RetrogeneDB ID: retro_chof_2453

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_77296:4264..5007(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CASC4
• Ensembl ID: ENSCHOG00000006998
• Aliases: None
• Description: cancer susceptibility candidate 4 [Source:HGNC Symbol;Acc:24892]

Sequence

>retro_chof_2453
GTTAAACTACACAACAACATATTATATCAAATGGCAGACATACGTCATTTAAAGGAGAAACTTGCCGAGCTTCGTCAGGA
GTTTCTTCAAGAAGATGAGCTTCATGACAACAGGAAAAATAACACTTAACTCCTGAAGAGGTTAGAATATGAGAGTTTTC
ATTGTGGACAAGACATAAAGGAATTAAGAACACAGCATGAAGCAAATATTAAAAAGTTAGCAGATCAGATTTTGCAGGAA
CAAAAACAAGAGGTACACAAGGTGCAATCAAATGATGGCAATGATTTGGGTATAAATGATCATGCAGTACCTAAAAATAT
TCCAGAAATAGCTGAGAATGCTTCAGATAAGAATGAAGAGCCTTCAAGCAATCATATTCCATGTGGGAAAGAACAAATCA
AATGAGGTGATGATGCAGAGATACCTGGGATAGAAGAGAATGACCTTGCAAAAGTTGAAGATCTTCACACTTCTTTAAAG
AAGCCCTCCTTCCAGTTTCTAAACATGAAAGTCATCAAGCAATCTCTCATCTTCCAACTGGAAAAGCTCTCTCCTCAGAT
ATGGCTCCAGGTTCACAAATGAACCACAATCGAAATCCTGGTACTTCAAAACAGATATCATCTAATTCCCTTCAGCATTT
AATTCCAGGCTCAAACTTGGAAAGTGAACCCAGAGTTCAAATAGATATGCTAAAGCAGGATACCAAGGATAGAGATGATT
TCCATAAATTTTAGCAAAGTAAG

Alignment

ORF - retro_chof_2453 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.29 %
• Parental protein coverage: 82.24 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VKLQNNISYQMADIHHLKEQLAELRQEFLRQEDQLQDYRKNNTYXXXXXXXXXFQCGQQIKELRTQHEEN
          VKL.NNI.YQMADI.HLKE.LAELRQEFL.QED.L.D.RKNNT..........F.CGQ.IKELRTQHE.N
Retrocopy VKLHNNILYQMADIRHLKEKLAELRQEFL-QEDELHDNRKNNT*LLKRLEYESFHCGQDIKELRTQHEAN

Parental  IKKLADQFVQEQKQEMHKVQSNDDKDLGINDHAVPKNIPKVAENAADKNEEPSSNHILHGKEHIKRGGDA
          IKKLADQ..QEQKQE.HKVQSND..DLGINDHAVPKNIP..AENA.DKNEEPSSNHI..GKE.IK.G.DA
Retrocopy IKKLADQILQEQKQEVHKVQSNDGNDLGINDHAVPKNIPEIAENASDKNEEPSSNHIPCGKEQIK*GDDA

Parental  GMPGIEENDLAKAEDLPTSLKKPP-LSVSKHGSHQAISRLATGQPLSPNMAPDSQMNHNRNPGTSKQISS
          ..PGIEENDLAK.EDL.TSLKKP..L.VSKH.SHQAIS.L.TG..LS..MAP.SQMNHNRNPGTSKQISS
Retrocopy EIPGIEENDLAKVEDLHTSLKKPS<LPVSKHESHQAISHLPTGKALSSDMAPGSQMNHNRNPGTSKQISS

Parental  NSLQRLIPGPNLESEPRVQTDMLKQDTKDRVGDFHKLKQSR
          NSLQ.LIPG.NLESEPRVQ.DMLKQDTKDR..DFHK..QS.
Retrocopy NSLQHLIPGSNLESEPRVQIDMLKQDTKDR-DDFHKF*QSK

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_2453 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006998	4 retrocopies	retro_chof_1422, retro_chof_1445, retro_chof_2453 , retro_chof_627,
Homo sapiens	ENSG00000166734	1 retrocopy	retro_hsap_1238,
Nomascus leucogenys	ENSNLEG00000005533	1 retrocopy	retro_nleu_2857,
Oryctolagus cuniculus	ENSOCUG00000005362	1 retrocopy	retro_ocun_1472,
Pongo abelii	ENSPPYG00000006428	1 retrocopy	retro_pabe_1083,
Pan troglodytes	ENSPTRG00000007010	1 retrocopy	retro_ptro_852,