RetrogeneDB ID: retro_chof_609

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_126622:1051..1273(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000004014
• Aliases: None
• Description: None

Sequence

>retro_chof_609
AATAAGGAGAGCTGTATTGAACCACGACTTTAGAAGGGAAAGAGTAGTAGGAGGACTCATGACAACAGTTAGAGCTTGGA
AAAGAGCATTCAGACCTATCTTCAGTCAACAAAGCCAATTGTTGACCTATATAAGGAAGTGAGGAAAGTCAAAAAAATAG
ATGCTTCTAAATCTGTTGATGAAGTTTTTGATGAAGCTGTGAAGATTTTTGACAAAGAAGGC

Alignment

ORF - retro_chof_609 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.03 %
• Parental protein coverage: 60.66 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NNEICIQRCLERGKSSGRTDDNRESLEKRIQTYLQSTKPIIDLYEEMGKVKKIDASKSVDEVFDEVVKIF
          N.E.CI...L..GKSS.RT.DN..SLEK.IQTYLQSTKPI.DLY.E..KVKKIDASKSVDEVFDE.VKIF
Retrocopy NKESCIEPRL*KGKSSRRTHDNS*SLEKSIQTYLQSTKPIVDLYKEVRKVKKIDASKSVDEVFDEAVKIF

Parental  DKEG
          DKEG
Retrocopy DKEG

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_609 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 17 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000012	2 retrocopies	retro_amel_1074, retro_amel_1711,
Canis familiaris	ENSCAFG00000004030	1 retrocopy	retro_cfam_1729,
Choloepus hoffmanni	ENSCHOG00000004014	2 retrocopies	retro_chof_609 , retro_chof_840,
Callithrix jacchus	ENSCJAG00000021250	2 retrocopies	retro_cjac_2652, retro_cjac_2992,
Cavia porcellus	ENSCPOG00000014747	4 retrocopies	retro_cpor_1070, retro_cpor_1295, retro_cpor_417, retro_cpor_799,
Felis catus	ENSFCAG00000025426	1 retrocopy	retro_fcat_1259,
Macaca mulatta	ENSMMUG00000017375	2 retrocopies	retro_mmul_1572, retro_mmul_66,
Mustela putorius furo	ENSMPUG00000012394	1 retrocopy	retro_mputfur_1061,
Mus musculus	ENSMUSG00000028719	1 retrocopy	retro_mmus_2576,
Otolemur garnettii	ENSOGAG00000026904	2 retrocopies	retro_ogar_1589, retro_ogar_3204,
Pongo abelii	ENSPPYG00000001380	1 retrocopy	retro_pabe_1369,
Rattus norvegicus	ENSRNOG00000007775	1 retrocopy	retro_rnor_1940,
Sorex araneus	ENSSARG00000009745	2 retrocopies	retro_sara_199, retro_sara_294,
Sus scrofa	ENSSSCG00000003885	1 retrocopy	retro_sscr_454,
Tupaia belangeri	ENSTBEG00000017494	2 retrocopies	retro_tbel_3597, retro_tbel_691,
Tarsius syrichta	ENSTSYG00000007511	1 retrocopy	retro_tsyr_319,
Vicugna pacos	ENSVPAG00000004127	2 retrocopies	retro_vpac_345, retro_vpac_373,