EARDSGAVSALTWSMSAYTCAXXXXXXXXXXXXXXXLVR-FLIMLALNIWVTATILRYRKTTTKDE
          EARDSGAVSALTWSMSAYTCA...............LVR.FLIMLALNIWVTATIL.YRKTTTKDE
Retrocopy EARDSGAVSALTWSMSAYTCATRVVTTLMTSQDLMVLVR<FLIMLALNIWVTATILLYRKTTTKDE

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_1167 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1167 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 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006017	3 retrocopies	retro_chof_1902, retro_chof_2195, retro_chof_717,
Callithrix jacchus	ENSCJAG00000006801	1 retrocopy	retro_cjac_3969,
Dasypus novemcinctus	ENSDNOG00000015960	1 retrocopy	retro_dnov_2157,
Macropus eugenii	ENSMEUG00000009376	1 retrocopy	retro_meug_1167 ,
Mus musculus	ENSMUSG00000045679	2 retrocopies	retro_mmus_1352, retro_mmus_2875,