RetrogeneDB ID: retro_chof_1005

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_183271:1779..2289(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000002721
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ZBTB8OS
• Ensembl ID: ENSCHOG00000004061
• Aliases: None
• Description: zinc finger and BTB domain containing 8 opposite strand [Source:HGNC Symbol;Acc:24094]

Sequence

>retro_chof_1005
AGAATGCCCAATGCTGCACTCATGGCACAGCAGTATTAAGATGTGAGAGACTACAATTTGACTGAGGAGCAGAAGGCAAT
CAAGGCCAAGTATCCTCCAGTCAATCAGAAGTACAAGTATTTGGATCATACAACTGATGTCCAGTTACCCACATGGGGAG
ATACTCTGGAGGAAGCATATGATCATGTATGTTTGGTTACATGGCAGATACTGGGGACTGTTGAGCCCCTCCAAACAGTA
GAAATAGAAACCCAAGGAGATGACTTACAGTCTCTTTTTCACTTTTTGGATGAATGGCTTTATAAATTCAGTGCTGATGA
GTTCTTGATACCCTGGGAAGTGAAAGTATTCAGTACTGACCAAAGAAATTTCAAATTACAGTCAATTGGGTGGGGAGACG
AGTTTTCATTGTCCTAGCATCCTCAGGGAACTGAAGTCAAGGCAATAACATATTCGTCAATGCAAGTCTATAGTGAAGGG
AAGCCAGAAGTTTTTGTGATCATTGACATT

Alignment

ORF - retro_chof_1005 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.74 %
• Parental protein coverage: 97.21 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RMPNATLMAQPEEDVRDYNLTEKQKAIKAKYPPVNRKYEYLDHTADVQLHAWGDTLEEAFEQCAMAMFGY
          RMPNA.LMAQ...DVRDYNLTE.QKAIKAKYPPVN.KY.YLDHT.DVQL..WGDTLEEA...........
Retrocopy RMPNAALMAQQY*DVRDYNLTEEQKAIKAKYPPVNQKYKYLDHTTDVQLPTWGDTLEEAYDHVCLVTWQI

Parental  MTDTGTVEPLQTVEVETQGDDLQSLLFHFLDEWLYKFSADEFFIPREVKVLNIDQRNFKLRSIGWGEEFS
          ....GTVEPLQTVE.ETQGDDLQS.LFHFLDEWLYKFSADEF.IP.EVKV...DQRNFKL.SIGWG.EFS
Retrocopy L---GTVEPLQTVEIETQGDDLQS-LFHFLDEWLYKFSADEFLIPWEVKVFSTDQRNFKLQSIGWGDEFS

Parental  LSKHPQGTEVKAITYSAMQVYSEEKPEVFVIIDI
          LS.HPQGTEVKAITYS.MQVYSE.KPEVFVIIDI
Retrocopy LS*HPQGTEVKAITYSSMQVYSEGKPEVFVIIDI

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_1005 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 16 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010550	1 retrocopy	retro_cfam_2152,
Choloepus hoffmanni	ENSCHOG00000004061	2 retrocopies	retro_chof_1005 , retro_chof_1158,
Cavia porcellus	ENSCPOG00000015349	2 retrocopies	retro_cpor_356, retro_cpor_903,
Dasypus novemcinctus	ENSDNOG00000001861	2 retrocopies	retro_dnov_1056, retro_dnov_2193,
Equus caballus	ENSECAG00000020982	1 retrocopy	retro_ecab_610,
Felis catus	ENSFCAG00000000700	1 retrocopy	retro_fcat_703,
Homo sapiens	ENSG00000176261	2 retrocopies	retro_hsap_2396, retro_hsap_2992,
Gorilla gorilla	ENSGGOG00000007519	2 retrocopies	retro_ggor_2072, retro_ggor_231,
Myotis lucifugus	ENSMLUG00000000745	5 retrocopies	retro_mluc_1961, retro_mluc_2533, retro_mluc_2570, retro_mluc_2617, retro_mluc_2622,
Macaca mulatta	ENSMMUG00000009939	1 retrocopy	retro_mmul_1915,
Monodelphis domestica	ENSMODG00000017419	2 retrocopies	retro_mdom_400, retro_mdom_901,
Mus musculus	ENSMUSG00000057572	1 retrocopy	retro_mmus_2631,
Oryctolagus cuniculus	ENSOCUG00000000940	1 retrocopy	retro_ocun_492,
Otolemur garnettii	ENSOGAG00000011630	1 retrocopy	retro_ogar_3231,
Pongo abelii	ENSPPYG00000001589	2 retrocopies	retro_pabe_13, retro_pabe_2478,
Tursiops truncatus	ENSTTRG00000014968	1 retrocopy	retro_ttru_1200,