RetrogeneDB ID: retro_meug_1384

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold38614:492..1807(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TOX4
• Ensembl ID: ENSMEUG00000010501
• Aliases: None
• Description: TOX high mobility group box family member 4 [Source:HGNC Symbol;Acc:20161]

Sequence

>retro_meug_1384
CTGCCCAGTCAGATGACAATTGTGGTAGAGTTAAGCAAAAAGCAGAAGACTCTGAAGAAAAAGAAGAAAGATCCCAATGA
ACACCAAAAACCAGTATCAACATATGCCTTGTTCTTCCATGACACACAGGCAGCCATCAAGGGATAGAATCCCATTGCTA
CTTTTGGGGAGGTATCGAAAATTGTGGTCTCCATGTGGGACAGTCTTAGAGAAGAACAAAAACAGGGTATATAAAAGGAA
AACTGAAACTGCCAAGAAGGAATACCTGAAGGCTTTGGCAGCGTATAAAGCCAATCAAGTGTGTCAGAATGCTGTGGAGA
CAGTGGAACTTGATCCAGTGACTCCTCAGCAGATGCTTCCCCCATTTCCTGCTGTAACAGTTGTTGTTCCAGCCTCTCCA
GCACCAGCACCAGCATGAGCACCAGCATCAATGGAACCCCCTTCCCTGTCCTCTTCCATTGTAGTTAAATCCACCCTCTC
ATTCTATATGACAAGCCAGACATCTGGTGGGATAGGGGCCCAGACCAGCATCACCAAGATCATTATATCCAAGCAGAAGT
TGACATCTAGCCAGTTGACTTCTTCTATTTCCATGTCCCAAGGGGGCATGGTTACAGTCATCCCAGCCACAATGGTGACT
TCCCAAGGGCTGCAGTTAAGCCAAATCCAGGCAGCTACCAGCACATCTGCCATTGATCAGAGCCAACAAGCCAAAATTTT
TACCAGATCTGTGTTGCAGGCAGCAATGGCTGCTGCTGTTTCTATGCAGTTGCTTTCACCTCGACTGCAGCCTCCTCTGC
TGCAACAGATGCCTCAGCCACCCAGTCAGCAACAAGTAACCATTCTGCAGCAGCCTCCCCCACTCCAGGCCATGCAGCAG
CCCCCATAGCAAAAGGTTCATCTTAGTCCCTAACAACCGCTTCCTCTGCAGATCAAGATTGTTCCTCCACCTACATTGTG
AATTCAGCCTGCCTCAGTCCCACCTGCTCTGGAGAGTAGCCCTGAACAGCCAGTTACTACTAGTCTTGAGCCCCATGCAG
TGGAGGCAATTTCTCCGGAGCCAATTGAGATGGTCACAGAAGTTGTACCTGAGGTTGAATCTCCTTCTCAGATGGATGTT
GAGCTGGTGACAGGGTCTCCTGTGACACTCTCCCCTCAGCCACGATGTGTGAAGTCAGGTTGTGAAAACCCTCTAGTTAT
GAATAAGGACTGAGACAATGAATAACGTAGCAATGAGTGTGTAGTGAAGCATTGCAAGGATGTATTCCTGGCCTGGGTGG
CATCCAGAAATTCAAGCATAATGGTGTTTGTGAAA

Alignment

ORF - retro_meug_1384 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.09 %
• Parental protein coverage: 69.59 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LPSQKTIVVESSKKQKTPKKKKKKDPNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDSL
          LPSQ.TIVVE.SKKQKT..KKKKKDPNE.QKPVS.YALFF.DTQAAIKG.NP.ATFGEVSKIV.SMWDSL
Retrocopy LPSQMTIVVELSKKQKT-LKKKKKDPNEHQKPVSTYALFFHDTQAAIKG*NPIATFGEVSKIVVSMWDSL

Parental  GEEQKQ-VYKRKTEAAKKEYLKALAAYKANQVCQTPVETVELDPVTPQQTPP--PSPAATVVVPASPAPA
          .EEQKQ.VYKRKTE.AKKEYLKALAAYKANQVCQ..VETVELDPVTPQQ..P..P.....V.........
Retrocopy REEQKQ>VYKRKTETAKKEYLKALAAYKANQVCQNAVETVELDPVTPQQMLPPFPAVTVVVPASXXXXXX

Parental  PAPASTEPPSLSSSIVVKSTLSSYVTSQTSGGTGAQTSITKIIISKQTLTSSQLTSSIAMSQGGMVTVIP
          ....S.EPPSLSSSIVVKSTLS.Y.TSQTSGG.GAQTSITKIIISKQ.LTSSQLTSSI.MSQGGMVTVIP
Retrocopy XXXXSMEPPSLSSSIVVKSTLSFYMTSQTSGGIGAQTSITKIIISKQKLTSSQLTSSISMSQGGMVTVIP

Parental  ATMVTSQGLQLSQIQAATSTSAIDQSQQAKIVTRSVLQAAAAAAASMQLPPPRLQPPPLQQMPQPPSQQQ
          ATMVTSQGLQLSQIQAATSTSAIDQSQQAKI.TRSVLQAA.AAA.SMQL..PRLQPP.LQQMPQPPSQQQ
Retrocopy ATMVTSQGLQLSQIQAATSTSAIDQSQQAKIFTRSVLQAAMAAAVSMQLLSPRLQPPLLQQMPQPPSQQQ

Parental  VTILQQPPPLQAMQQPPQQKVRLSLQQPPPLQIKIVPPPTLHIQPASVPPALESSPEQPVTTSPEPHAVE
          VTILQQPPPLQAMQQPP.QKV.LS..QP.PLQIKIVPPPTL.IQPASVPPALESSPEQPVTTS.EPHAVE
Retrocopy VTILQQPPPLQAMQQPP*QKVHLSP*QPLPLQIKIVPPPTL*IQPASVPPALESSPEQPVTTSLEPHAVE

Parental  ATSPEPIEMITDVVPEVESPSQMDVELVTGSPVTLSPQPRCVRSGCENPPVVSKDWDNEYCSNECVVKHC
          A.SPEPIEM.T.VVPEVESPSQMDVELVTGSPVTLSPQPRCV.SGCENP.V..KD.DNE..SNECVVKHC
Retrocopy AISPEPIEMVTEVVPEVESPSQMDVELVTGSPVTLSPQPRCVKSGCENPLVMNKD*DNE*RSNECVVKHC

Parental  RDVFLACVASRNSSTVVFVK
          .DVFLA.VASRNSS..VFVK
Retrocopy KDVFLAWVASRNSSIMVFVK

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_1384 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1384 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 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006261	1 retrocopy	retro_amel_858,
Canis familiaris	ENSCAFG00000005647	2 retrocopies	retro_cfam_1625, retro_cfam_1698,
Choloepus hoffmanni	ENSCHOG00000000714	2 retrocopies	retro_chof_2239, retro_chof_631,
Homo sapiens	ENSG00000092203	1 retrocopy	retro_hsap_2970,
Macropus eugenii	ENSMEUG00000010501	1 retrocopy	retro_meug_1384 ,
Mustela putorius furo	ENSMPUG00000000181	1 retrocopy	retro_mputfur_718,
Mus musculus	ENSMUSG00000016831	1 retrocopy	retro_mmus_11,
Nomascus leucogenys	ENSNLEG00000014556	1 retrocopy	retro_nleu_2027,
Pongo abelii	ENSPPYG00000005598	1 retrocopy	retro_pabe_2463,
Pan troglodytes	ENSPTRG00000006126	1 retrocopy	retro_ptro_2008,
Sus scrofa	ENSSSCG00000029203	1 retrocopy	retro_sscr_361,