RetrogeneDB ID: retro_chof_2387

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_70713:5340..5878(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD14
• Ensembl ID: ENSCHOG00000002556
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, non-ATPase, 14 [Source:HGNC Symbol;Acc:16889]

Sequence

>retro_chof_2387
CAGTCAGGAACAGGTGTCAGTGTGGAGGCAGTTGATCCAGTATTCCAAATCAAAATGTTGGATATTTTGAATCAGACAGG
AAGGCCTGAGATGATTATTGGTTGGTATCACAGTCACCCTGGCTTTCGCTTGTTGACTTTCTGGTGTGGATATCAACACT
CAACGGAGCTTTGAAGCCTTGTCAGAGAGAGCCATGGCAGTGGTTGTGGATCCCATTCAGAGTGCAAAAGGAAAGGTTGT
TATTGATGCCTTCAGATTGATCAATGCTAATATGATGGTCTTAGGACATAAACCAAGACAAACAACTTCAAATCTGGATC
ACTTAAACAAGCCATCTATCCAGGCATTAATTAATGGACTAAACAGACATTATTACTCCATTACTATTAACTATTGGAAA
AATGAACTGGAACAGAAGATGTTGTTAAATTTGTATAAGAAGAGTTGGATGGAAGGTTTAACACTTCAGGACTACAGAGA
ACACTATATACATAATGAATCAGTGGTAAAAGAAATGTTGGCATTAGTCAAGAATTAC

Alignment

ORF - retro_chof_2387 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.33 %
• Parental protein coverage: 60.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QSGTGVSVEAVDPVFQAKMLDMLKQTGRPEMVVGWYHSHPGF-GCWLSGVDINTQQSFEALSERAVAVVV
          QSGTGVSVEAVDPVFQ.KMLD.L.QTGRPEM..GWYHSHPGF..C.LSGVDINTQ.SFEALSERA.AVVV
Retrocopy QSGTGVSVEAVDPVFQIKMLDILNQTGRPEMIIGWYHSHPGF>AC*LSGVDINTQRSFEALSERAMAVVV

Parental  DPIQSVKGKVVIDAFRLINANMMVLGHEPRQTTSNLGHLNKPSIQALIHGLNRHYYSITINYRKNELEQK
          DPIQS.KGKVVIDAFRLINANMMVLGH.PRQTTSNL.HLNKPSIQALI.GLNRHYYSITINY.KNELEQK
Retrocopy DPIQSAKGKVVIDAFRLINANMMVLGHKPRQTTSNLDHLNKPSIQALINGLNRHYYSITINYWKNELEQK

Parental  MLLNLHKKSWMEGLTLQDYSEHCKHNESVVKEMLELAKNY
          MLLNL.KKSWMEGLTLQDY.EH..HNESVVKEML.L.KNY
Retrocopy MLLNLYKKSWMEGLTLQDYREHYIHNESVVKEMLALVKNY

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_2387 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002556	1 retrocopy	retro_chof_2387 ,
Callithrix jacchus	ENSCJAG00000005572	1 retrocopy	retro_cjac_1434,
Gorilla gorilla	ENSGGOG00000015747	1 retrocopy	retro_ggor_1710,
Mus musculus	ENSMUSG00000026914	1 retrocopy	retro_mmus_701,
Otolemur garnettii	ENSOGAG00000004933	2 retrocopies	retro_ogar_2955, retro_ogar_3213,
Pongo abelii	ENSPPYG00000012881	1 retrocopy	retro_pabe_2100,
Pan troglodytes	ENSPTRG00000012575	1 retrocopy	retro_ptro_1636,
Rattus norvegicus	ENSRNOG00000004911	1 retrocopy	retro_rnor_1271,
Tupaia belangeri	ENSTBEG00000014118	1 retrocopy	retro_tbel_3917,