RetrogeneDB ID: retro_meug_1550

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold44886:6548..7550(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLR3D
• Ensembl ID: ENSMEUG00000000465
• Aliases: None
• Description: polymerase (RNA) III (DNA directed) polypeptide D, 44kDa [Source:HGNC Symbol;Acc:1080]

Sequence

>retro_meug_1550
GGGTGCTGACCCTTGCTGCCAGGGATCCAAGGGATGATTGGGCAGTGGCCTGCAGCCCCCCTATTCCCAGGCTGCTTCCT
TTCTGTCCATTCTGGAGGCCTCACTCTCAGCATCAAGAGGAAAACCTTCACTCCTAACATCATTAGCCTGAAGGTAAATG
AAGAGCCAAAGGAAGAAATATCAGTTAAGAAAGAGAAATGAGTGAGGAATCAAGATCAACCACAAGATGGGCATGGTTGA
GGGAGGGGTTGTCAAGAAGTGATCCAATCCCAATCCATTTTTGAGCAGAGTCCTGCAGAAATTATGAAGAAGAAAGGCAA
ATAGAATAAGATAATGGATGTTTCAGATTTTGACCCATCTCGTATTATCAATATTAAAAAGGAGAAGAGGGAAATGGGTG
AGGAAACTAAACAAATTCTACACATGCTAGAGAAGGATAATTTTATACATGACCCAGGGCTCAAGAATAATACATGAAAC
AAGCCTGTGCAGCTTCATCTGGCTCAACCAAGGTGGTTCTTTATGGAAGAGACTGAAGAACCTGATGTCAAGCTCAGGCT
GGGGAGAGCCAAGGAAGAGAACATGGAGGTGGATATGCCAGGACTGAAAGTAAAAGAGGAACCACAAGATGAGGATGAGA
CCAAGGCAACTGCCCCCTCCAGGCCTGACAGAAGGGTGCCTGGACTTCCTCAAGATGTGTCTGTGGCAGATTTATTCAGG
GAACTGAGCTTTGACAAGGAGGAAGAGCTTTTATTCCTGCAGCAGCCTAACATGCTTCCTGGTCAACCTCCTACCCATGA
CATCAAGCCCATCAAGACAGAGCTTTAAGGAGAAGATGGGCAGATGGTGCTCATGAAGACAGAGAAAAACAGGGATACTA
CACTGGCAGAAAACCTATGTATACTAAGTGACCTGACAGAGGATCATGTGAGAAAACTACTTAACCAAAAATCTGGAAAG
GTGCAACTGCTTCTGAGCAAAGTGACTCTGGATGTAACACTC

Alignment

ORF - retro_meug_1550 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.84 %
• Parental protein coverage: 84.38 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GSRPSLPGARGLIGRRPAAPLTPGRLPSIRSRDLTLGGVKKKTFTPNIISRKIKEEPKEEISVKKEKRER
          G..P.LPG..G.IG..PAAPL.PG...S..S..LTL...K.KTFTPNIIS.K..EEPKEEISVKKEK..R
Retrocopy GC*PLLPGIQGMIGQWPAAPLFPGCFLSVHSGGLTLS-IKRKTFTPNIISLKVNEEPKEEISVKKEK*VR

Parental  DRDRQRDGHGRGRGRPEVIQSHSIFEQGPAEMMKKKGNWDKTVDVSDFGPSHIINIKKEKRETDEETKQI
          ..D...DGHG.GRG..EVIQS.SIFEQ.PAE.MKKKG...K..DVSDF.PS.IINIKKEKRE..EETKQI
Retrocopy NQDQPQDGHG*GRGCQEVIQSQSIFEQSPAEIMKKKGK*NKIMDVSDFDPSRIINIKKEKREMGEETKQI

Parental  LRMLEKDDFIDDPGLKNDTRNKPVQLPLAHSGWLFKEETEEPDVKPWLGRAKEESMEVDVPALKVKEEPR
          L.MLEKD.FI.DPGLKN.T.NKPVQL.LA...W.F.EETEEPDVK..LGRAKEE.MEVD.P.LKVKEEP.
Retrocopy LHMLEKDNFIHDPGLKNNT*NKPVQLHLAQPRWFFMEETEEPDVKLRLGRAKEENMEVDMPGLKVKEEPQ

Parental  DEHEAKAAAPSRPGRTAPGLPPDVSVADLLRELSFAKEEELLFLQLPDTLPGQPPTQDIKPIKTEVQGED
          DE.E.KA.APSRP.R..PGLP.DVSVADL.RELSF.KEEELLFLQ.P..LPGQPPT.DIKPIKTE..GED
Retrocopy DEDETKATAPSRPDRRVPGLPQDVSVADLFRELSFDKEEELLFLQQPNMLPGQPPTHDIKPIKTEL*GED

Parental  GQMVLVKPEKDREAKLAENLCTLSDLTEGQVGKLLIRKSGKVQLLLGKVTLDVTV
          GQMVL.K.EK.R...LAENLC.LSDLTE..V.KLL..KSGKVQLLL.KVTLDVT.
Retrocopy GQMVLMKTEKNRDTTLAENLCILSDLTEDHVRKLLNQKSGKVQLLLSKVTLDVTL

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_1550 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1550 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 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000013488	1 retrocopy	retro_dnov_1681,
Equus caballus	ENSECAG00000025090	1 retrocopy	retro_ecab_43,
Erinaceus europaeus	ENSEEUG00000007632	2 retrocopies	retro_eeur_277, retro_eeur_705,
Homo sapiens	ENSG00000168495	1 retrocopy	retro_hsap_596,
Macropus eugenii	ENSMEUG00000000465	1 retrocopy	retro_meug_1550 ,
Myotis lucifugus	ENSMLUG00000002109	1 retrocopy	retro_mluc_2339,
Macaca mulatta	ENSMMUG00000023226	1 retrocopy	retro_mmul_2449,
Monodelphis domestica	ENSMODG00000009491	1 retrocopy	retro_mdom_988,
Nomascus leucogenys	ENSNLEG00000015502	1 retrocopy	retro_nleu_2218,
Pongo abelii	ENSPPYG00000018419	1 retrocopy	retro_pabe_594,
Pan troglodytes	ENSPTRG00000020056	1 retrocopy	retro_ptro_439,
Tursiops truncatus	ENSTTRG00000012745	1 retrocopy	retro_ttru_1189,