RetrogeneDB ID: retro_chof_1834

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_399305:1..989(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000005083
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000006026
• Aliases: None
• Description: None

Sequence

>retro_chof_1834
AGCAACCAAGTTGTAAAAGGATATATTGGTAAAAGCTGATCTTCAGACAAGTTCTCAGCTTGTAAATCTTTCAGCCTCCA
ATGCTGCAGTGGCTGAACTTAAACCTGATTGTTGTATTGATGATGTAATACATCATGAAGTAAAGGAAATTGGAACACAC
ATCTTGGTGTGTGCAGTGAGTTATACAACTCAAAGTGGAGAAAAAATGTATTTTAGAAAGTTCTTCAAATTTCAGGTTCT
CAAACCATTGGATGTGAAAACCAAATTTTACAATGCAGAGAGTGACCTCAGTTCTGTGACTGATGAAGTATTTCTCGAAG
CCCAGATTCAGAATATTACAACCTCACCCATGTTTATGGAGAAGGTTTCATTGGAGCCATCTATAATGTACAATGTAGCA
GAACTAAATTCTGTGGACCAAGCTGGAGAATGTGCGTCTACATTTGGATCAAGAGCCTATTTTCAACCAATGGATACACA
CCAGTACTTATACTGCCTAAAGCCCAAGAAAGAGTTTGCAGAAAAGGCAGGCATCATTAAGGGAGTAACTGTAATTGGAA
AATTGGATATAGTATGGAAAACAAATCTGGGTGAAAGAGGAAGGTTACAGACCAGCCAACTTCAAAGAATGGCTCCAGGT
TATGGAGATGTTAGATTATCTTTGGAGGCAATCCCAGATATCGTAAACCTAGAAGAACCTTTTCATATTACCTGTAAAAT
AACAAACTGCAGCAGTGAAAGGACTATGGATCTTGTTTTGGAGATGTGCAATACCAATTCCATCCACTGGTGTGGCGTTT
CAGGAAGACAGCATGGAAAGCTACATCCAAGTTCCTCTCTCTGCCTTGCCCTTACTCTGCTGTCTTCAGTACAGGGACTG
CAAAGTGTTTCCGGCTTAAGACTGACAGACACTTTCCTAAAGAGAACATACGAATATGATGACATTGCACAAGTCTGTGT
GGTATCTTCGGCCATTAAAGTGGAAAGC

Alignment

ORF - retro_chof_1834 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.75 %
• Parental protein coverage: 92.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SNQVVK-DILVKADLQTSSQRLNLSASNAAVAELKPDCCIDDVIHHEVKEIGTHI-VCAVSYTTQSG-KM
          SNQVVK.DILVKADLQTSSQ..NLSASNAAVAELKPDCCIDDVIHHEVKEIGTHI.VCAVSYTTQSG.KM
Retrocopy SNQVVK>DILVKADLQTSSQLVNLSASNAAVAELKPDCCIDDVIHHEVKEIGTHILVCAVSYTTQSGEKM

Parental  YFR---KFFFGLPLDVKTKFYNAEVSIADMTTDEVFLEAQIQNITTSPMFMEKVSLEPSIMYNVAELNSV
          YFR...KF....PLDVKTKFYNAE......T.DEVFLEAQIQNITTSPMFMEKVSLEPSIMYNVAELNSV
Retrocopy YFRKFFKFQVLKPLDVKTKFYNAESDLSSVT-DEVFLEAQIQNITTSPMFMEKVSLEPSIMYNVAELNSV

Parental  DQAGECASTFGSRAYLQPMDTRQYLYCLKPKKEFAEKAGIIKGVTVIGKLDIVWKTNLGERGRLQTSQLQ
          DQAGECASTFGSRAY.QPMDT.QYLYCLKPKKEFAEKAGIIKGVTVIGKLDIVWKTNLGERGRLQTSQLQ
Retrocopy DQAGECASTFGSRAYFQPMDTHQYLYCLKPKKEFAEKAGIIKGVTVIGKLDIVWKTNLGERGRLQTSQLQ

Parental  RMAPGYGDVRLSLEAIPDTVNLEEPFHITCKITNC-SERTMDLVLEMCNTNSIHWCGVSGRQLGKLHPSS
          RMAPGYGDVRLSLEAIPD.VNLEEPFHITCKITNC.SERTMDLVLEMCNTNSIHWCGVSGRQ.GKLHPSS
Retrocopy RMAPGYGDVRLSLEAIPDIVNLEEPFHITCKITNCSSERTMDLVLEMCNTNSIHWCGVSGRQHGKLHPSS

Parental  SLCLALTLLSSVQGLQSVSGLRLTDTFLKRTYEYDDIAQVCVVSSAIKVES
          SLCLALTLLSSVQGLQSVSGLRLTDTFLKRTYEYDDIAQVCVVSSAIKVES
Retrocopy SLCLALTLLSSVQGLQSVSGLRLTDTFLKRTYEYDDIAQVCVVSSAIKVES

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_1834 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006026	1 retrocopy	retro_chof_1834 ,
Dasypus novemcinctus	ENSDNOG00000006386	1 retrocopy	retro_dnov_1288,
Equus caballus	ENSECAG00000011983	1 retrocopy	retro_ecab_1074,
Otolemur garnettii	ENSOGAG00000010787	1 retrocopy	retro_ogar_3287,
Procavia capensis	ENSPCAG00000005623	1 retrocopy	retro_pcap_370,
Pteropus vampyrus	ENSPVAG00000008275	1 retrocopy	retro_pvam_980,
Sorex araneus	ENSSARG00000000639	1 retrocopy	retro_sara_394,
Ictidomys tridecemlineatus	ENSSTOG00000021318	1 retrocopy	retro_itri_1455,
Tarsius syrichta	ENSTSYG00000004582	1 retrocopy	retro_tsyr_18,
Tursiops truncatus	ENSTTRG00000006537	1 retrocopy	retro_ttru_1068,