RetrogeneDB ID: retro_chof_631

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_12844:8601..9557(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TOX4
• Ensembl ID: ENSCHOG00000000714
• Aliases: None
• Description: TOX high mobility group box family member 4 [Source:HGNC Symbol;Acc:20161]

Sequence

>retro_chof_631
GCCATAGTGGAGACAGTGGAATTGGATCCTGTGCCACCACCCCAGACTCCTTCTCCATCTGCTATGGCTACTGTTAACCT
AGCATTTCTAGCACCAGCCTCAACAGACCCCCTGCCTTGTCACCTTCCATTGTTGTTTACTCAACTCTTTCATCCTATGT
GGCAAACCAGGCATCTTCTGGAGCTGGGAGTCAGCCCAATATTGCCACATTGATTATTACCAAACAGATGTTACCCTCTT
CTATTACCATGTCTGAAGGAGGGGTGGCTACCATTACCCCAGCCACAATTGTGACCTCCTGGGGGCTCCAGGTAGGCCAA
ACCATTACAGCTACTATCCAACCCAGTCAACAAGCTCAGGTAGTCACTCAGTCAGTGTTGCAGGCAGTAGCAGCTGCTGC
TGCTTCTATGCAACTGCCTCTAACCTGACTACATCCCCTTCCATTATAATAGGTGTCTTAGCCCCCCACTCAGCAGCAAG
TGACCGGTCTGCAGCAGCCTCTCTTACTCCAGTCCATGCAAAAGCCCCCACCTCAGAAAGCTCAAATAAATTTACAACAG
CCACCTCCTCTGCAGATCAAGAATATGCCTCCACCCCCTCCAAAAATGCAGGCTACCTTAGTCCCACCAGCTGTGGAAAG
TAGTCCTGAGTGGCCTATGAACAACAGCCCTGAGGCCCTTACAGTGGAGGCAACATCTCCTGGGATAATCTATGAGATGA
TTACAGATGTAGTTCCTGAGGAAGTCTCCTTCTCAGATGGATGTTCAATTGCTGAGTGGCTCTCTGGTGACACTCTCGCC
CCAGCCTTGATGTGTAAGGTTAGGTTGTGAGAAACCTACCATTGTAAGAACTGGGACAATGAGTACTGAAGCAATGAGTG
TGTGGTGAGGCACTGCAGGGATGTATTCTTAGCCTGGGTAGCCTCCAGAAATTCAAACACAATCATGTTTGTGAAA

Alignment

ORF - retro_chof_631 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.47 %
• Parental protein coverage: 51.94 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ATVETVELDPVPAPQTPSPPPVATVNPASPAPASTEP-PALSPSIVVNSTLSSYVANQASSGAGGQPNIT
          A.VETVELDPVP.PQTPSP...ATVN.A..APAST.P.PALSPSIVV.STLSSYVANQASSGAG.QPNI.
Retrocopy AIVETVELDPVPPPQTPSPSAMATVNLAFLAPASTDP<PALSPSIVVYSTLSSYVANQASSGAGSQPNIA

Parental  KLIITKQMLPSSITMSQGGMVTVIPATVVTSRGLQLGQTSTATIQPSQQAQIVTRSVLQAAAAAAASMQL
          .LIITKQMLPSSITMS.GG..T..PAT.VTS.GLQ.GQT.TATIQPSQQAQ.VT.SVLQA.AAAAASMQL
Retrocopy TLIITKQMLPSSITMSEGGVATITPATIVTSWGLQVGQTITATIQPSQQAQVVTQSVLQAVAAAAASMQL

Parental  PPPRLQPPPLQQMPQPPTQQQVTILQQPPPLQAMQQPPPQKVRINLQQQPPPLQIKNMPPPTLKMQATLV
          P...L.P.PL.....PPTQQQVT.LQQP..LQ.MQ.PPPQK..INLQQ.PPPLQIKNMPPP..KMQATLV
Retrocopy PLT*LHPLPL**VS*PPTQQQVTGLQQPLLLQSMQKPPPQKAQINLQQ-PPPLQIKNMPPPPPKMQATLV

Parental  PPAVESSPERPMNSSPETHTVETTSPEIICEMITDVVPEVES-PQMDVQLVSGSPMTLSPQPRCVRSGCE
          PPAVESSPE.PMN.SPE..TVE.TSP.II.EMITDVVPE..S..QMDVQL.SGS..TLSPQP.CVR.GCE
Retrocopy PPAVESSPEWPMNNSPEALTVEATSPGIIYEMITDVVPEEVS>SQMDVQLLSGSLVTLSPQP*CVRLGCE

Parental  NPPVV-SKDWDNEYCSNECVVKHCRDVFLAWVASRNSNTVVFVK
          ..P....K.WDNEY.SNECVV.HCRDVFLAWVASRNSNT..FVK
Retrocopy K-PTI<CKNWDNEY*SNECVVRHCRDVFLAWVASRNSNTIMFVK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Choloepus hoffmanni was not studied using RNA-Seq expression data.

ChIP-Seq

Choloepus hoffmanni was not studied using ChIP-Seq data.

EST

Choloepus hoffmanni was not studied using EST data.

TSS

Choloepus hoffmanni was not studied using FANTOM5 data.

Lab

retro_chof_631 was not experimentally validated.

Homology

Retrocopy orthology:

Choloepus hoffmanni 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,