RetrogeneDB ID: retro_chof_2460

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_78025:3574..3970(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000007947
• Aliases: None
• Description: None

Sequence

>retro_chof_2460
GAGAGTTTCAAGTGGTTTGATAAATCAAATATGACATTTGTTAAGTGGACAGACCAAGATGGTGAGACTCTAGTCGACAC
CTGTGTTTTTCTGCACATGAAGACAGGTGAATAGAAAAAAGGAAACTGTGAACTTTCTTCTGTGGAAGGAACCCTTTGTA
AAGCAGTTACTCTATATCAAAAGAAATATTTATCAGACAGCCACATTTTAATAACAGCTTTGGTGATCTCTAGTACTGTA
ATCTTGACAGTTTGGGGAGCAATGATTTGGTTCCTGTACAAAAGAAATTCAGATTCTGGTTTCATCACAGTTTTTTCAGC
TGCACATCAATCACCTTATAAGGACAACTGTGTCTGGGTAGTTGCAAAAGCAAATGAATATGCTATTCAATTTGAT

Alignment

ORF - retro_chof_2460 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.58 %
• Parental protein coverage: 57.14 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ESFKWSDKSNMTFVKWADQDGETLVDTCAFLQMKTGEWKKGNCELSSVEGTLCKAVIPYQKKYLSDNHIL
          ESFKW.DKSNMTFVKW.DQDGETLVDTC.FL.MKTGE.KKGNCELSSVEGTLCKAV..YQKKYLSD.HIL
Retrocopy ESFKWFDKSNMTFVKWTDQDGETLVDTCVFLHMKTGE*KKGNCELSSVEGTLCKAVTLYQKKYLSDSHIL

Parental  ISALVIASTLILTVLGAVIWFLYKRSADSGFTTVFSAAPQSPYNDDCVLVVAEENEYAVQFD
          I.ALVI.ST.ILTV.GA.IWFLYKR..DSGF.TVFSAA.QSPY.D.CV.VVA..NEYA.QFD
Retrocopy ITALVISSTVILTVWGAMIWFLYKRNSDSGFITVFSAAHQSPYKDNCVWVVAKANEYAIQFD

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_2460 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007947	2 retrocopies	retro_chof_224, retro_chof_2460 ,
Oryctolagus cuniculus	ENSOCUG00000016361	1 retrocopy	retro_ocun_927,
Tarsius syrichta	ENSTSYG00000002564	1 retrocopy	retro_tsyr_71,