RetrogeneDB ID: retro_meug_1828

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold63156:7225..8023(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DSCR3
• Ensembl ID: ENSMEUG00000007920
• Aliases: None
• Description: Down syndrome critical region gene 3 [Source:HGNC Symbol;Acc:3044]

Sequence

>retro_meug_1828
ATGGGGACCGTCCTGGACATCAAAATCAAAAGGGCCAATAAAGTATATTACGCCGGGGAAGTGCTCTCTGGAGTGGTGGT
TATATCTAGTAAAGATCCAGTACAACACCAGGGTATTTTATTAACAATGGAAAGATAGGTAAACCTGCAGCTCAGTGCCA
AAAGTGTTGGTATGTTTGAGGCTTTCTGTAACTCTGTTAAGCCTATCCAAGTTATTAACAGTTCAATAAAAATTGTGAAG
CCAGGAAAATTTCCCAGTGGCAAAACAGAAATTCCTTTTGAGATCCCTCTGCATGTGAAGGGCAACAAAGTTTTGTATGA
GACGTATCATGGTGTATTTGTCAACATTTATCATACCCTCCGGTGTGACCTGAGACACTCTCTTTTGGCCAAGGATTTGA
CAAAGATATGTGAATTCATCATTCATTCTGCTCCTCAGAAGGGCAAATCAACTCCAAGTCCTGTGGATTTTACAATTACA
CCTGAAACCTTACAGAATGTTAAAGAGAGAGCTTCCCTCCCCAAATTTCTCATAAGAGGACATCTCAACTCCACCAACTG
TGTTATTACACAGACACTAACAGGGTAGCTGGTGATTGAGTATTCAGAAGCTGCCATTAAAAACATAGAGTTGCAGTTAG
TATGAGTGGAAACCTGTGAAGGATATGCCAGAGATGCCACAGAGATTCAGAATATTCAAACTGCTGATGGGGATGTTTGC
AGGAGTCTTACTGTTCCCATATATATGATATTCCCCAGACTTTTCACTTGCCCTACCCTTGAAACTACCAATTTCAAA

Alignment

ORF - retro_meug_1828 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.48 %
• Parental protein coverage: 99.63 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGTVVDIKIKRANKVYYAGEVLSGVVVISSKDPVQHQGILLTMEGLVNLQLSAKSVGMFEAFCNSVKPIQ
          MGTV.DIKIKRANKVYYAGEVLSGVVVISSKDPVQHQGILLTME..VNLQLSAKSVGMFEAFCNSVKPIQ
Retrocopy MGTVLDIKIKRANKVYYAGEVLSGVVVISSKDPVQHQGILLTMER*VNLQLSAKSVGMFEAFCNSVKPIQ

Parental  VITSSIEIVKPGKFPSGKTEIPFEFPLHVKGNKVLYETYHGVFVNIQXXXXXXXXXXXXXXDLTKICEFI
          VI.SSI.IVKPGKFPSGKTEIPFE.PLHVKGNKVLYETYHGVFVNI...............DLTKICEFI
Retrocopy VINSSIKIVKPGKFPSGKTEIPFEIPLHVKGNKVLYETYHGVFVNIYHTLRCDLRHSLLAKDLTKICEFI

Parental  IHSAPQKGKSTPSPVDFTITPETLQNVKERASLPKFLIRGHLNSTNCVITQPLTGELVVEYSEAAIKNIE
          IHSAPQKGKSTPSPVDFTITPETLQNVKERASLPKFLIRGHLNSTNCVITQ.LTG.LV.EYSEAAIKNIE
Retrocopy IHSAPQKGKSTPSPVDFTITPETLQNVKERASLPKFLIRGHLNSTNCVITQTLTG*LVIEYSEAAIKNIE

Parental  LQLVRVETCGCAEGYARDATEIQNIQIADGDVCRGLSVPIYMIFPRLFTCPTLETTNFK
          LQLV.VETC...EGYARDATEIQNIQ.ADGDVCR.L.VPIYMIFPRLFTCPTLETTNFK
Retrocopy LQLV*VETC---EGYARDATEIQNIQTADGDVCRSLTVPIYMIFPRLFTCPTLETTNFK

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_1828 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1828 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002626	1 retrocopy	retro_cjac_2878,
Macropus eugenii	ENSMEUG00000007920	1 retrocopy	retro_meug_1828 ,
Nomascus leucogenys	ENSNLEG00000004717	1 retrocopy	retro_nleu_696,
Pan troglodytes	ENSPTRG00000013900	1 retrocopy	retro_ptro_2418,
Rattus norvegicus	ENSRNOG00000001681	1 retrocopy	retro_rnor_1897,