RetrogeneDB ID: retro_meug_1387

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold3872:17865..18447(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC17
• Ensembl ID: ENSMEUG00000005641
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily C, member 17 [Source:HGNC Symbol;Acc:25556]

Sequence

>retro_meug_1387
GTGAAGAAAGCATATAAACAAAGGCCCTCACCTGCCATCCAGACAAAAATCCAGAGAATCCCCAAGCAGGTGAGCTCTTC
CACCAGCTCTCCCAGGTCTTGGACATGTTGACAGAAGCTGCAGCCCAGGCAGCCTATAACAACGGCAGGAAAGCCAAGAA
GCAGGAGGCTGAGAGGAATCAGAAACTTGATGAGAGAAGGAAAAAGCTAAAGCTTGATCTTGGGGCCTAGGAGAGGCAAG
CCCAGGCCCAAGGGAGGGAGGTGGAGCAGAACAGTGGAAGTACCAGGACATTAGAAGAAAAGATTTCATGCCTACAGGAA
TAAGGTACCAGGCAGCTAGAAGAACAACAGAGGCTGATCCAGGAGCAGATAGGCCAAGACTGGGAACAGAGATTCCAAGG
AAGGACAGAACATCCTGAAGGCAAAGCAACACCTAAACTGAAGCTAAAGTGGAAATGTCCCAAAGAGGATGAGAACAAAT
GTGGTTACTCCAAGGACATCCTCTTGAGGATTCTGCAGGAGTATGGTGAAAATGCTCAGCCTGCTCATCTCCAGTAAGAA
GTCTGGGAGGGCTGTGGCGGAA

Alignment

ORF - retro_meug_1387 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.51 %
• Parental protein coverage: 80.5 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VKKAYRQ-KALTCHPDKNPDNPQAAELFHQLSQALEVLTDAAARAAYDKVRKAKKQAAERTQKLDERRKK
          VKKAY.Q.KALTCHPDKNP.NPQA.ELFHQLSQ.L..LT.AAA.AAY...RKAKKQ.AER.QKLDERRKK
Retrocopy VKKAYKQ<KALTCHPDKNPENPQAGELFHQLSQVLDMLTEAAAQAAYNNGRKAKKQEAERNQKLDERRKK

Parental  VKLDLEARERQAQAQGSEVEEDNRSTRTLEQEIARLREEGSRQLEEQQRLIQEQIRQDREQRLKGKTENP
          .KLDL.A.ERQAQAQG.EVE....STRTLE..I..L.E.G.RQLEEQQRLIQEQI.QD.EQR..G.TE.P
Retrocopy LKLDLGA*ERQAQAQGREVEQNSGSTRTLEEKISCLQE*GTRQLEEQQRLIQEQIGQDWEQRFQGRTEHP

Parental  EGKGTPKLKLKWKCKKEDETKGGYSKDVLLRILQKYGE-VLNLVISSKKMGCAVVE
          EGK.TPKLKLKWKC.KEDE.K.GYSKD.LLRILQ.YGE..L.L.ISSKK.G.AV.E
Retrocopy EGKATPKLKLKWKCPKEDENKCGYSKDILLRILQEYGE>MLSLLISSKKSGRAVAE

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_1387 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1387 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 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020803	4 retrocopies	retro_cjac_1013, retro_cjac_4017, retro_cjac_738, retro_cjac_820,
Cavia porcellus	ENSCPOG00000014110	1 retrocopy	retro_cpor_693,
Homo sapiens	ENSG00000104129	2 retrocopies	retro_hsap_2363, retro_hsap_3468,
Gorilla gorilla	ENSGGOG00000000051	1 retrocopy	retro_ggor_2340,
Macropus eugenii	ENSMEUG00000005641	2 retrocopies	retro_meug_1387 , retro_meug_2001,
Myotis lucifugus	ENSMLUG00000014835	1 retrocopy	retro_mluc_317,
Macaca mulatta	ENSMMUG00000013160	1 retrocopy	retro_mmul_1574,
Mus musculus	ENSMUSG00000034278	1 retrocopy	retro_mmus_3346,
Nomascus leucogenys	ENSNLEG00000003257	1 retrocopy	retro_nleu_343,
Pongo abelii	ENSPPYG00000006360	1 retrocopy	retro_pabe_2864,
Pan troglodytes	ENSPTRG00000006929	2 retrocopies	retro_ptro_1729, retro_ptro_2351,
Rattus norvegicus	ENSRNOG00000012368	2 retrocopies	retro_rnor_18, retro_rnor_2319,