RetrogeneDB ID: retro_chof_1445

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_295620:275..858(+)
• 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_1445
TGTGGACAAGAAAAAATGGAATTAAAACCACGTCATGAATCTAATATTAAAAAGTTAGCAAATCCTGTTTTGCAGGATCA
ACTGCAAGAGGTGCACAAGGTTCAGTCAAATGATGACACTGATTTGGGTATAAATGATCATGCACTACCTGGAATTATGC
CGGAATTAGCTGATAATGCTTCCCATAAGAATGAAGAGCCTTCAAGCAATCATATTCCTTGTGGAAAGAATAAATCAAAT
GAGGTGATGATGCAGAGATGCCTGAGATCAAGAGAATGACCTTGCAAAAGTTGAAGATCTTCCCACTTCTTTAAAGAAGC
CCCCCCTTTCAGTTTCTAAACATGAAAGTCATCAAGCAATCTCTCATCTTCCAACTGGAAAATCTCTCTCCTCAGATATG
GCTCCAGGTTCACAAATGAACCACAATCAAAATCCTGGTACTTCAAAACAGATATGATCTAATTCCCTTCAGCGTTTAAT
TCCAGGCTCAAATTTGGAAAGTGAACCCAGAGTTCAAACAGATATGCTAAAGCAGGATACCAAGGATAGAGTTGGTGATT
TCCATAAATTCAAGCAAAGTAAG

Alignment

ORF - retro_chof_1445 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.63 %
• Parental protein coverage: 64.14 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CGQQIKELRTQHEENIKKLADQFVQEQKQEMHKVQSNDDKDLGINDHAVPKNIPKVAENAADKNEEPSSN
          CGQ...EL...HE.NIKKLA....Q.Q.QE.HKVQSNDD.DLGINDHA.P...P..A.NA..KNEEPSSN
Retrocopy CGQEKMELKPRHESNIKKLANPVLQDQLQEVHKVQSNDDTDLGINDHALPGIMPELADNASHKNEEPSSN

Parental  HILHGK-EHIKRGGDAGMPGI-EENDLAKAEDLPTSLKKPPLSVSKHGSHQAISRLATGQPLSPNMAPDS
          HI..GK.E.IK.G.DA.MP.I..ENDLAK.EDLPTSLKKPPLSVSKH.SHQAIS.L.TG..LS..MAP.S
Retrocopy HIPCGK<E*IK*GDDAEMPEI<QENDLAKVEDLPTSLKKPPLSVSKHESHQAISHLPTGKSLSSDMAPGS

Parental  QMNHNRNPGTSKQISSNSLQRLIPGPNLESEPRVQTDMLKQDTKDRVGDFHKLKQSR
          QMNHN.NPGTSKQI.SNSLQRLIPG.NLESEPRVQTDMLKQDTKDRVGDFHK.KQS.
Retrocopy QMNHNQNPGTSKQI*SNSLQRLIPGSNLESEPRVQTDMLKQDTKDRVGDFHKFKQSK

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_1445 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,