RetrogeneDB ID: retro_chof_1467

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_301020:806..1256(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM3C
• Ensembl ID: ENSCHOG00000003224
• Aliases: None
• Description: family with sequence similarity 3, member C [Source:HGNC Symbol;Acc:18664]

Sequence

>retro_chof_1467
AAAATTTGCCTAGAAGCAGCCAACGTGGTTGGGACCACTCTTTTCTTAATGACTGGTGTTGAGAATAATGTTGGAAGAGG
GATCATTGTTACCTGGGCAAATGGGAAAAGAGAAGTATTAGACAATAAATACTTTGGCATATGGGGAGGAGATGTAGAAC
CATTTATTGAGTTTCTGATGTCCATACAAGATGGTACAATTGTCTTAATGGGAACATACGATGATGGAGCAACTAAACTC
AATGATGAGGCGCAGCAGCTCGTTGCTGAATTCGGGAGTACGTATATTACTAATCTTGGTTCCAGAGACAGCTGGATCTT
CTGTAGTAGAAAAGGCATTAAGACAAACAGCCCTTTTGAACAGCACATAAAGAACAATAAGGATGCAAATTAGTGTGAAG
GATGGCCTAAAGTCATAGAATTGGAAGCATTCATCCCCCAGAAGCAAGAC

Alignment

ORF - retro_chof_1467 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.93 %
• Parental protein coverage: 68.3 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KMASGAANVVGPKICLELMSGVKNNVGRGINVALANGKTGEVLDTKYFDMWGGDVAPFIEFLKSIHDGSV
          K....AANVVG....L.LM.GV.NNVGRGI.V..ANGK..EVLD.KYF..WGGDV.PFIEFL.SI.DG..
Retrocopy KICLEAANVVGTT--LFLMTGVENNVGRGIIVTWANGKR-EVLDNKYFGIWGGDVEPFIEFLMSIQDGTI

Parental  VLMATYDDGATKLNDEARRLIADLGSTSIVNLGFRDNWVFCGGKGIKTKSPFEQHIKNNKDTNKYEGWPE
          VLM.TYDDGATKLNDEA..L.A..GST.I.NLG.RD.W.FC..KGIKT.SPFEQHIKNNKD.N..EGWP.
Retrocopy VLMGTYDDGATKLNDEAQQLVAEFGSTYITNLGSRDSWIFCSRKGIKTNSPFEQHIKNNKDAN*CEGWPK

Parental  VVEMEGCIPQKQD
          V.E.E..IPQKQD
Retrocopy VIELEAFIPQKQD

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_1467 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003224	1 retrocopy	retro_chof_1467 ,
Felis catus	ENSFCAG00000023087	1 retrocopy	retro_fcat_1392,
Homo sapiens	ENSG00000196937	1 retrocopy	retro_hsap_4657,
Loxodonta africana	ENSLAFG00000010029	1 retrocopy	retro_lafr_1169,
Macropus eugenii	ENSMEUG00000006906	2 retrocopies	retro_meug_2057, retro_meug_536,
Monodelphis domestica	ENSMODG00000015478	1 retrocopy	retro_mdom_1392,
Sarcophilus harrisii	ENSSHAG00000015103	1 retrocopy	retro_shar_6,
Tursiops truncatus	ENSTTRG00000016229	2 retrocopies	retro_ttru_1219, retro_ttru_855,