RetrogeneDB ID: retro_meug_945

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold24081:18768..19398(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PGAM2
• Ensembl ID: ENSMEUG00000012920
• Aliases: None
• Description: phosphoglycerate mutase 2 (muscle) [Source:HGNC Symbol;Acc:8889]

Sequence

>retro_meug_945
CAGGCGCTGCAAGATGCTGGCTATGAATTTGATATCTGCTTCACCTCTGTCCAGAAGAGAGCAATTCTTACCCTTTGGAC
AGTACTATACGCCATTGACCAGATGTGGCTGCTTGTAGTGAGGACTTGATGCCTCAATGAGCAGCAGTATGGAGGTCTGA
CAGGCCTCAACAAAGCAGAGACCGCTACTAAGCATGGTGAGGCCTAGGTGAAGATCTGGTGATGATCCTATGACATCCTA
CCACCTCCAGTGGAGCCTGACCACCCCTTCTACAGGAACATCAGCAAGGACCTTTGCTATGCAGATCTGACTGAGGATCA
GCTGCTTTCCTGTGAGAACCTGAAAGACACCATTGCCAGGCTCTACCTTTCTGGAATGAGGAAATCGTCTCCCAGATCAA
GGAAGGCAAACCTGTTCTGATTGCAGCCCATGGCAATAGTCTTTGAAGGATTGTCAAACATCTTGAAAGTCTGTCTGAAG
AAGCAATCATGAAACTGAATCTGCCCACTGGCATTCCCATCATGTGCGAGCTGGACAAGAACATGAAACCCATCAAGCCC
ATGCAGTTCCTCCTCTTCAGAGACTGCATGCAAAGCCATGGAAGCCGTGGCAGCCCAAGGCAAGACCAAA

Alignment

ORF - retro_meug_945 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.73 %
• Parental protein coverage: 83.4 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QAVKEAGLQFDICYTSVLKRAIRTLWIIMDGIDQMWLPVIRTWRLNERHYGGLTGLNKAETAAKHGEAQV
          QA...AG..FDIC.TSV.KRAI.TLW.....IDQMWL.V.RT..LNE..YGGLTGLNKAETA.KHGEA.V
Retrocopy QALQDAGYEFDICFTSVQKRAILTLWTVLYAIDQMWLLVVRT*CLNEQQYGGLTGLNKAETATKHGEA*V

Parental  KIWRRSFDIPPPPMDETHPYHAVISKERRYASLKPGELPTCESLKDTIAR-ALPFWNEQIVPQIKSGKRV
          KIW..S.DI.PPP....HP....ISK...YA.L....L..CE.LKDTIAR.ALPFWNE.IV.QIK.GK.V
Retrocopy KIW**SYDILPPPVEPDHPFYRNISKDLCYADLTEDQLLSCENLKDTIAR<ALPFWNEEIVSQIKEGKPV

Parental  LIAAHGNSLRGIVKHLEGMSDEAIMELNLPTGIPIVYELDDHLK-PTKPMQFLGDEETVRKAMEAVAAQG
          LIAAHGNSL..IVKHLE..S.EAIM.LNLPTGIPI..ELD...K.P..P.......ET..KAMEAVAAQG
Retrocopy LIAAHGNSL*RIVKHLESLSEEAIMKLNLPTGIPIMCELDKNMK>PSSPCSS-SSSETACKAMEAVAAQG

Parental  KAK
          K.K
Retrocopy KTK

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_945 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_945 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 7 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000024480	1 retrocopy	retro_dnov_34,
Macropus eugenii	ENSMEUG00000012920	8 retrocopies	retro_meug_1044, retro_meug_1303, retro_meug_1636, retro_meug_1838, retro_meug_202, retro_meug_2152, retro_meug_251, retro_meug_945 ,
Otolemur garnettii	ENSOGAG00000006713	1 retrocopy	retro_ogar_164,
Procavia capensis	ENSPCAG00000002181	1 retrocopy	retro_pcap_13,
Rattus norvegicus	ENSRNOG00000013532	1 retrocopy	retro_rnor_2889,
Tupaia belangeri	ENSTBEG00000004587	1 retrocopy	retro_tbel_3939,
Drosophila melanogaster	FBgn0014869	1 retrocopy	retro_dmel_57,