RetrogeneDB ID: retro_chof_582

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_123669:748..1304(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000006376
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000000939
• Aliases: None
• Description: None

Sequence

>retro_chof_582
ATGTCTGCTGCATGTTGGAGTGTGAAGGACTTGGTAGCAGTGATAACTGGAGGAGCCTGGGGCCTAGGTCTGGCCACAGC
AGAGCAACTGGTGAGACAGCAGATCACTGCTGTGCTTCTGGACCTGCCCAACTTGGATGAGGATGCCCTTGCCAAAAAGT
TAGGGAAGAGCTGCACCTTTGTCCCTGCTGACGTGACCCCAAAGAAGGATGTACAAGCAGCTCTGACCCTAGCAAAAGAA
AAGTTTGGCCATGTGGATGTGACAGTCAACCATGCAGGCATTACAGTGGCCAATAAGACATACAACCTAAGGAAGAGAAA
AGCCCTTTCCTTGGAGGACTTCCAGAAAGTTCTCAATGTGAATCTGATAGGCTATTTCAATGTGATTTGCCTGAGGGCTG
GCGAGATGGGCCAGAATGAACAAAACCAGGGAGGCCAATGTGGGATCATCAATACTGCCAGTATGGCTGCCTTCAAGGGC
CAGGTTATACAAACTGCATACTGTGTTTTAAGGGGGTATGGTGGGCATGATGCTGCCCATTGCTCAAGATCTGGCT

Alignment

ORF - retro_chof_582 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.19 %
• Parental protein coverage: 72.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAGCRSVKGLVALITGGASGLGLATAERLVRQGAAAVLLDLPSSDGEAQAKKLGSSCTFAPADVTSEKD
          M.A.C.SVK.LVA.ITGGA.GLGLATAE.LVRQ...AVLLDLP..D..A.AKKLG.SCTF.PADVT..KD
Retrocopy MSAACWSVKDLVAVITGGAWGLGLATAEQLVRQQITAVLLDLPNLDEDALAKKLGKSCTFVPADVTPKKD

Parental  VQAALTLAIEKFGRVDVAVNCAGIAVANKTYSLKKRKAHSLEDFQQVLNVNLIGTFNVIRLVAGEMGQNE
          VQAALTLA.EKFG.VDV.VN.AGI.VANKTY.L.KRKA.SLEDFQ.VLNVNLIG.FNVI.L.AGEMGQNE
Retrocopy VQAALTLAKEKFGHVDVTVNHAGITVANKTYNLRKRKALSLEDFQKVLNVNLIGYFNVICLRAGEMGQNE

Parental  PDQGGQRGVIINTASVAAFEGQGQAIVSASKQGIVG-MTLPIAGDLA
          ..QGGQ.G.IINTAS.AAF.GQ..........G..G.M.LPIA.DLA
Retrocopy QNQGGQCG-IINTASMAAFKGQVIQTAYCVLRGYGG>MMLPIAQDLA

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_582 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.

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005036	1 retrocopy	retro_amel_371,
Canis familiaris	ENSCAFG00000016277	1 retrocopy	retro_cfam_545,
Choloepus hoffmanni	ENSCHOG00000000939	1 retrocopy	retro_chof_582 ,
Cavia porcellus	ENSCPOG00000009594	1 retrocopy	retro_cpor_535,
Dipodomys ordii	ENSDORG00000004051	1 retrocopy	retro_dord_532,
Erinaceus europaeus	ENSEEUG00000005080	1 retrocopy	retro_eeur_379,
Felis catus	ENSFCAG00000013899	1 retrocopy	retro_fcat_1827,
Macropus eugenii	ENSMEUG00000008565	1 retrocopy	retro_meug_2184,
Myotis lucifugus	ENSMLUG00000000175	1 retrocopy	retro_mluc_4,
Otolemur garnettii	ENSOGAG00000002951	1 retrocopy	retro_ogar_1823,
Tarsius syrichta	ENSTSYG00000005340	3 retrocopies	retro_tsyr_1000, retro_tsyr_1542, retro_tsyr_2078,
Xenopus tropicalis	ENSXETG00000007721	1 retrocopy	retro_xtro_39,