RetrogeneDB ID: retro_chof_1611

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_33885:5577..6695(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000008413
• Aliases: None
• Description: None

Sequence

>retro_chof_1611
GACATTCATCATTTCAAGCCAATGAGATGGTGGCCAGTATAGAAGAAATGTTATATCACCTACAGAATCAACAACTACAC
TCCGACCTGGCATATACGGATGTTGACTACACCATCCAGAAGGCTTTTCAAGCATGGAGTGATTTGACTACCCCCCCTGA
AATTCAGAAGGATTAATGCAGGTGAGGCTGACATTATGATCTCTTTTTCACGTGGAGCTCATGGAGACTTCTACCCTTTT
GATGGAAAAAGTGCAGTTTTAGCCCAGGCTTTTGGACCTGGAGCTGGTGTTGGAGTAGATGCGCCTTTTGATGAGGATGA
AATCTGGACTAAAATCTCCAGAGGCATCAACTTAAGTGTTGCAGTTCATGAGATTGGCCATGCCTTGGGTCTTGACCATT
CCAACGACCCAAGGGCCTTAATGTTTGCCACCTACAATTATACTGATCCCCATACCTTTAGCCTCTCTACTGATGACATA
TATGGCACTTGTTTCCTCTATGGAGGCCCAGAACAGCACCAACCCAAGCCAGATCCCGACAGTACAGAACTGTCTATCTG
TGACCCTAATTTGAGGTTCGATGCTGTTGCTACAGTTGGAAATAAAATCTTTTTCTTCAAAGTCAGGTTCTTCCAGTGGA
AGCATGCTGAGACACCTAAGATCAGTGTTATTTTAATTTCTAACTTATGGCCAATTTTGCCATCGGGTATTCAAGCTGCT
TATGAAATTGGAGCTAGAAATGAAGTTTTTCTTTTTAAAGATGACAAGTACTGGTTAGTCAGCAATTTAAGAACACATAC
GAACTATCCCAAGAGCATATATTCTTTGGGTTTCCCTGACTCTGTGAAAAAAATTGATGCAGCCGTTTTTCACCCACTTC
TCTACAAGACCTACTTCTTTGTAGATAACTGGTATTGGAGGTATGATGAGAGGAGATAACTCATGGACCCCAATTATCCC
AAATTGATTACCAAAACTTTCCAGGAATTGGACCTAAAATTGATGCAGTCTTGTACTCCAAAGGACACTATTTCTTCCAA
GGATCTCACCAACTTGATTATAACATCCTATCCAATAGTGTCACCAGGAGGTTGAAAAGCAATAGCGGATTGGGTTGT

Alignment

ORF - retro_chof_1611 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.72 %
• Parental protein coverage: 79.61 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NVVEFKTMRGGPVWKKHFITYRINNYT-TDLARADVDDAIQKAFQVWSDV-TPLKFRR-ISAGEADIMIL
          ....FK.MR..PV.KK..ITYRINNYT..DLA..DVD..IQKAFQ.WSD..TP......I.AGEADIMI.
Retrocopy DIHHFKPMRWWPV*KKCYITYRINNYT<SDLAYTDVDYTIQKAFQAWSDLTTPPEIQK>INAGEADIMIS

Parental  FSRREHGDFYPFDGKNGILAHAFGPGAGIGGDAHFDDDEIWTKNSRGHNFFLVAVHEIGHSLGLDHSNDP
          FSR..HGDFYPFDGK...LA.AFGPGAG.G.DA.FD.DEIWTK.SRG.N...VAVHEIGH.LGLDHSNDP
Retrocopy FSRGAHGDFYPFDGKSAVLAQAFGPGAGVGVDAPFDEDEIWTKISRGIN-LSVAVHEIGHALGLDHSNDP

Parental  KAIMFPTYRYVDLHTFSLSSDDIRGIQFLYGGPEQHQPKPVPDE---DVCDPNLRFNAVTTVGNKIFFFK
          .A.MF.TY.Y.D.HTFSLS.DDI.G..FLYGGPEQHQPKP.PD......CDPNLRF.AV.TVGNKIFFFK
Retrocopy RALMFATYNYTDPHTFSLSTDDIYGTCFLYGGPEQHQPKPDPDSTELSICDPNLRFDAVATVGNKIFFFK

Parental  DRFFWWKHVETPKISISSISNLWPTLPSGIQAAYEIGARNEVFLFKDDKYWLISNLRIHPDYPKSIYSLG
          .RFF.WKH.ETPKIS...ISNLWP.LPSGIQAAYEIGARNEVFLFKDDKYWL.SNLR.H..YPKSIYSLG
Retrocopy VRFFQWKHAETPKISVILISNLWPILPSGIQAAYEIGARNEVFLFKDDKYWLVSNLRTHTNYPKSIYSLG

Parental  LPASVKKIDAAVFHPVLYKTYFFVDNWYWRYDERRQLMDSDYPKLITK-NFPGIGPKIDAAFYYKGHYYF
          .P.SVKKIDAAVFHP.LYKTYFFVDNWYWRYDERR.LMD..YPKLITK.NFPGIGPKIDA..Y.KGH.YF
Retrocopy FPDSVKKIDAAVFHPLLYKTYFFVDNWYWRYDERR*LMDPNYPKLITK<NFPGIGPKIDAVLYSKGH-YF

Parental  FQGSHQLEFNTLSNRVTRRLKSNSGLGC
          FQGSHQL..N.LSN.VTRRLKSNSGLGC
Retrocopy FQGSHQLDYNILSNSVTRRLKSNSGLGC

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_1611 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 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008413	6 retrocopies	retro_chof_1424, retro_chof_1611 , retro_chof_2207, retro_chof_325, retro_chof_595, retro_chof_645,
Equus caballus	ENSECAG00000019445	1 retrocopy	retro_ecab_153,
Loxodonta africana	ENSLAFG00000010062	1 retrocopy	retro_lafr_147,
Macaca mulatta	ENSMMUG00000004250	1 retrocopy	retro_mmul_2325,
Otolemur garnettii	ENSOGAG00000010221	1 retrocopy	retro_ogar_965,