RetrogeneDB ID: retro_chof_73

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_1287:120928..121225(-)
• Located in intron of: ENSCHOG00000000284

Retrocopy information

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

Parental gene information

• Parental gene symbol: C3orf14
• Ensembl ID: ENSCHOG00000004965
• Aliases: None
• Description: chromosome 3 open reading frame 14 [Source:HGNC Symbol;Acc:25024]

Sequence

>retro_chof_73
GTGACTTCCTTGTTTGCACAAGAAATTCACCTATCTAAAGGACATGAAGAAATAGTATCACAAAGATTAATGTTACTTCA
ACAAAAGGACAGTAGATTTGGAGATCAAAACATGGAAAAGGCATCTCAGATGCAAGCAGCTAACACTTGCTTATAAAACG
AATCTTAGTCTCTTAAATTATATAGGAGCAGCAGAGAAGTCTCTACAAACCAGGATTCATCCACATCTCAGCCTGGGGTG
GTTTCTCTCGAGACTCCTTACTGGGCATCGGTAGAAGAATATATTCCCAAATGGAAA

Alignment

ORF - retro_chof_73 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.22 %
• Parental protein coverage: 76.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MTSLFAQEIRLSKRHEEIVSQRLMLLQQMDNRFGDQNLDKASQMQAAKT-AYKRNVSLLKDIEAAAKSLQ
          .TSLFAQEI.LSK.HEEIVSQRLMLLQQ.D.RFGDQN..KASQMQAA.T.AYK.N.SLL..I.AA.KSLQ
Retrocopy VTSLFAQEIHLSKGHEEIVSQRLMLLQQKDSRFGDQNMEKASQMQAANT>AYKTNLSLLNYIGAAEKSLQ

Parental  TRIHP-LSQPEVVSLETHY-ASV-EYIPKWE
          TRIHP..SQP.VVSLET.Y.ASV.EYIPKW.
Retrocopy TRIHP<TSQPGVVSLETPYWASVEEYIPKWK

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_73 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 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015374	1 retrocopy	retro_amel_1312,
Canis familiaris	ENSCAFG00000007123	1 retrocopy	retro_cfam_1485,
Choloepus hoffmanni	ENSCHOG00000004965	7 retrocopies	retro_chof_138, retro_chof_2082, retro_chof_423, retro_chof_536, retro_chof_659, retro_chof_73 , retro_chof_96,
Erinaceus europaeus	ENSEEUG00000000474	1 retrocopy	retro_eeur_656,
Felis catus	ENSFCAG00000027983	1 retrocopy	retro_fcat_577,
Macropus eugenii	ENSMEUG00000013085	2 retrocopies	retro_meug_1990, retro_meug_2091,
Microcebus murinus	ENSMICG00000016406	1 retrocopy	retro_mmur_461,
Mustela putorius furo	ENSMPUG00000016914	1 retrocopy	retro_mputfur_751,
Mus musculus	ENSMUSG00000033111	1 retrocopy	retro_mmus_1255,
Otolemur garnettii	ENSOGAG00000008107	2 retrocopies	retro_ogar_484, retro_ogar_485,
Tupaia belangeri	ENSTBEG00000017312	1 retrocopy	retro_tbel_1713,