RetrogeneDB ID: retro_chof_2320

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_65810:1340..1672(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000013877
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LAPTM4A
• Ensembl ID: ENSCHOG00000011200
• Aliases: None
• Description: lysosomal protein transmembrane 4 alpha [Source:HGNC Symbol;Acc:6924]

Sequence

>retro_chof_2320
CTCAGTTGCCTGGTTGCTATCAGCACTCTCACTTATTTGCCAAGAATCCAAGAATATCTGGATCAATTACCTGATTTTCC
CCACAAAGATGGCCTTCTGGCATTGGACTCCATCTGCCTTTTCTTCATTGTTGTTGTATGCTTTGCCTTATTCATTGTGT
TTAAGGCTTATCTAATAAACTATGTTTGGAACGGCTATAAATATATTAACAACAGAAGTGTGCTGGAGATTGCTGTGTAC
CCTGCCTTTGAAGCATCTCCAAGTATGTTTTGCGAACCAATGAAATGGCAATGAAGATGCCTGAAAAAGAACCATCGGCT
CCTTACATACCT

Alignment

ORF - retro_chof_2320 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.68 %
• Parental protein coverage: 56.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LSCLVAISSLTYLPRIKEYLDQLPDFPYKDDLLALDSSCLLFIVLLFFVLFILFKAYLINCVWNCYKYIN
          LSCLVAIS.LTYLPRI.EYLDQLPDFP.KD.LLALDS.CL.FIV...F.LFI.FKAYLIN.VWN.YKYIN
Retrocopy LSCLVAISTLTYLPRIQEYLDQLPDFPHKDGLLALDSICLFFIVVVCFALFIVFKAYLINYVWNGYKYIN

Parental  NRNVPEIAVYPAFEAPP-QEVLPTYEMAVKMPEKHPAPPYIP
          NR.V.EIAVYPAFEA.P...VL.T.EMA.KMPEK.P..PYIP
Retrocopy NRSVLEIAVYPAFEASP<KYVLRTNEMAMKMPEKEPSAPYIP

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_2320 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020894	1 retrocopy	retro_btau_575,
Choloepus hoffmanni	ENSCHOG00000011200	2 retrocopies	retro_chof_1916, retro_chof_2320 ,
Callithrix jacchus	ENSCJAG00000007433	1 retrocopy	retro_cjac_839,
Echinops telfairi	ENSETEG00000002569	1 retrocopy	retro_etel_591,
Mustela putorius furo	ENSMPUG00000013714	1 retrocopy	retro_mputfur_657,
Ochotona princeps	ENSOPRG00000012401	2 retrocopies	retro_opri_356, retro_opri_474,
Pteropus vampyrus	ENSPVAG00000002909	3 retrocopies	retro_pvam_779, retro_pvam_847, retro_pvam_873,