RetrogeneDB ID: retro_chof_456

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_111251:3225..3700(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NFU1
• Ensembl ID: ENSCHOG00000005978
• Aliases: None
• Description: NFU1 iron-sulfur cluster scaffold homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:16287]

Sequence

>retro_chof_456
GGTGGGGTCCCTGCGGTGCTGGGGAGCTGCAGGTGATTCTGTCATATAATGATGAATCCACACACCAGTAAGAAACAGTC
TCTTCATTAATTTGTACAAAGATCACTTTTCCTACTACCTGCAACCATACATAACACAGTCAGATGCATGTCATTCAGAC
AAAAGGTATCCCAAATCCCCACAGTTTAAACTTTATTCCAGGAAAACCAGTTCTTGAGACAAGGACCATGGATTTTTCTA
CACCAGCTGCAGCTTTTCACTCCCCTCTGGCCAGGAAGTTATTCAGAATATAAGGCTAAAAGGTGCCTTCTTTGGACCAG
ATTTCATCACTGTTACAAAGAAAAATGAAGAGTTAGACTGAAATTTCCTGAAACCAGATATTTATGCAACAATCATGGAC
TTCTTTGAATCTGATTTACCTCTAGTTACTGAGGAAACATCTTCAGAAGTATCCGAAGAAGATGACGAAGTTGTG

Alignment

ORF - retro_chof_456 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.46 %
• Parental protein coverage: 63.39 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GAAAAAAGLRRRFCHVKMNPHTIKKQSLHQFVQRSLFLLPATLYNTVRYM-FIQTQDTPNPNSLKFIPGK
          G...A..G..R.FCH..MNPHT.KKQSLH.FVQRSLFLLPAT..NTVR.M..IQT...PNP.SL.FIPGK
Retrocopy GGVPAVLGSCR*FCHIMMNPHTSKKQSLH*FVQRSLFLLPATIHNTVRCM<VIQTKGIPNPHSLNFIPGK

Parental  PVLETRTMDFPTPAAAFCSPLARQLFRIEG-VKSVFFGPDFITVTKENEELDWNLIKPDIYATIMDFFAS
          PVLETRTMDF.TPAAAF.SPLAR.LFRI.G..K..FFGPDFITVTK.NEELD.N..KPDIYATIMDFF.S
Retrocopy PVLETRTMDFSTPAAAFHSPLARKLFRI*G<LKGAFFGPDFITVTKKNEELD*NFLKPDIYATIMDFFES

Parental  GLPLVTEETSSGEAASEEDDEVV
          .LPLVTEETSS....SEEDDEVV
Retrocopy DLPLVTEETSS--EVSEEDDEVV

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_456 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.

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005978	1 retrocopy	retro_chof_456 ,
Callithrix jacchus	ENSCJAG00000019156	1 retrocopy	retro_cjac_1573,
Echinops telfairi	ENSETEG00000019002	1 retrocopy	retro_etel_1371,
Homo sapiens	ENSG00000169599	1 retrocopy	retro_hsap_2638,
Macaca mulatta	ENSMMUG00000000435	1 retrocopy	retro_mmul_1524,
Monodelphis domestica	ENSMODG00000011805	1 retrocopy	retro_mdom_1395,
Mustela putorius furo	ENSMPUG00000006663	1 retrocopy	retro_mputfur_67,
Mus musculus	ENSMUSG00000029993	1 retrocopy	retro_mmus_1401,
Nomascus leucogenys	ENSNLEG00000010101	1 retrocopy	retro_nleu_646,
Ochotona princeps	ENSOPRG00000016760	2 retrocopies	retro_opri_380, retro_opri_48,
Pongo abelii	ENSPPYG00000012339	1 retrocopy	retro_pabe_2329,
Pan troglodytes	ENSPTRG00000012016	1 retrocopy	retro_ptro_1778,
Tupaia belangeri	ENSTBEG00000008616	1 retrocopy	retro_tbel_525,
Tarsius syrichta	ENSTSYG00000013765	1 retrocopy	retro_tsyr_108,