RetrogeneDB ID: retro_chof_2136

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_52531:336..827(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HDHD1
• Ensembl ID: ENSCHOG00000001318
• Aliases: None
• Description: haloacid dehalogenase-like hydrolase domain containing 1 [Source:HGNC Symbol;Acc:16818]

Sequence

>retro_chof_2136
ACTGAATGGCTGTATTCCAGTAGTGTTTCAAGAAGTATGTGGTCGCTATGAGGAGAAATACACCTGGGATGTAAAATCCC
TGGTGATGGGGAAAACTGCATTAGAAAAGGCACAAGGTGGTAATCGAGGTCTTGCAGCTTCCAGTGACTAAAGTGGAGCT
GATGGAAGAAAACCAAATGAAGTTCAAACCACTGGTCCCCACAGCTGCCTTGTGCCAGGTGTCAAAAAACTGATTCACCA
CATATGAAAACACAACATTCATTTTGTTCTTGCTACCAGCTCAGGGCCTGCATCTTTTGAAATGAAAACAAGTAGACACA
AAGAGTTTTTCAGTTTGTTTCACCATTTCGTTTTGGGAGATGATACTGAAGTGATGACTGACAAACCCGATCCTGCCATA
TTTCTAGCTTGCGCAAAGAGATTTTCTTCTTTGCTTCCGTGGAAAAATGCCTTGTATTTGAAGATGCCCCAATGGGATGG
AGGCGGCCCTG

Alignment

ORF - retro_chof_2136 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.51 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  TERLYS-VVFQEICGRYDKQYTWDVKSLVMGKTALEAAQ-VIIEVLQLPVTKEELVEESQTKLKQLFPTA
          TE.LYS.VVFQE.CGRY...YTWDVKSLVMGKTALE.AQ.V.IEVLQLPVTK.EL.EE.Q.K.K.L.PTA
Retrocopy TEWLYS>VVFQEVCGRYEEKYTWDVKSLVMGKTALEKAQ>VVIEVLQLPVTKVELMEENQMKFKPLVPTA

Parental  A-LLPGVEKLIHHLRKYNIPFALATSSGSASFEMKTSSHKEFFSLFHHIVLGDDPEVTSGKPDPAIFLTC
          A.L.PGV.KLIHH..K.NI.F.LATSSG.ASFEMKTS.HKEFFSLFHH.VLGDD.EV...KPDPAIFL.C
Retrocopy A<LVPGVKKLIHHI*KHNIHFVLATSSGPASFEMKTSRHKEFFSLFHHFVLGDDTEVMTDKPDPAIFLAC

Parental  AKRFSPSAP-VEKCLVFEDA-PNGVEAAL
          AKRFS...P.VEKCLVFEDA.PNG.EAAL
Retrocopy AKRFSSLLP<VEKCLVFEDA<PNGMEAAL

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_2136 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 10 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000004616	1 retrocopy	retro_acar_48,
Choloepus hoffmanni	ENSCHOG00000001318	5 retrocopies	retro_chof_1597, retro_chof_1855, retro_chof_1883, retro_chof_2136 , retro_chof_2168,
Homo sapiens	ENSG00000130021	2 retrocopies	retro_hsap_2469, retro_hsap_454,
Gorilla gorilla	ENSGGOG00000004425	1 retrocopy	retro_ggor_1537,
Microcebus murinus	ENSMICG00000017082	1 retrocopy	retro_mmur_1321,
Macaca mulatta	ENSMMUG00000017377	1 retrocopy	retro_mmul_244,
Monodelphis domestica	ENSMODG00000017505	2 retrocopies	retro_mdom_1374, retro_mdom_52,
Pongo abelii	ENSPPYG00000020105	2 retrocopies	retro_pabe_1837, retro_pabe_280,
Pteropus vampyrus	ENSPVAG00000011149	1 retrocopy	retro_pvam_1165,
Tarsius syrichta	ENSTSYG00000013238	4 retrocopies	retro_tsyr_2013, retro_tsyr_345, retro_tsyr_542, retro_tsyr_931,