RetrogeneDB ID: retro_meug_288

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: GeneScaffold_9557:65774..66442(-)
• Located in intron of: ENSMEUG00000002345

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX39B
• Ensembl ID: ENSMEUG00000008264
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B [Source:HGNC Symbol;Acc:13917]

Sequence

>retro_meug_288
ATGCATCAGGATGTCCAGGAAATTTTCTGCATGACCCACCATGAGAAGCAGGTCATGATGTTCAGTGCCACCCTGAGCAA
GTAGATCTGCCCTGTCTGCTGCAAGTTCACACAAGACCCAGTGGAGATCTTCGTGGATGATGAGATGAAGTTGATGCTGC
ATGGGCTGCAGCAGTACTGTTGTGAAGCTGAAGGACAAGGAGAAGAACCGAAAACTCTTTGACTTCCTGGACATTCTGGT
GTTCAACCAGAGGGTGATCTTTGTGAAATCTGTGCAGCGTTGCATTGCCCTGGCCCACCTCCTAGTGAAATAGAACTTCC
CAGCCATTACTATCCATCATGGAATGTCCCAAGAGGAGAGATTGTCCTTGGTATCAGCAGTTCAAGGATTTCCAGCATTG
TATCCTTATGGCCACCAACCTGTTTGGCCAGGGCATGAATATTGAACGAGTAAACATCACCTTCAACTATGACATGCCAG
AGGACTCAGACACCTACTTACACAGGGTGGCTAGGGCAGGCTGGTTTGGTACGAAGGGTTTTACCATCATATTTGTGTCA
GATGAAAATGACACCAAAATCCTCCTTGGTGATATCCAGGATTGCTTCGAGATCAACATCAGTGAACCGCCTGATGAGAT
AGACATTCTTTCCTACTTTGAGCAGAGT

Alignment

ORF - retro_meug_288 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.46 %
• Parental protein coverage: 51.64 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQY-YVKLKDNEKN
          M..DVQEIF.MT.HEKQVMMFSATLSK.I.PVC.KF.QDP.EIFVDDE.KL.LHGLQQY..VKLKD.EKN
Retrocopy MHQDVQEIFCMTHHEKQVMMFSATLSK*ICPVCCKFTQDPVEIFVDDEMKLMLHGLQQY>VVKLKDKEKN

Parental  RKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSR-YQQFKDFQRRILVAT
          RKLFD.LD.L.FNQ.VIFVKSVQRCIALA.LLV..NFPAI.IH.GM.QEERLS..YQQFKDFQ..IL.AT
Retrocopy RKLFDFLDILVFNQRVIFVKSVQRCIALAHLLVK*NFPAITIHHGMSQEERLSL>YQQFKDFQHCILMAT

Parental  NLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKI-LNDVQDRFEVNISE
          NLFG.GM.IERVNI.FNYDMPEDSDTYLHRVARAG.FGTKG..I.FVSDEND.KI.L.D.QD.FE.NISE
Retrocopy NLFGQGMNIERVNITFNYDMPEDSDTYLHRVARAGWFGTKGFTIIFVSDENDTKILLGDIQDCFEINISE

Parental  LPDEIDISSYIEQT
          .PDEIDI.SY.EQ.
Retrocopy PPDEIDILSYFEQS

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_288 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_288 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.

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003152	1 retrocopy	retro_cjac_1461,
Gorilla gorilla	ENSGGOG00000005989	1 retrocopy	retro_ggor_752,
Macropus eugenii	ENSMEUG00000008264	2 retrocopies	retro_meug_1623, retro_meug_288 ,
Macaca mulatta	ENSMMUG00000008839	1 retrocopy	retro_mmul_1126,
Nomascus leucogenys	ENSNLEG00000006094	1 retrocopy	retro_nleu_2418,
Pongo abelii	ENSPPYG00000016433	1 retrocopy	retro_pabe_804,