RetrogeneDB ID: retro_chof_2664

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_95325:2476..2867(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL48
• Ensembl ID: ENSCHOG00000003662
• Aliases: None
• Description: mitochondrial ribosomal protein L48 [Source:HGNC Symbol;Acc:16653]

Sequence

>retro_chof_2664
CTAAGGTTCAAAACTTCAGGAGAGAATCCCATCAGTTCTTCATAGGGCATTCTCCTGAGCACCAGTCAGCACTCTGAGAC
AAACCCACCCACGGCAACAGAAGATACAAGAGCCTAACTACAGCACAAGAGCCCAGAAGAAGAGGGGAAAAGTGGAAGCG
AGATCCGTTAATCTGGAGACAGATTACGAATATGGGGTTTTAAACATTCACCTGACAGCACATGACATGGCCCCATCAGA
GAGTTATGCCCAATATGCTCACAACCTCTGCAACGATCTCTCCACTAGAGTTGAGGAAAGTCGCACGAGGCCCATCAAAA
CCATGGAGGTGCTGCGGCTGCAGGACTAAGGCAGAAAAACATTCCTGGGCTCAGGCCTTACCACCCATGAG

Alignment

ORF - retro_chof_2664 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.93 %
• Parental protein coverage: 68.95 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LIFRTSGENPICSSGGILLSISRQYKT-KPTHGIGRYKYLITAQEPK-KKRGKVEVRPINLGTDYEYGVL
          L.F.TSGENPI.SS.GILLS.S....T.KPTHG..RYK.L.TAQEP..KKRGKVE.R..NL.TDYEYGVL
Retrocopy LRFKTSGENPISSS*GILLSTSQHSET<KPTHGNRRYKSLTTAQEPR<KKRGKVEARSVNLETDYEYGVL

Parental  NVHLTAYDMALAESYAQYVHNLCNDLSIKVEESYAMPTKTMEVLQLQDQGRKMFLDSVLTTHE
          N.HLTA.DMA..ESYAQY.HNLCNDLS..VEES...P.KTMEVL.LQD.GRK.FL.S.LTTHE
Retrocopy NIHLTAHDMAPSESYAQYAHNLCNDLSTRVEESRTRPIKTMEVLRLQD*GRKTFLGSGLTTHE

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_2664 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005585	1 retrocopy	retro_cfam_1437,
Choloepus hoffmanni	ENSCHOG00000003662	1 retrocopy	retro_chof_2664 ,
Mustela putorius furo	ENSMPUG00000009716	1 retrocopy	retro_mputfur_38,
Oryctolagus cuniculus	ENSOCUG00000009302	1 retrocopy	retro_ocun_39,
Otolemur garnettii	ENSOGAG00000004771	1 retrocopy	retro_ogar_234,