RetrogeneDB ID: retro_chof_595

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_124935:65..1175(-)
• 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_595
GACGTTCATAATTTCAAGACAATGAGAGGGGGGCCAGTATGGAAGAAACATTTTATCACCTACAGAATCAACAACTACAC
TCTTGACCTGACACATGCAGATGTCGACTATGCCATCCAGAAGGCTTTTCAAGTATGGAGTGATGTGAGCCCCTGAAATT
CAAGAAGATTAGTGCAGGCGAAGCTGACATTATGATCTTTTCACGCAGAGAGCATGGAGACTTCTACCCTTTTGATGGAA
AAAATGGAGTTTTAGCCCATGCTTTTGGACCTGGAGCTGGTATTGGAGGAGACACTCATTTTGATGAGGATGAAATCTGG
ACTAAAAACTCCAGAGGCACAAACTTATTTCTTGTTGCAGTTCATGAGATTGGCCATTCCTTGGGTCTTGACCATTCCAA
TGATCCAAAGGCCATAATGTTTCCCACCTACAGTTATGTTGGCCCCCACACATTTAGCCTCTCTTCTGGTGACATACATA
GCATTCAGTTCTCTATGGAGGCCCAGAACAGCACCAACCCAAGCCAGATTCCCACCAGGTAGACATCTGTGACCCCAATT
TGAAATTCGATGCTGTCACTACATTTGGAAATAAAATCTTTTTCTTTGAAGACAGGTTCTTGTGGTGGAAGCGTGCTGAG
ACACCTAAGATCAGTGTTAGTTCAATTTCTAACTTATGGCCAACTTTGCCATCTGGTGTTCAAGCTGCCTGTGAAATTGG
AGCTAGAAATGAAGTTTTTCTTTTTAAAGTTGACAGGTACTGGTTAATCAGCAATTTAAGAATACATCCAAATTATCCCA
AGAGCATATATTCTTTGGGTTTCCTGTCTCTGTGAAAAAAATTGATTCAGCCATTTTCCACCCAGTTTTCTACAAGACCT
ACTTCTTTGTAGATAACTGGTATTGGAGGTATGATGAGAGGAGACAACTCATGGACCCTGATTATCCCAAACTGATTACC
AAAAGCTTTCCAGGAATTGGACCTAAAATCAATGCAGGCTTCTACTCCAGGGGACACTGCTATTTCTTCCAGGGATCTTA
CCAACTTGAATATAACATCCTATTCAACCATGTCACAAGAAGGTTGAAAAGCAATAGCGGATTGGGTTGT

Alignment

ORF - retro_chof_595 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.73 %
• Parental protein coverage: 79.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NVVEFKTMRGGPVWKKHFITYRINNYTTDLARADVDDAIQKAFQVWSDVTP-LKFRRISAGEADIMILFS
          .V..FKTMRGGPVWKKHFITYRINNYT.DL..ADVD.AIQKAFQVWSDV.P.LKF..ISAGEADIMI.FS
Retrocopy DVHNFKTMRGGPVWKKHFITYRINNYTLDLTHADVDYAIQKAFQVWSDVSP<LKFKKISAGEADIMI-FS

Parental  RREHGDFYPFDGKNGILAHAFGPGAGIGGDAHFDDDEIWTKNSRGHNFFLVAVHEIGHSLGLDHSNDPKA
          RREHGDFYPFDGKNG.LAHAFGPGAGIGGD.HFD.DEIWTKNSRG.N.FLVAVHEIGHSLGLDHSNDPKA
Retrocopy RREHGDFYPFDGKNGVLAHAFGPGAGIGGDTHFDEDEIWTKNSRGTNLFLVAVHEIGHSLGLDHSNDPKA

Parental  IMFPTYRYVDLHTFSLSSDDIRGIQF-LYGGPEQHQPKPVPDE-DVCDPNLRFNAVTTVGNKIFFFKDRF
          IMFPTY.YV..HTFSLSS.DI..IQF.LYGGPEQHQPKP.....D.CDPNL.F.AVTT.GNKIFFF.DRF
Retrocopy IMFPTYSYVGPHTFSLSSGDIHSIQF<LYGGPEQHQPKPDSHQVDICDPNLKFDAVTTFGNKIFFFEDRF

Parental  FWWKHVETPKISISSISNLWPTLPSGIQAAYEIGARNEVFLFKDDKYWLISNLRIHPDYPKSIYSL-GLP
          .WWK..ETPKIS.SSISNLWPTLPSG.QAA.EIGARNEVFLFK.D.YWLISNLRIHP.YPKSIYSL.G.P
Retrocopy LWWKRAETPKISVSSISNLWPTLPSGVQAACEIGARNEVFLFKVDRYWLISNLRIHPNYPKSIYSL<GFP

Parental  ASVKKIDAAVFHPVLYKTYFFVDNWYWRYDERRQLMDSDYPKLITKNFPGIGPKIDAAFYYKGHYYFFQG
          .SVKKID.A.FHPV.YKTYFFVDNWYWRYDERRQLMD.DYPKLITK.FPGIGPKI.A.FY..GH.YFFQG
Retrocopy VSVKKIDSAIFHPVFYKTYFFVDNWYWRYDERRQLMDPDYPKLITKSFPGIGPKINAGFYSRGHCYFFQG

Parental  SHQLEFNTLSNRVTRRLKSNSGLGC
          S.QLE.N.L.N.VTRRLKSNSGLGC
Retrocopy SYQLEYNILFNHVTRRLKSNSGLGC

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_595 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,