RetrogeneDB ID: retro_chof_68

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_1162:114770..115437(+)
• Located in intron of: ENSCHOG00000010116

Retrocopy information

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

Parental gene information

• Parental gene symbol: SCO1
• Ensembl ID: ENSCHOG00000007572
• Aliases: None
• Description: SCO1 cytochrome c oxidase assembly protein [Source:HGNC Symbol;Acc:10603]

Sequence

>retro_chof_68
ATGGTGGGGCTGCTACTGGCCCCTGGCTGGGTCATACAGCCTCCGGATGGCCAACTTTGGTGTTTCCTGTCTCATGGACT
TGGGCTTTGGGGCCTGGCTGGGGCGACCACGAGAACCTGGCCAAAGCAGTTCTGCATGTGGTGAGAGGAAGCCTGGCGGG
CCTCGGGGCTCGCAGGCAGCTGCCTGGGAATCTGGCCACTCAGCACAGTGGTGCCGTCATTCCCGGGGTCGTCAGGGCCC
AGGCTGAAGGGGTTGCAGAGACCCCACACTCCCCTCGCAGCCTAGGTCTGTTTCTTGGAAGTCCACAATCGCTTTTGGAG
GCACTTTACTGGCTGGAATGAAATACTTCAAGAAAGAAAAGACAGAAAAGGTGTAGAAGGAACAGCAGCGAAGCCTAGGA
AAGACTTCACTCCGGGGACCATTTTCCCTCACAATTCATATCGGAAAGCCTAAACCTGACAAGGACTATCTGGCCCAGTG
GATACTGATTTATTTTGGTTTCACTCATTGCCCTGATATCTGTCCAGAAAAACTAGAAAAAAGCATTCAAGTCATGGATG
AAATAGATAGTATTCCATCTCTGCTAAATTTAACTCTGCTTTTCATCACTATTGACCCACAGAGGGGTACAAAATCTAAC
TTATGCAACTTTAAATTTAACTTTAAC

Alignment

ORF - retro_chof_68 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.81 %
• Parental protein coverage: 73.77 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAGLLVVLGRVVRLPDGRLWRFLCRGVERWGPAEATARASPRQLCVRREEAWRGSGLAGSCLGSRALGTA
          M.GLL...G.V...PDG.LW.FL..G...WG.A.AT.R..P.Q.C...EEAWR.SGLAGSCLG...L.T.
Retrocopy MVGLLLAPGWVIQPPDGQLWCFLSHGLGLWGLAGATTRTWPKQFCMW*EEAWRASGLAGSCLGIWPLSTV

Parental  MPPPPGSSGPESKGL-RDPTRPSQPGPVSWKSLALTFAVGGALLAGMKYFKKEKAEKLEKERQRSLGKPL
          .P..PGSSGP..KGL.RDPT.PSQP..VSWKS...T.A.GG.LLAGMKYFKKEK.EK..KE.QRSLGK..
Retrocopy VPSFPGSSGPRLKGL>RDPTLPSQPRSVSWKS---TIAFGGTLLAGMKYFKKEKTEKV*KEQQRSLGKTS

Parental  LGGPFSLTTHIGEPKTDKDYLGQWVLIYFGFTHCPDICPEELEKMIQVVDEIDSIPSLPNLTPLFITIDP
          L.GPFSLT.HIG.PK.DKDYL.QW.LIYFGFTHCPDICPE.LEK.IQV.DEIDSIPSL.NLT.LFITIDP
Retrocopy LRGPFSLTIHIGKPKPDKDYLAQWILIYFGFTHCPDICPEKLEKSIQVMDEIDSIPSLLNLTLLFITIDP

Parental  ERDTKEAIATYVKEFS
          .R.TK.........F.
Retrocopy QRGTKSNLCNFKFNFN

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_68 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 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000325	1 retrocopy	retro_amel_67,
Bos taurus	ENSBTAG00000021780	1 retrocopy	retro_btau_393,
Choloepus hoffmanni	ENSCHOG00000007572	7 retrocopies	retro_chof_2118, retro_chof_2547, retro_chof_2648, retro_chof_447, retro_chof_516, retro_chof_68 , retro_chof_827,
Danio rerio	ENSDARG00000067593	1 retrocopy	retro_drer_14,
Equus caballus	ENSECAG00000025151	1 retrocopy	retro_ecab_50,
Erinaceus europaeus	ENSEEUG00000011060	1 retrocopy	retro_eeur_4,
Felis catus	ENSFCAG00000003959	1 retrocopy	retro_fcat_36,
Homo sapiens	ENSG00000133028	1 retrocopy	retro_hsap_1112,
Gallus gallus	ENSGALG00000013382	1 retrocopy	retro_ggal_14,
Loxodonta africana	ENSLAFG00000005056	1 retrocopy	retro_lafr_567,
Oreochromis niloticus	ENSONIG00000009584	1 retrocopy	retro_onil_50,
Oryzias latipes	ENSORLG00000001047	1 retrocopy	retro_olat_14,