RetrogeneDB ID: retro_chof_1847

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_402702:454..1052(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000007181
• Aliases: None
• Description: None

Sequence

>retro_chof_1847
AAGCAATATATCATCAATGGAAAGAAAATCATTATTTACAACCACACAGATTAGCAGAAGAAGGACCATGAAAAAGTTGA
ATTTGAGGTACATGAAATACATGCCCTGGATATTCTTGTCAGCTCAGGAGAGGGCAAGGCAAAGGATGCAGGACAGAGAA
ACACCATTCACAGACGAGACCCCTCTAAACAATATGGCCTGAAAATGAAAACCTCACATGCCTTTTTCGGTGAAGTAGAA
AGATGTTTGATGCCATTCCATTTACTTTGAGAATTTCAAGATGAGAAGGCTGACTGGATATGGTGGAGTGTGCCAAACAT
GAACTGCCACAACCATTTAATGCTCTTTATGAGAAGAAGGGCGAATTTGTTGCCCAGTTTAAATTTACAGTTCTGCTCAT
GCCCAATGGCTCCATGTGGATAACTAGTGGTCCCTTCGAGCCTGACCGCTACAAGTCTGAGATGGAAGCCCAGGATGCAG
AGCTGAAGGCTCTTTTCCAGAAGTCTGCAAGTTAGAAAACCCATAAAAAGGAAAAGAAAAGAAGGCCTCCAAGACTGCAG
AGAATACTACCAGTGGGGAAACACTAGAAGAGACTGAG

Alignment

ORF - retro_chof_1847 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.75 %
• Parental protein coverage: 54.72 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KQHVIDGEKTIIQNPTD--QQDHEKAEFEVHEVYAVDVLVSSGEGKAKDAGQRTTIYKRDPSKQYGLKMK
          KQ..I.G.K.II.N.TD....DHEK.EFEVHE..A.D.LVSSGEGKAKDAGQR.TI..RDPSKQYGLKMK
Retrocopy KQYIINGKKIIIYNHTD*QKKDHEKVEFEVHEIHALDILVSSGEGKAKDAGQRNTIHRRDPSKQYGLKMK

Parental  TSRAFFSEVER-RFDAMPFTLRAFDEKKRMGVVECAKHELLQPFNVLYEKEGEFVAQFKFTVLLMPNGPM
          TS.AFF.EVER..FDA.PFTLR..........VECAKHEL.QPFN.LYEK.GEFVAQFKFTVLLMPNG.M
Retrocopy TSHAFFGEVER<MFDAIPFTLRISR*EG*LDMVECAKHELPQPFNALYEKKGEFVAQFKFTVLLMPNGSM

Parental  RITSGPFEPDLYKSEMEVQDAELKALLQSSASRKT-QKKKK-KKASKTAENATSGETLEEND
          .ITSGPFEPD.YKSEME.QDAELKAL.Q.SAS.KT..K.KK.KKASKTAEN.TSGETLEE..
Retrocopy WITSGPFEPDRYKSEMEAQDAELKALFQKSAS*KTHKKEKK<KKASKTAENTTSGETLEETE

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_1847 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 13 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007181	2 retrocopies	retro_chof_1089, retro_chof_1847 ,
Callithrix jacchus	ENSCJAG00000011811	2 retrocopies	retro_cjac_4214, retro_cjac_4215,
Homo sapiens	ENSG00000170515	6 retrocopies	retro_hsap_1930, retro_hsap_2413, retro_hsap_2868, retro_hsap_3646, retro_hsap_4191, retro_hsap_4895,
Macaca mulatta	ENSMMUG00000002164	2 retrocopies	retro_mmul_1168, retro_mmul_2631,
Mus musculus	ENSMUSG00000025364	1 retrocopy	retro_mmus_2803,
Nomascus leucogenys	ENSNLEG00000017544	6 retrocopies	retro_nleu_1212, retro_nleu_1260, retro_nleu_163, retro_nleu_3024, retro_nleu_506, retro_nleu_612,
Oryctolagus cuniculus	ENSOCUG00000017342	1 retrocopy	retro_ocun_1733,
Pongo abelii	ENSPPYG00000025851	7 retrocopies	retro_pabe_1595, retro_pabe_1778, retro_pabe_2375, retro_pabe_2869, retro_pabe_2993, retro_pabe_3430, retro_pabe_3807,
Pan troglodytes	ENSPTRG00000005076	6 retrocopies	retro_ptro_1289, retro_ptro_1389, retro_ptro_1940, retro_ptro_2471, retro_ptro_2846, retro_ptro_3263,
Sus scrofa	ENSSSCG00000000377	1 retrocopy	retro_sscr_338,
Sus scrofa	ENSSSCG00000022666	2 retrocopies	retro_sscr_1143, retro_sscr_337,
Tarsius syrichta	ENSTSYG00000006777	1 retrocopy	retro_tsyr_746,
Vicugna pacos	ENSVPAG00000009523	1 retrocopy	retro_vpac_2,