RetrogeneDB ID: retro_chof_2518

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_82110:193..664(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHMP4B
• Ensembl ID: ENSCHOG00000007288
• Aliases: None
• Description: charged multivesicular body protein 4B [Source:HGNC Symbol;Acc:16171]

Sequence

>retro_chof_2518
CTCCAGGCACTAAAGCGCAAGGGGTATGAGAAGCAGTTGGCACAGATTGATGGCATACTATCCACCATCAAGTTCTAGCA
GGAGGCCCTGGAGAATGGCAACACCAACACCAAGATGCTCAAGAACATGGGCTATGCTTCCAAGGCCATGATGGCTGCTC
ATGACAACATGGAAATGGGTAAAGTCAAGGAGTTAATGCAGAACATTGCTGACCAGCAAGAACTTGCAGAGGAGATTTCA
ACAGCTATTTCCAGACCTGTAGGGTTTGGAGAAGAATTTGATGAGGATGAGCTTATGGCAGAATTAGAAGAATTAGAACA
GGAAGAACTAGATAAGAATTTGCTGGAAATCAGTGGACCCAAAACAGTCCCTCTACCAAATGATCCCTCTATAGCCTTAC
CATCAAAACCAACCAAGAAGAAGGAAGAGGAAGATGATAACATGATGGAATTGGAGAACAGGGCTGGATCC

Alignment

ORF - retro_chof_2518 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.08 %
• Parental protein coverage: 98.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LQALKRKKRYEKQLAQIDGTLSTIEFQREALENANTNTEVLKNMGYAAKAMKAAHDNMDIDKVDELMQDI
          LQALKRK..YEKQLAQIDG.LSTI.F..EALEN.NTNT..LKNMGYA.KAM.AAHDNM...KV.ELMQ.I
Retrocopy LQALKRKG-YEKQLAQIDGILSTIKF*QEALENGNTNTKMLKNMGYASKAMMAAHDNMEMGKVKELMQNI

Parental  ADQQELAEEISTAISKPVGFGEEFDEDELMAELEELEQEELDKNLLEISGPETVPLPNVPSIALPSKPTK
          ADQQELAEEISTAIS.PVGFGEEFDEDELMAELEELEQEELDKNLLEISGP.TVPLPN.PSIALPSKPTK
Retrocopy ADQQELAEEISTAISRPVGFGEEFDEDELMAELEELEQEELDKNLLEISGPKTVPLPNDPSIALPSKPTK

Parental  KKEEEDDDMKELENWAGS
          KKEEEDD.M.ELEN.AGS
Retrocopy KKEEEDDNMMELENRAGS

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_2518 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 15 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009038	1 retrocopy	retro_amel_1612,
Canis familiaris	ENSCAFG00000007478	1 retrocopy	retro_cfam_1304,
Choloepus hoffmanni	ENSCHOG00000007288	1 retrocopy	retro_chof_2518 ,
Equus caballus	ENSECAG00000008311	1 retrocopy	retro_ecab_496,
Felis catus	ENSFCAG00000025893	1 retrocopy	retro_fcat_1835,
Homo sapiens	ENSG00000101421	1 retrocopy	retro_hsap_1339,
Gorilla gorilla	ENSGGOG00000007775	1 retrocopy	retro_ggor_29,
Macaca mulatta	ENSMMUG00000008084	1 retrocopy	retro_mmul_2178,
Mustela putorius furo	ENSMPUG00000017821	2 retrocopies	retro_mputfur_1302, retro_mputfur_697,
Nomascus leucogenys	ENSNLEG00000010020	1 retrocopy	retro_nleu_1822,
Pongo abelii	ENSPPYG00000010931	1 retrocopy	retro_pabe_1111,
Pan troglodytes	ENSPTRG00000013408	1 retrocopy	retro_ptro_915,
Pteropus vampyrus	ENSPVAG00000010293	1 retrocopy	retro_pvam_973,
Rattus norvegicus	ENSRNOG00000046585	1 retrocopy	retro_rnor_61,
Tarsius syrichta	ENSTSYG00000013212	1 retrocopy	retro_tsyr_1453,