RetrogeneDB ID: retro_chof_645

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_130519:4119..5144(+)
• 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_645
GCAGATGTCAATTATGCCATCCAGAAGACTTTTCAAGTATGGAGTGATGTGACCCCTGTGAAATTCAAAAAGATTAATGC
AGGCGAAACTGACATTATGATCTTTTCTTCATGTGGAGAGCAAAGACTTCTACCCTTTTGATGGAAAAAGTGGAGGTTTA
GCCCATGCTTTTGAATACCAGCTGGAGCTGGTATTGGAGGAGATGCTCATCTTGATGAGGATGAAATATGGACTAAAAAC
TCCAGAGGCATAAACTTGTTACTTGTTGCAGTTCATGAGATTGGCCATTCCTTGGGTCTCGACCATTCCAATGATCCAAA
GGCCATAATGTTTCCACCTACAATTATGTTGACCCCCACACACTTAGCCTCTCTTCTGATGACACACGTGGCATTCAGTT
CCTCTATGGAGGCCCAGTACAGCACCAACCCAAGCCAGAGCCCCACCAGATAGTCATCTGTGACCCCAATTTGAGGTTTG
ATGCTGTCACTACAGTTGGAAATAAAATCTTTTTTCTTTAAAGACAATTTCTTCCGGTGGAAGCATGCTGAGACACCTAA
GATTAGTGTTAGTTTAATTTCTAACTTATAGCCAACTTTGCCATCTGATATTCAAGCTGCCTATGAAATTGGAGCTAGAA
ATGAAGTTTTTCTTTTTAAAGATGACAAGTACTGGTTAATCAGCAATTTAAGAATACATCTAAGCTATCCCAAGAACATA
TATTCTTTGGGTTTCCCTGCCTCTGTGAAAAAAAAATTGATGCAGCTGTTTTTCATCCAGTTTTCTACGAGACCTACTTC
TTTGTAGATAACTGGTATTGGAAGTATGATGAGAGGAAACAACTCGTGGACCCTGATTATCCCAAGTTGATTACCAAAAG
CTTTCCAGGAATTGGACCAAAAATCAATGCAACCTTCTTCTCCAAGGGACACACCTATTTCTTCCAAGGATCTCACCAAC
TTGAATATAACATCCAGTCCAACCGTGTCACCAGAATGTTGAAAAGCAATAGTGGATTGGGTTGT

Alignment

ORF - retro_chof_645 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.01 %
• Parental protein coverage: 72.75 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ADVDDAIQKAFQVWSDVTPLKFRRISAGEADIMILFSRREHGDFYPFDGKNGILAHAF--GPGAGIGGDA
          ADV..AIQK.FQVWSDVTP.KF..I.AGE.DIMI.FS........PF..K.......F....GAGIGGDA
Retrocopy ADVNYAIQKTFQVWSDVTPVKFKKINAGETDIMI-FSSCGEQRLLPF*WKKWRFSPCF*IPAGAGIGGDA

Parental  HFDDDEIWTKNSRGHNFFLVAVHEIGHSLGLDHSNDPKAIMFP-TYRYVDLHTFSLSSDDIRGIQFLYGG
          H.D.DEIWTKNSRG.N..LVAVHEIGHSLGLDHSNDPKAIMFP.TY.YVD.HT.SLSSDD.RGIQFLYGG
Retrocopy HLDEDEIWTKNSRGINLLLVAVHEIGHSLGLDHSNDPKAIMFP<TYNYVDPHTLSLSSDDTRGIQFLYGG

Parental  PEQHQPKPVPDEDV-CDPNLRFNAVTTVGNKIFF-FKDRFFWWKHVETPKISISSISNLWPTLPSGIQAA
          P.QHQPKP.P...V.CDPNLRF.AVTTVGNKIFF.FKD.FF.WKH.ETPKIS.S.ISNL.PTLPS.IQAA
Retrocopy PVQHQPKPEPHQIVICDPNLRFDAVTTVGNKIFF>FKDNFFRWKHAETPKISVSLISNL*PTLPSDIQAA

Parental  YEIGARNEVFLFKDDKYWLISNLRIHPDYPKSIYSL-GLPA-SVKKIDAAVFHPVLYKTYFFVDNWYWRY
          YEIGARNEVFLFKDDKYWLISNLRIH..YPK.IYSL.G.P.......DAAVFHPV.Y.TYFFVDNWYW.Y
Retrocopy YEIGARNEVFLFKDDKYWLISNLRIHLSYPKNIYSL<GFPCLCXXXXDAAVFHPVFYETYFFVDNWYWKY

Parental  DERRQLMDSDYPKLITKNFPGIGPKIDAAFYYKGHYYFFQGSHQLEFNTLSNRVTRRLKSNSGLGC
          DER.QL.D.DYPKLITK.FPGIGPKI.A.F..KGH.YFFQGSHQLE.N..SNRVTR.LKSNSGLGC
Retrocopy DERKQLVDPDYPKLITKSFPGIGPKINATFFSKGHTYFFQGSHQLEYNIQSNRVTRMLKSNSGLGC

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_645 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,