RetrogeneDB ID: retro_meug_2040

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold82459:1491..3273(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX41
• Ensembl ID: ENSMEUG00000014375
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box polypeptide 41 [Source:HGNC Symbol;Acc:18674]

Sequence

>retro_meug_2040
GAGGATGAGGATTATGTGCCTTAAGTGCCTGTCAAGCAGAGAAAGCAGCAAATGCTACAGAAGATGCTGCAGATGCAATG
GAAGGGAGCAGCAGAGGAGGAGCAGAAAGACAGCAGCAGTGAGCTCTGAGGAGATGAAGATGACATTCCCTTGGGCTGCT
AGTCCCGTGTCAGCCTCCTGGACCAGCACCAACACCTGAAGGAGAAGGCAGAAGCCCAGAAAGAGTCTGCCAAGGAGAAG
CAGCTGAATGAGGAGGAGAAGATCTTAGAGAGTGTGGCAGAGGGTAGAGGTCTCATGTTGGTGAAAGAGATGATGAAAGG
AATCACCTATGATGATACCATCAAAACCATTTGGAAAGCTCCTCAAATGTGCTGATCATGCCTGAAGTCTGGCATGACTG
TGTTTGTAAGAAGTACCATATCTTGGTGGAAGGAGAAGGGATTCCATTCTTCCTCAAGAGCTTCAAGGAAATGAAGTTTC
CTGCAGCCATTCTGAGGGGTCTGAAGTAGAAGGGAATCTACCACCCTACTCCTATTCAGATCCAGGGCATCCCTACCATC
CTTTCTGGCTGTGACATGATTGGCATGGCTTTCACTGGCTCTGGCGGGACATTAGTGTTCACTCTGCCTGTCATCATGTT
TTGCCTGGAACAGGAGAAAACATTTACCCTTCTCCAACAGGGAAGGGCCCTATGGGATCATTATCTGCCCTTTGTGAAAA
CTGGACCCTCAGACCCATGGAATTTTGGAGCATTACTGTCGGCTACTCCAGGAAGACAGCTTGCCCCCTTGTGCTGTACT
CTCTGCATTGGGGGCATGTTACTCAAGGAGTAGATGGAAACCATCCAGCATGGGGTGCACATGATGGTAGTCACCCCAGG
GCATCTCATGGACCTGCTGCAAAAGAAGATGGTGAGTCTGGACATCTGCCACTACTTGGCCCTGGATGAGGCTGATAAAA
TGATTGACATGGGCTTTGAGGGGGGACGTCCAAACCATCTTCTCCTACTTCAAGGGCCAGCGACAGACACTGATTTTCAG
TGCTACCATGCCCCCAAAGATCCAAAACTTTGCTAAGAGTGCCCTGGTAAAGCCTATCACCATCAACATGGGCTGGGCAG
GCACTGTTGGTTTGGACGTCATACAGGTGGTGGAGTATGTGAAGGAAGAGACCAAGATGGTATACTTGCTTCAGTGTCTA
CAAAAGACTCCCCCACCAGTGCTGATCTTTCCAGAGAAGAAGGCAGATGTAGATGCTATCCATGAATACTTGTTTCTCAA
GGGTGTGGAGGCTGTAGCCATCCATAGAGGCAAAGATCAAGAAGAACGGACCAAGGCCATTGAGGCATTCCAGGATGGCA
AGAAAGATGTCTTAGTGGCCACCAATATGGCCTCCAAGGGCCTGGACTTTCCAGTCATTCAGCACATCACCAATTATGGT
ATGCCTGAGGAGACTGAGAATTATGTTCATTGGACTGGCTGCACAGGGCGCTCTGGGAATACAGGCATCGCCACCACCTT
TATCAACAAGGCCTGTGATGAGTCAGTACTCATGGATCTCAAAGTCCCCCTGCTTGAAGCCAAGCAGAAGGTGCCTCCCA
TGCTGCCAGTCCTACGCTGTGGAGATGAGTCTATGCTGGACATTGGAGGAGAAAGAGACCGGACCTTTTTCAGGGATCTG
GGCCATCGCATCACTGAATGAGCCAAGCTGGAAGCCATGCAGATCAAACTGGTCAGCAACACTGGCCGCGAGGACTACCT
GACCCACAGCTCCATGGACTTC

Alignment

ORF - retro_meug_2040 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.44 %
• Parental protein coverage: 95.65 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EDEDYVPYVPVKQRKQQMLQKLLQMRRKGVAEEEQKDSGSEPRGDEDDIPLGPQSNVSLLDQHQHLKEKA
          EDEDYVP.VPVKQRKQQMLQK.LQM..KG.AEEEQKDS.SE..GDEDDIPLG..S.VSLLDQHQHLKEKA
Retrocopy EDEDYVP*VPVKQRKQQMLQKMLQMQWKGAAEEEQKDSSSEL*GDEDDIPLGC*SRVSLLDQHQHLKEKA

Parental  EARKESAKEKQLKEEEKILESVAEGRALMSVKEMAKGITYDDPIKTSWKAPRY-VLSMSEARHDRVRKKY
          EA.KESAKEKQL.EEEKILESVAEGR.LM.VKEM.KGITYDD.IKT.WKAP...VL.M.E..HD.V.KKY
Retrocopy EAQKESAKEKQLNEEEKILESVAEGRGLMLVKEMMKGITYDDTIKTIWKAPQM<VLIMPEVWHDCVCKKY

Parental  HILVEGEGIPPPLKSFREMKFPAAILRGLKKKGIHHPTPIQIQGIPTILSGRDMIGIAFTGSGKTLVFTL
          HILVEGEGIP..LKSF.EMKFPAAILRGLK.KGI.HPTPIQIQGIPTILSG.DMIG.AFTGSG.TLVFTL
Retrocopy HILVEGEGIPFFLKSFKEMKFPAAILRGLK*KGIYHPTPIQIQGIPTILSGCDMIGMAFTGSGGTLVFTL

Parental  PVIMFCLEQEK-RLPFSKREGPYGLIICPSRELARQTHGILEYYCRLLQEDSSPP-LRCALCIGGMSVKE
          PVIMFCLEQEK..LPFS.REGPYG.IICP...L..QTHGILE.YCRLLQEDS.PP.L.C.LCIGGM..KE
Retrocopy PVIMFCLEQEK>HLPFSNREGPYGIIICPL*KLDPQTHGILEHYCRLLQEDSLPP<LCCTLCIGGMLLKE

Parental  QMETIRHGVHMMVATPGRLMDLLQKKMVSLDICRYLALDEADRMIDMGFEG-DIRTIFSYFKGQRQTLLF
          .METI.HGVHMMV.TPG.LMDLLQKKMVSLDIC.YLALDEAD.MIDMGFEG.D..TIFSYFKGQRQTL.F
Retrocopy *METIQHGVHMMVVTPGHLMDLLQKKMVSLDICHYLALDEADKMIDMGFEG>DVQTIFSYFKGQRQTLIF

Parental  SATMPKKIQNFAKSALVKPVTINVGRAGAASLDVIQEVEYVKEEAKMVYLLECLQKTPPPVLIFAEKKAD
          SATMP.KIQNFAKSALVKP.TIN.G.AG...LDVIQ.VEYVKEE.KMVYLL.CLQKTPPPVLIF.EKKAD
Retrocopy SATMPPKIQNFAKSALVKPITINMGWAGTVGLDVIQVVEYVKEETKMVYLLQCLQKTPPPVLIFPEKKAD

Parental  VDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFRDGKKDVLVATDVASKGLDFPAIQHVINYDMPEEIE
          VDAIHEYL.LKGVEAVAIH.GKDQEERTKAIEAF.DGKKDVLVAT..ASKGLDFP.IQH..NY.MPEE.E
Retrocopy VDAIHEYLFLKGVEAVAIHRGKDQEERTKAIEAFQDGKKDVLVATNMASKGLDFPVIQHITNYGMPEETE

Parental  NYVHRIGRTGRSGNTGIATTFINKACDESVLMDLKALLLEAKQKVPPVLQVLHCGDESMLVLGGERGCTF
          NYVH..G.TGRSGNTGIATTFINKACDESVLMDLK..LLEAKQKVPP.L.VL.CGDESML..GGER..TF
Retrocopy NYVHWTGCTGRSGNTGIATTFINKACDESVLMDLKVPLLEAKQKVPPMLPVLRCGDESMLDIGGERDRTF

Parental  CGGLGHRITDCPKLEAMQTKQVSNIGRKDYLAHSSMDF
          ...LGHRIT...KLEAMQ.K.VSN.GR.DYL.HSSMDF
Retrocopy FRDLGHRITE*AKLEAMQIKLVSNTGREDYLTHSSMDF

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_2040 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_2040 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000008770	1 retrocopy	retro_cpor_1521,
Loxodonta africana	ENSLAFG00000026418	1 retrocopy	retro_lafr_689,
Macropus eugenii	ENSMEUG00000014375	1 retrocopy	retro_meug_2040 ,
Otolemur garnettii	ENSOGAG00000011123	1 retrocopy	retro_ogar_1801,
Rattus norvegicus	ENSRNOG00000012771	1 retrocopy	retro_rnor_2396,
Sarcophilus harrisii	ENSSHAG00000014005	1 retrocopy	retro_shar_53,