RetrogeneDB ID: retro_chof_334

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_7535:36550..37054(-)
• Located in intron of: ENSCHOG00000002553

Retrocopy information

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

Parental gene information

• Parental gene symbol: PHYH
• Ensembl ID: ENSCHOG00000002160
• Aliases: None
• Description: phytanoyl-CoA 2-hydroxylase [Source:HGNC Symbol;Acc:8940]

Sequence

>retro_chof_334
TATACTCTAGTTAAGAATGTTCTGAGCCAGAAACAAGAGACAATTTTATGAAGAAAATGGCTTTCTTGTCCTTAAAAATC
TAGTGTCCAGTGCTGATATCTAACACTTTAGGGATGAGTTTGGAAAATTCTGCACAAAGGAGGTGAAGCCAATGGAATAA
ATGGTCATAAGAAATGTGCCCACTGCAAAGTCAGAATCTATTTCAAATGAAAAAGTGGTCATGAAGGTCCAAGATTTCCA
GGAAGACAAAGAACTCTTCAGACACTGCACCCTCTGGGGAATTCTGAAATATGTGGAGTGTGCCACTGAACTCAGTATTC
TGGCCATGCTGGTAAACAGACCTCGGGATTCAGGCAAGAAGACATCCCACCATCCCTTGGACCAGGATCTGCACTAACTC
CCCTTCAGGACTAGCAATCAGTCGTGGGTGCATAGACGGCCTTGGAGCACACTGACCCCAACAGCAGCTGTCTGCTTGCA
CCCTTGGGCACACACGGAATTCCA

Alignment

ORF - retro_chof_334 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.71 %
• Parental protein coverage: 58.64 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YTLDNNVLTLEQ-RQFYEENGFLIIKNLVSDADIQRFRNEFEKICRKEVKPMGLTVMRDVTIAKSEYIPS
          YTL..NVL...Q.RQFYEENGFL..KNLVS.ADI..FR.EF.K.C.KEVKPM...V.R.V..AKSE.I..
Retrocopy YTLVKNVLSQKQ>RQFYEENGFLVLKNLVSSADI*HFRDEFGKFCTKEVKPME*MVIRNVPTAKSESISN

Parental  EEVVSKVQDFQEDEELFRYCSLPEILKYVECFTGPDIMAVHTMLINKPPDSGNCKKTSRHPLHQDLHYFP
          E.VV.KVQDFQED.ELFR.C.L..ILKYVEC.T...I.A...ML.N.P.DSG..KKTS.HPL.QDLH..P
Retrocopy EKVVMKVQDFQEDKELFRHCTLWGILKYVECATELSILA---MLVNRPRDSG--KKTSHHPLDQDLH*LP

Parental  FRPSNH-IVCAWTAMEHIDRSNGCLVVLPGTHKGP
          FR.SN...V.A.TA.EH.D....CL....GTH..P
Retrocopy FRTSNQ<VVGA*TALEHTDPNSSCLLAPLGTHGIP

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_334 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002160	1 retrocopy	retro_chof_334 ,
Cavia porcellus	ENSCPOG00000007582	1 retrocopy	retro_cpor_161,
Rattus norvegicus	ENSRNOG00000018044	1 retrocopy	retro_rnor_542,
Tursiops truncatus	ENSTTRG00000011113	1 retrocopy	retro_ttru_1844,