RetrogeneDB ID: retro_chof_1738

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_371878:447..843(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000010042
• Aliases: None
• Description: None

Sequence

>retro_chof_1738
ATGTTGGTCCCCTGCAAGGAGTTGGTCGCCGACCTTGCGGGCTTCACCCATCTGATGGGGTATCTGTTGGAAATTGACCA
CCTTGCAATAGATCTAATTATTTCCACACTGAATATATCTAAGATTCATTACTTCTGTACCAGTTGTCTTGTGCGGATGG
TTGGAAACAATCCATATGCAACTGCAGAAGAAAATTCAGCAGAGCTCAGTACAGATGCCGAAGTTTATTCATTGCCTTCA
AAGAAACTAGTGATTCTTCAGTTAAGATCCATTTTTATTAAGTATAAATCCAAGCCATTCTGTGAAAAACTGCTTTCCTG
GGTAAGAAGTGCTGACTGTGCCAGAGTTGTTCTTTCAAGCAGTCATTCATATCACAGCAATGATCTCCAGCATCGA

Alignment

ORF - retro_chof_1738 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.74 %
• Parental protein coverage: 51.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MFVPCGESVPDLAGFTLLMPAVSVGNVGQLAIDLIISTLNMSKIGYFYTDCLVPMVGNNPYATAEENSAE
          M.VPC.E.V.DLAGFT.LM..........LAIDLIISTLN.SKI.YF.T.CLV.MVGNNPYATAEENSAE
Retrocopy MLVPCKELVADLAGFTHLMGYLL--EIDHLAIDLIISTLNISKIHYFCTSCLVRMVGNNPYATAEENSAE

Parental  LSTNAEVYSLPSQKLVALQLRSIFIKYKSKPFCEKLLSWVRSADCARVVVLSSSHSYHRNDLQLR
          LST.AEVYSLPS.KLV.LQLRSIFIKYKSKPFCEKLLSWVRSADCARVV.LSSSHSYH.NDLQ.R
Retrocopy LSTDAEVYSLPSKKLVILQLRSIFIKYKSKPFCEKLLSWVRSADCARVV-LSSSHSYHSNDLQHR

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_1738 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018855	1 retrocopy	retro_cfam_424,
Choloepus hoffmanni	ENSCHOG00000010042	1 retrocopy	retro_chof_1738 ,
Myotis lucifugus	ENSMLUG00000017744	1 retrocopy	retro_mluc_2496,
Macaca mulatta	ENSMMUG00000021855	1 retrocopy	retro_mmul_198,
Nomascus leucogenys	ENSNLEG00000009063	1 retrocopy	retro_nleu_1753,
Oryctolagus cuniculus	ENSOCUG00000005086	1 retrocopy	retro_ocun_1448,
Sus scrofa	ENSSSCG00000021827	2 retrocopies	retro_sscr_1008, retro_sscr_763,