RetrogeneDB ID: retro_chof_2586

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_88162:2245..3400(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP3M1
• Ensembl ID: ENSCHOG00000004510
• Aliases: None
• Description: adaptor-related protein complex 3, mu 1 subunit [Source:HGNC Symbol;Acc:569]

Sequence

>retro_chof_2586
ATGATCCACAGTCTATTACTTATAAACTGTTCCGGTGACATATTTCTAGAAAAGCACTGGAAGAGTGTTGTGAGTCAGTC
TGTCTGTGATTATTTCTTTGAAGCTCAAGAGAAAGCTGCTGATGTTGAAAATGTACCACCTGTCATTCCAACGCCTCACC
ATTACCTCATCAGTATCTACCGGGACAAGCTCTTCTTTGTTTTTGTCATACAGACTGAGGTGCCACCTCTCTTTGTAATT
GAGTTCCTACATTGAGTTGCTGACACTTTTCAGGACTACTTTGGTGAGTGTTCAGAGGCTGCAATTAAGGATAATGTGGT
CATAGTATATGAACTCTTAGAGGAAATGTTAGGCAATGGATTTCCACTGGCTACTGAATCTAACATTTTGAAAGAACTGA
TTAAACCACCAACAATTCTCCGTTCTGTCATCAACTCTATTATAGGTAGTAGTAATGTTGGGGACACACTCCCCACTGGG
CAGCTATCCAACATCCCATGGCGCCGCGCAGGGGTAAAGTACACAAACAATGAAGCCTATTTTGATGTAATTGAAGAAAT
AGACGCAATTATAGATAAATCAGGGTCTACAGTCTTTGCAGAAATTAAGGGGGTCATTGATGCTTGCATTAAACTGTCTG
GAATGCCTGATCTTTCCCTTTCCTTCATGAACCCAAGGCTTCTGGATGATGTCAGCTTCCACCCCTGCGTCAGGTTTAAG
AGTTGGGAGTCTGAAAGAGTTTTGTCATTTATTCCTCCAGATGGAAATTTCCGACTCATATCGTACCGTGTCAGCTCACA
AAATCTAGTGGCAATTCCAGTGTATGTGAAACACAGCATCAGCTTTAAGGAGAACAGTTCTTGTGGCAGATTTGATATTA
CCATTGGACCAAAGCAGAATATGGGAAAAACTATTGAAGGAATCACAGTGACAGTTCACATGCCAAAAGTTGTGCTGAAT
ATGAACCTGACACCAACACAAGGCAGCTATACATTTGATCCAGTCACCAAGGTACTAACATGGGATGTGGGGAAAATTAC
TCCACAGAAGCTCCCAAGTCTTAAAGGACTAGTCAATTTACAGTCTGGAGCACCCAAGCCAGAAGAGAATCCAAGCCTCA
ACATTCAATTCAAGATCCAGCAACTTGCTATTTCA

Alignment

ORF - retro_chof_2586 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.88 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MIHSLFLINCSGDIFLEKHWKSVVSQSVCDYFFEAQEKAADVENVPPVIPTPHHYLISIYRDKLFFVSVI
          MIHSL.LINCSGDIFLEKHWKSVVSQSVCDYFFEAQEKAADVENVPPVIPTPHHYLISIYRDKLFFV.VI
Retrocopy MIHSLLLINCSGDIFLEKHWKSVVSQSVCDYFFEAQEKAADVENVPPVIPTPHHYLISIYRDKLFFVFVI

Parental  QTEVPPLFVIEFLHRVADTFQDYFGECSEAAIKDNVVIVYELLEEMLDNGFPLATESNILKELIKPPTIL
          QTEVPPLFVIEFLH.VADTFQDYFGECSEAAIKDNVVIVYELLEEML.NGFPLATESNILKELIKPPTIL
Retrocopy QTEVPPLFVIEFLH*VADTFQDYFGECSEAAIKDNVVIVYELLEEMLGNGFPLATESNILKELIKPPTIL

Parental  RSVVNSITXXXNVGDTLPTGQLSNIPWRRAGVKYTNNEAYFDVIEEIDAIIDKSGSTVFAEIQGVIDACI
          RSV.NSI....NVGDTLPTGQLSNIPWRRAGVKYTNNEAYFDVIEEIDAIIDKSGSTVFAEI.GVIDACI
Retrocopy RSVINSIIGSSNVGDTLPTGQLSNIPWRRAGVKYTNNEAYFDVIEEIDAIIDKSGSTVFAEIKGVIDACI

Parental  KLSGMPDLSLSFMNPRLLDDVSFHPCIRFKRWESERVLSFIPPDGNFRLISYRVSSQNLVAIPVYVKHSI
          KLSGMPDLSLSFMNPRLLDDVSFHPC.RFK.WESERVLSFIPPDGNFRLISYRVSSQNLVAIPVYVKHSI
Retrocopy KLSGMPDLSLSFMNPRLLDDVSFHPCVRFKSWESERVLSFIPPDGNFRLISYRVSSQNLVAIPVYVKHSI

Parental  SFKENSSCGRFDITIGPKQNMGKTIEGITVTVHMPKVVLNMNLTPTQGSYTFDPVTKVLTWDVGKITPQK
          SFKENSSCGRFDITIGPKQNMGKTIEGITVTVHMPKVVLNMNLTPTQGSYTFDPVTKVLTWDVGKITPQK
Retrocopy SFKENSSCGRFDITIGPKQNMGKTIEGITVTVHMPKVVLNMNLTPTQGSYTFDPVTKVLTWDVGKITPQK

Parental  LPSLKGLVNLQSGAPKPEENPSLNIQFKIQQLAIS
          LPSLKGLVNLQSGAPKPEENPSLNIQFKIQQLAIS
Retrocopy LPSLKGLVNLQSGAPKPEENPSLNIQFKIQQLAIS

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_2586 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004510	1 retrocopy	retro_chof_2586 ,
Monodelphis domestica	ENSMODG00000000660	1 retrocopy	retro_mdom_1564,
Mus musculus	ENSMUSG00000021824	1 retrocopy	retro_mmus_580,
Ictidomys tridecemlineatus	ENSSTOG00000012881	1 retrocopy	retro_itri_1276,