RetrogeneDB ID: retro_chof_123

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_2630:16061..16616(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000013897
• Aliases: None
• Description: None

Sequence

>retro_chof_123
ATGTCTCCCAGCCTTCAGGAAGGTGCTTAGCTTGGGGAAAGCAAACCCTCACCCTGCTCCTTTTCCATTGATAGCATCTT
AGGACGGGACCAGAAGCAAGACTGTGGCCCATCAATGAAACCTCACAGGCCCTGGGCAGACACCTGTGGCTCCTCAGGGA
AAGATGGAATCCTACACCTACATGTCCCCAGTCTTCCCAGTGGGATCTCATTCCCTTGTACTGTGGATCACCCAATGCTG
GAAGAAAGAGTTCTGAAACATGAAAATTACTTTTCGCTGTCAGAAAAACTGTTTTTGAAAAGAGAGTTGAGTTGGTATAG
AGGCTGAAGACCAAGAACTGCTTTTACTCAAAACCAGATTGACGTTTTGGAAAAGGTCTTTAGCGTAAACTGCTATCCTG
GCATCGATATTAGAGAAGACTTGGCCCGAAAACTGAATCTAGAGGAAGACAGAATCCAGATCTGGTTCCAAAATCGGAGT
GCAAAGCTGAAAAGGTCCCATAGAGAATCACAGTTTCTAACGGCAAAAAAAAATTTCAATACAAATCTCCTGGAA

Alignment

ORF - retro_chof_123 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.43 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSPSLQEGAQLGESKPSPCSFSIDSILGRDQKQDCGPSMKPHRPWADTCGSSGKDGILHLHVPGLPSGIS
          MSPSLQEGA.LGESKPSPCSFSIDSILGRDQKQDCGPSMKPHRPWADTCGSSGKDGILHLHVP.LPSGIS
Retrocopy MSPSLQEGA*LGESKPSPCSFSIDSILGRDQKQDCGPSMKPHRPWADTCGSSGKDGILHLHVPSLPSGIS

Parental  FPCTVDHPMLEERVLKHENYFSPSEKLSSKRELSWYRGRRPRTAFTQNQIEVLEKVFSVNCYPGIDIRED
          FPCTVDHPMLEERVLKHENYFS.SEKL..KRELSWYRG.RPRTAFTQNQI.VLEKVFSVNCYPGIDIRED
Retrocopy FPCTVDHPMLEERVLKHENYFSLSEKLFLKRELSWYRG*RPRTAFTQNQIDVLEKVFSVNCYPGIDIRED

Parental  LARKLNLEEDRIQIWFQNRRAKLKRSHRESQLLMAKKNFNTNLLE
          LARKLNLEEDRIQIWFQNR.AKLKRSHRESQ.L.....FNTNLLE
Retrocopy LARKLNLEEDRIQIWFQNRSAKLKRSHRESQFLTXXXXFNTNLLE

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_123 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
Ailuropoda melanoleuca	ENSAMEG00000011722	1 retrocopy	retro_amel_862,
Canis familiaris	ENSCAFG00000007995	2 retrocopies	retro_cfam_1907, retro_cfam_954,
Choloepus hoffmanni	ENSCHOG00000013897	1 retrocopy	retro_chof_123 ,
Callithrix jacchus	ENSCJAG00000010981	1 retrocopy	retro_cjac_891,
Cavia porcellus	ENSCPOG00000012741	1 retrocopy	retro_cpor_1067,
Dasypus novemcinctus	ENSDNOG00000003677	1 retrocopy	retro_dnov_58,
Mustela putorius furo	ENSMPUG00000016854	2 retrocopies	retro_mputfur_112, retro_mputfur_174,
Tupaia belangeri	ENSTBEG00000017505	1 retrocopy	retro_tbel_339,