RetrogeneDB ID: retro_chof_1328

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_263378:1054..1876(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000009274
• Aliases: None
• Description: None

Sequence

>retro_chof_1328
TGGCTTCTGTCCCACATCGAGCACCCACCTCAAGGGGCAGTGATCTGTGGCTCTGGGTTAGGAGGTCTGGCGGATAAAGT
AACTCAGGCCCAGGCCTTTGAATACAGTGAGATACCCAACTTTCCTCAAAGTACAGTACCACGTCATGCTGGACGACTGG
TGTTTGGGTTCCTGAATGGCCGAGCCTGTGTGGTGATACAGGGCAGATTCCACTTTTATGAAGGCTACCCACTCTGGAAG
GTAATATTCCCAGTGAGGGTTTTCCAGCTTATGGGTGTGGACACCCTAGTGGTCACCAATGCAGCTGGAGGGCTTAACCC
CAGGTTTGAGGTTGGAGATATCATGATGATCCGTGATCATATCAACATGCTTGGTTTCTTTGGCCAGAACCCTCTCAGAG
GCCCCAGTGATGAAAGGTTTGGCCCTCGTTTTCCTGTCGTGTCTGATGCTTATGACCGCAATCTGAGGCAGAAGGCTCAC
TGGGCCTGGAAACAAATGGGGGAGCAGTGAGAGCTACAGGAAGGCACCTGTGTGATGTTGGGAGGCCCCAACTTTGAAAC
CATTGCAGAGTGTCGTCTGCTGCTGAACCTGGGGGCTGACGCTGTTGGCATGAGCACAGTACCACAAGTTATAGTTGCAC
GGCACTGTGGACTTCGAGTTTTTGGCTTTTCTCTCATCACTAACAAGGTTATTATGAGTTATGAGAGCTTAGAGAAGGCT
AATCATGAGGAAGTACTGGAATCCGCGAAACAAGCTGCACAGAAATTGGAACAGTTTGTCTCCATTCTTATGGCTAACAT
TCCACCCTCTGACAAGGCCATT

Alignment

ORF - retro_chof_1328 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.21 %
• Parental protein coverage: 96.17 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WLLSHTEHRPQVAVICGSGLGGLADKVTQAQAFEYSEIPNFPQSTVPGHAGRLVFGFLNGRACVVMQGRF
          WLLSH.EH.PQ.AVICGSGLGGLADKVTQAQAFEYSEIPNFPQSTVP.HAGRLVFGFLNGRACVV.QGRF
Retrocopy WLLSHIEHPPQGAVICGSGLGGLADKVTQAQAFEYSEIPNFPQSTVPRHAGRLVFGFLNGRACVVIQGRF

Parental  HFYEGYPLWKFAFKVTFPARVFRLMGVDILVVTNAAGGLNPRFEVGDIMLIRDHINMLGFSGQSPLRGPN
          HFYEGYPLW....KV.FP.RVF.LMGVD.LVVTNAAGGLNPRFEVGDIM.IRDHINMLGF.GQ.PLRGP.
Retrocopy HFYEGYPLW----KVIFPVRVFQLMGVDTLVVTNAAGGLNPRFEVGDIMMIRDHINMLGFFGQNPLRGPS

Parental  DERFGPRFPAVSDAYDHNLRQKAHCAWKQMGEQ-EL-EGTYVMAGGPNFETIAECHLLLNLGADAVGMST
          DERFGPRFP.VSDAYD.NLRQKAH.AWKQMGEQ.EL.EGT.VM.GGPNFETIAEC.LLLNLGADAVGMST
Retrocopy DERFGPRFPVVSDAYDRNLRQKAHWAWKQMGEQ*ELQEGTCVMLGGPNFETIAECRLLLNLGADAVGMST

Parental  VPEVIVARHCGLRVFGFSLITNKVIMSYKSLEKANHEEVLQSGKQAAQKLEQFVSILMATIPPSDKAI
          VP.VIVARHCGLRVFGFSLITNKVIMSY.SLEKANHEEVL.S.KQAAQKLEQFVSILMA.IPPSDKAI
Retrocopy VPQVIVARHCGLRVFGFSLITNKVIMSYESLEKANHEEVLESAKQAAQKLEQFVSILMANIPPSDKAI

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_1328 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 20 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005373	1 retrocopy	retro_amel_1666,
Bos taurus	ENSBTAG00000012317	1 retrocopy	retro_btau_1463,
Choloepus hoffmanni	ENSCHOG00000009274	5 retrocopies	retro_chof_1328 , retro_chof_1595, retro_chof_1827, retro_chof_1933, retro_chof_348,
Callithrix jacchus	ENSCJAG00000009676	2 retrocopies	retro_cjac_1195, retro_cjac_1511,
Dasypus novemcinctus	ENSDNOG00000011630	1 retrocopy	retro_dnov_322,
Erinaceus europaeus	ENSEEUG00000002411	1 retrocopy	retro_eeur_541,
Felis catus	ENSFCAG00000006934	1 retrocopy	retro_fcat_1368,
Homo sapiens	ENSG00000198805	1 retrocopy	retro_hsap_2282,
Gorilla gorilla	ENSGGOG00000002126	1 retrocopy	retro_ggor_1695,
Macropus eugenii	ENSMEUG00000014512	3 retrocopies	retro_meug_1282, retro_meug_1560, retro_meug_211,
Macaca mulatta	ENSMMUG00000019126	1 retrocopy	retro_mmul_287,
Mustela putorius furo	ENSMPUG00000018119	2 retrocopies	retro_mputfur_420, retro_mputfur_822,
Nomascus leucogenys	ENSNLEG00000010969	1 retrocopy	retro_nleu_1964,
Otolemur garnettii	ENSOGAG00000013344	4 retrocopies	retro_ogar_1631, retro_ogar_2141, retro_ogar_3083, retro_ogar_594,
Pongo abelii	ENSPPYG00000005567	1 retrocopy	retro_pabe_1938,
Pan troglodytes	ENSPTRG00000006095	1 retrocopy	retro_ptro_1616,
Pteropus vampyrus	ENSPVAG00000010734	1 retrocopy	retro_pvam_1302,
Rattus norvegicus	ENSRNOG00000009982	1 retrocopy	retro_rnor_891,
Tupaia belangeri	ENSTBEG00000016378	1 retrocopy	retro_tbel_4632,
Tarsius syrichta	ENSTSYG00000000748	3 retrocopies	retro_tsyr_2057, retro_tsyr_2127, retro_tsyr_235,