RetrogeneDB ID: retro_chof_457

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_111297:914..1407(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RHOQ
• Ensembl ID: ENSCHOG00000000549
• Aliases: None
• Description: ras homolog family member Q [Source:HGNC Symbol;Acc:17736]

Sequence

>retro_chof_457
GCGGGCGGGCCCGGCGCACTGATGCTCACGGGCGTGGTGGTCGGCCTCGGGGTGGTGGGCAGCCCGCGCCTGCTCGCGAG
GGGCGCCGAGGACCCTTCCCCGAGGAGGACGTGCCCGCCTCTGCGACCACCACGCGGTTGGCGTCCCCGTGGGGCAAGGG
CACCTCGTGGACTCGGTGACGCGGGGGGACAGGAGACTTGCCCGCCCGAGGCCATCATCCCATCCCATGGCTGATCTCTT
CCTTACAAGCCTCTCTGCAGTAACTCCAGCCTCATCCAAAACGTGAAAGAGGAGGGGGTACCAGAACCTAAGGAATGTCC
ACCAAATGTACCTGTTATTAATAGGAACTCAGATTCATCTCCCAGATGACCCCAAAACTTGAGCAAGACTGACTGACATG
AAAGAAAAACCTGTATGTGTGGAACAAGGACAGAAACTAGAGGTAGGAGCTTGCTGCCACGTGGAATGTTCAGCTTCAAC
CCGGAAGAGACTA

Alignment

ORF - retro_chof_457 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.65 %
• Parental protein coverage: 82.93 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AHGPGALMLKCVVVGDGAVGKTCLLMSYANDA-FPEEYVPT-VFDHYAVSVTVGGKQYLLGLYDTAGQED
          A.GPGALML..VVVG.G.VG...LL...A.D..FPEE.VP....DH.AV.V.V.G...L.....T.G...
Retrocopy AGGPGALMLTGVVVGLGVVGSPRLLARGAEDP<FPEEDVPA<LCDHHAVGVPV-GQGHLVDSV-TRGDRR

Parental  YDRLRPLSYPMTDVFLICFSVVNPASFQNVKEEWVPELKEYAPNVPFLLIGTQIDLRDDPKTLARLNDMK
          ..R.RP.S.PM.D.FL...S.V.PAS....K......L.........LLIGTQI.L.DDPKT.ARL.DMK
Retrocopy LARPRPSSHPMADLFLTSLSAVTPASSKT*KRRGYQNLRN-VHQMYLLLIGTQIHLPDDPKT*ARLTDMK

Parental  EKPICVEQGQKLAKEIGACCYVECSALTQKGL
          EKP.CVEQGQKL..E.GACC.VECSA.T.K.L
Retrocopy EKPVCVEQGQKL--EVGACCHVECSASTRKRL

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_457 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 18 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006082	1 retrocopy	retro_amel_383,
Choloepus hoffmanni	ENSCHOG00000000549	3 retrocopies	retro_chof_2030, retro_chof_457 , retro_chof_914,
Choloepus hoffmanni	ENSCHOG00000005306	10 retrocopies	retro_chof_103, retro_chof_1044, retro_chof_1195, retro_chof_1853, retro_chof_2055, retro_chof_2105, retro_chof_2331, retro_chof_2407, retro_chof_50, retro_chof_800,
Callithrix jacchus	ENSCJAG00000000685	1 retrocopy	retro_cjac_2403,
Erinaceus europaeus	ENSEEUG00000015226	1 retrocopy	retro_eeur_129,
Echinops telfairi	ENSETEG00000019234	3 retrocopies	retro_etel_1468, retro_etel_596, retro_etel_672,
Felis catus	ENSFCAG00000015608	1 retrocopy	retro_fcat_795,
Homo sapiens	ENSG00000119729	3 retrocopies	retro_hsap_1333, retro_hsap_2158, retro_hsap_2316,
Loxodonta africana	ENSLAFG00000004327	1 retrocopy	retro_lafr_316,
Microcebus murinus	ENSMICG00000009124	1 retrocopy	retro_mmur_29,
Myotis lucifugus	ENSMLUG00000001567	1 retrocopy	retro_mluc_595,
Otolemur garnettii	ENSOGAG00000033272	1 retrocopy	retro_ogar_742,
Pongo abelii	ENSPPYG00000012439	2 retrocopies	retro_pabe_1107, retro_pabe_2195,
Pteropus vampyrus	ENSPVAG00000013691	1 retrocopy	retro_pvam_611,
Rattus norvegicus	ENSRNOG00000015415	1 retrocopy	retro_rnor_473,
Sus scrofa	ENSSSCG00000008439	1 retrocopy	retro_sscr_102,
Tarsius syrichta	ENSTSYG00000002837	1 retrocopy	retro_tsyr_1609,
Tursiops truncatus	ENSTTRG00000011892	1 retrocopy	retro_ttru_805,