RetrogeneDB ID: retro_chof_1851

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_40340:10593..11288(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RABGGTB
• Ensembl ID: ENSCHOG00000009456
• Aliases: None
• Description: Rab geranylgeranyltransferase, beta subunit [Source:HGNC Symbol;Acc:9796]

Sequence

>retro_chof_1851
ATGGGCACACCACAGAAGGATGTTATCAAGCCAGATGCACCTGATACCCTATTAGTAGAGAAACATTCAGGTTATATTGC
ATCCTATGGTTCAGAGAAAGATGAATATGAATACCGTATCTCTGTATAATTGAGAATGAGTGGCCTCTATTGGGGTCTCA
CATAATGGATCTCATGGAACAACTTCATTGCATGAATAGAGAGGAAATTCTAACATTCATTCAGTCATGCCATGAGTGTG
GTGGAATAGGTGCAAATATTGGAAATGATACTCATCTTTTGTACACTCTTGGTGCTGCCCAGATTCTTACATTGTATGAT
AGTATTAATGTTATTGGCAAAAAGAAAGTGTGTAATGTGTTCAAAGTCTACAGAGATAAGATGGGTCTTTTGCAGGAGAC
ATTTCTGGAGAAATTGACACAAGATTTTTTTTCTGTGTAGTGGCAGCTCTGGCTCTATTAGGGAAACTGGAAGCTATTAA
TGTGGAAAAAGCAATTGATTTGCTTTGTCCTGTATGAACTTTGATAGTGGATTTGGTTGAAGTCCAGGTTCTGTATCCCA
TGTTGGGCAGATGTACTATTGCACAGGATTCTTGGCTATTACTAGTCAATTGCATCAAGTAAATTCTGATTTACTGGGTT
GGTGGCTTTATGAACTACAATTAGCATCAGGGGACCCAATGAAAGGCCAGAGAAG

Alignment

ORF - retro_chof_1851 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.41 %
• Parental protein coverage: 71.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MGTPQKDVVIKPDAPGTLLVEKHADYIASYGSKKDDYEYCMSEYLRMSGIYWGLT-VMDLMGQLHRMNRE
          MGTPQKDV.IKPDAP.TLLVEKH..YIASYGS.KD.YEY..S..LRMSG.YWGLT..MDLM.QLH.MNRE
Retrocopy MGTPQKDV-IKPDAPDTLLVEKHSGYIASYGSEKDEYEYRISV*LRMSGLYWGLT<IMDLMEQLHCMNRE

Parental  EILTFIKSCQHECGGISASIGHDPHLLYTLSAVQILTLYDSINVIDVNKVVEY-VQSLQKEDGSFAGDIW
          EILTFI.SC.HECGGI.A.IG.D.HLLYTL.A.QILTLYDSINVI...KV....VQSLQ..DGSFAGDI.
Retrocopy EILTFIQSC-HECGGIGANIGNDTHLLYTLGAAQILTLYDSINVIGKKKVCNV<VQSLQR*DGSFAGDIS

Parental  GEIDTRFSFCAVATLALLGKLDAINVEKAID-FVLSCMNFDGGFGCRPGSESHAGQIYCCTGFLAITSQL
          GEIDTR...C.VA.LALLGKL.AINVEKAID.F.LSCMNFD.GFG..PGS.SH.GQ.Y.CTGFLAITSQL
Retrocopy GEIDTRXXXCVVAALALLGKLEAINVEKAID<FALSCMNFDSGFG*SPGSVSHVGQMYYCTGFLAITSQL

Parental  HQVNSDLLGWWLCERQLPSG-GLNGRPEK
          HQVNSDLLGWWL.E.QL.SG.G.N.RPEK
Retrocopy HQVNSDLLGWWLYELQLASG<GPNERPEK

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_1851 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000011052	1 retrocopy	retro_acar_155,
Canis familiaris	ENSCAFG00000020392	1 retrocopy	retro_cfam_2104,
Choloepus hoffmanni	ENSCHOG00000009456	2 retrocopies	retro_chof_1851 , retro_chof_260,
Mus musculus	ENSMUSG00000038975	1 retrocopy	retro_mmus_1030,
Otolemur garnettii	ENSOGAG00000007665	1 retrocopy	retro_ogar_1089,
Sorex araneus	ENSSARG00000007392	1 retrocopy	retro_sara_207,
Ictidomys tridecemlineatus	ENSSTOG00000021824	1 retrocopy	retro_itri_484,
Tursiops truncatus	ENSTTRG00000014126	3 retrocopies	retro_ttru_1391, retro_ttru_1767, retro_ttru_214,