RetrogeneDB ID: retro_chof_2061

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_470576:454..782(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000011485
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ZNRD1
• Ensembl ID: ENSCHOG00000007328
• Aliases: None
• Description: zinc ribbon domain containing 1 [Source:HGNC Symbol;Acc:13182]

Sequence

>retro_chof_2061
CTGTCTATCATGGACCTCACCAACACCTGCTCCAGCTTCCAGTTGGACCTAGATTTCTGCCCAGACTGTGGCTCAGTTCT
ATCTCTGCCTGGGACTCAGGATACGGTCATTTGTACTTGCTGTGGCTTCTCCATCAACGTGCAGGACTTCAAAGGGAAGG
TTGTGAAGACCTCATTTGTGTTCCACAAACTGGGAACAGCCATGCCTACATCAGTGGAAGAAGGACCAGAGTTCCAAGGG
CCCATGGTTGACAGACACTGCTCTCGATTGTGGTCATGAAGGAATGGCATACCACACCAGACAGATGTGCTATGCCAATG
AGGGGCAG

Alignment

ORF - retro_chof_2061 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.55 %
• Parental protein coverage: 86.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LSVMDLAKTCSSFQSDLDFCPDCGSVLPLPGTQDTVICTRCGFSINVRDFEGKVVKTSFVFHKLGRAVPM
          LS.MDL..TCSSFQ.DLDFCPDCGSVL.LPGTQDTVICT.CGFSINV.DF.GKVVKTSFVFHKLG.A.P.
Retrocopy LSIMDLTNTCSSFQLDLDFCPDCGSVLSLPGTQDTVICTCCGFSINVQDFKGKVVKTSFVFHKLGTAMPT

Parental  SVEEGPEFQGPVVDRRCSR-CGHEGMAYHTRQMRSADEGQ
          SVEEGPEFQGP.VDR.CSR.CGHEGMAYHTRQM..A.EGQ
Retrocopy SVEEGPEFQGPMVDRHCSR>CGHEGMAYHTRQMCYANEGQ

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_2061 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 8 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007328	2 retrocopies	retro_chof_1997, retro_chof_2061 ,
Dasypus novemcinctus	ENSDNOG00000015720	9 retrocopies	retro_dnov_1020, retro_dnov_1103, retro_dnov_1472, retro_dnov_1726, retro_dnov_1798, retro_dnov_1881, retro_dnov_2400, retro_dnov_2420, retro_dnov_933,
Myotis lucifugus	ENSMLUG00000007272	1 retrocopy	retro_mluc_126,
Monodelphis domestica	ENSMODG00000016023	1 retrocopy	retro_mdom_1799,
Mustela putorius furo	ENSMPUG00000007474	1 retrocopy	retro_mputfur_968,
Rattus norvegicus	ENSRNOG00000000779	1 retrocopy	retro_rnor_978,
Sorex araneus	ENSSARG00000009716	2 retrocopies	retro_sara_431, retro_sara_745,
Sarcophilus harrisii	ENSSHAG00000001554	1 retrocopy	retro_shar_796,