RetrogeneDB ID: retro_meug_292

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: GeneScaffold_9689:231611..232805(+)
• Located in intron of: ENSMEUG00000001674

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJA4
• Ensembl ID: ENSMEUG00000015982
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily A, member 4 [Source:HGNC Symbol;Acc:14885]

Sequence

>retro_meug_292
AAAATGGTGAAGGAGACGACTTACTATGACGTTCTGGGGGTGAAGCCCAATGCCTCCCAGGAGGAGCTGAAGAAGGCGGA
CCGAAAACTGGCCCTGAAGTATCACCCGGATAAGAACCCGAACGAAGGAGAGAAGTTCAAGCAGATTTCTCAAGCTTACG
AAGTGCTTTCTGATGCCAAGAAAAGAGACTTGTATGACAAAGGTGGAGAACAAGCCATCAAAGAGGGCGGCTCTGGGGGT
GGCTTCGGTTCTCCCATGGACATCTTTGACATGTTTTTTGGAGGAGGTGGAAGAATGCAGCGGGAATGGAGAGGTAAAAA
TGTTGTTCATCAATTGTCAGTGACTTTAGAAGATTTATATAATGGTGCAACGAGAAAACTGGCTTTGCAAAAGAATGTGA
TTTGTGATAAATGTGAAGGACGGGGTGGAAAAAAAGGAGCTGTAGAATGCTGTCCCAATTGCAGAGGTGCTGGAATGCAA
ATAAGAATTCATCAGATAGGACCTGGAATGGTTCAGCAAATTCAGTCAGTTTGCATGGAATGCCAAGGGCATGGGGAACG
AATCAGCCCTAAAGATAGATGTAAAAGCTGTAATGGAAGGAAAATTGTCCAAGAGAAGAAAATTCTGGAGGTTCATATTG
ACAAGGGCATGAAAGATGGTCAAAAGATAACATTCCATGGTGAAGGTGAGCAGGAGCCAGGACTTGAGCCAGGAGATATC
ATTGTTTTGGATCAGAAGGATAATGCTGTATTTACAGGACGTGGTGAGGACCTTTTCACGTGTGTGAATATCCAATTGGT
TGAAGCATTGTGTGGCTTTCAGAAACCAATAACAACTCTTGATAATAGAACTATAGTCATTACTTCTCATCCTGGTCAGA
TTGTTAAACATGGAGATATCAAATGTGTGCTGAATGAAGGTATGCCCATTTATTGCCGACCTTATGAGAAAGGAATTCTA
ATAATTGAATTTAAGGTAAACTTCCCAGAGAATGGCTTTCTTTCATCAGATAAGCTGTCTTTGTTGGAAAAATTACTGCC
TGAAAGAAAGGAAGTAGAGGTGACTGAAGATATGGATCAGGTAGAACTGGTGGACTTTGACCCATCTCAAGAAAGAAGAC
GCCATTACAATGGAGAAGTGTATGAGGATGATGAGCATCATCCCAGAGGAGGTGGGGTTCAATGTCAGACCTCT

Alignment

ORF - retro_meug_292 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.0 %
• Parental protein coverage: 99.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KMVKETEYYDILGVKPSAAQEEIKKAYRKLALKYHPDKNPDEGEKFKLISQAYEVLSDVKKREIYDQGGE
          KMVKET.YYD.LGVKP.A.QEE.KKA.RKLALKYHPDKNP.EGEKFK.ISQAYEVLSD.KKR..YD.GGE
Retrocopy KMVKETTYYDVLGVKPNASQEELKKADRKLALKYHPDKNPNEGEKFKQISQAYEVLSDAKKRDLYDKGGE

Parental  QAIKEGGTTSGNFSSPMDIFDMFFGGGGRMTRERRGKNVVHQLSVSLEDIYNGVTRKLALQKNVICDKCE
          QAIKEGG...G.F.SPMDIFDMFFGGGGRM.RE.RGKNVVHQLSV.LED.YNG.TRKLALQKNVICDKCE
Retrocopy QAIKEGGS-GGGFGSPMDIFDMFFGGGGRMQREWRGKNVVHQLSVTLEDLYNGATRKLALQKNVICDKCE

Parental  GIGGKKGSVEKCPICKGRGMQIHIQQIGPGMVQQIQTVCLECKGQGERINPKDRCENCNGCKVVREKKII
          G.GGKKG.VE.CP.C.G.GMQI.I.QIGPGMVQQIQ.VC.EC.G.GERI.PKDRC..CNG.K.V.EKKI.
Retrocopy GRGGKKGAVECCPNCRGAGMQIRIHQIGPGMVQQIQSVCMECQGHGERISPKDRCKSCNGRKIVQEKKIL

Parental  EVHIEKGMKDGQKIMFHGEGDQEPELEPGDVIIVLDQKDHGVFQRRGHDLIMKMKIQLTEALCGFKKTIK
          EVHI.KGMKDGQKI.FHGEG.QEP.LEPGD.IIVLDQKD..VF..RG.DL.....IQL.EALCGF.K.I.
Retrocopy EVHIDKGMKDGQKITFHGEGEQEPGLEPGD-IIVLDQKDNAVFTGRGEDLFTCVNIQLVEALCGFQKPIT

Parental  TLDNRTLVITSKAGEVIKHGDLKCVRNEGMPIYKAPLEKGSLIIQFLVIFPEKHWLSQDKLPQLEALLPP
          TLDNRT.VITS..G...KHGD.KCV.NEGMPIY..P.EKG.LII.F.V.FPE...LS.DKL..LE.LLP.
Retrocopy TLDNRTIVITSHPGQIVKHGDIKCVLNEGMPIYCRPYEKGILIIEFKVNFPENGFLSSDKLSLLEKLLPE

Parental  RQKIRITDDMDQVELKEFNPNEQNWRH-SAEAYEEDDEGPR-AGVQCQTA
          R.....T.DMDQVEL..F.P.....RH...E.YE.D...PR..GVQCQT.
Retrocopy RKEVEVTEDMDQVELVDFDPSQERRRHYNGEVYEDDEHHPRGGGVQCQTS

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_292 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_292 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 10 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012576	1 retrocopy	retro_amel_1659,
Dipodomys ordii	ENSDORG00000005972	4 retrocopies	retro_dord_245, retro_dord_280, retro_dord_333, retro_dord_533,
Echinops telfairi	ENSETEG00000004320	4 retrocopies	retro_etel_1010, retro_etel_1031, retro_etel_1067, retro_etel_608,
Macropus eugenii	ENSMEUG00000015982	4 retrocopies	retro_meug_1059, retro_meug_1893, retro_meug_292 , retro_meug_624,
Microcebus murinus	ENSMICG00000008789	6 retrocopies	retro_mmur_1242, retro_mmur_1460, retro_mmur_39, retro_mmur_482, retro_mmur_496, retro_mmur_578,
Mus musculus	ENSMUSG00000032285	1 retrocopy	retro_mmus_2632,
Otolemur garnettii	ENSOGAG00000006752	5 retrocopies	retro_ogar_1760, retro_ogar_1985, retro_ogar_221, retro_ogar_2656, retro_ogar_841,
Ochotona princeps	ENSOPRG00000007594	1 retrocopy	retro_opri_1028,
Tupaia belangeri	ENSTBEG00000009268	9 retrocopies	retro_tbel_2276, retro_tbel_2308, retro_tbel_2790, retro_tbel_2831, retro_tbel_3242, retro_tbel_4322, retro_tbel_4735, retro_tbel_772, retro_tbel_796,
Tarsius syrichta	ENSTSYG00000008600	1 retrocopy	retro_tsyr_1752,