RetrogeneDB ID: retro_chof_1995

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_447560:122..634(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000007262
• Aliases: None
• Description: None

Sequence

>retro_chof_1995
GAAAGGCAGAGAGTTGTGCAGCGATACCATCCTGCCAACCAAGGAGAATATCAGAGTTCTGGACTAGAAGATGACTTTGA
ATCTTGTTTGAGAAATGTAAAGTCACAGTACGAAGTTTGTCGAAGTAGTAGACTCTCATCAGATGCTACAGTTTTGACAC
CAAATAAAGAAAGGAGTTGTGATTTAATGACCAAAACTAAACCACCAGTAGAAATGATGACAGCACATCCTTAGATCTAG
AGTGGGAAGGTGAAGATGGAATGAATAGAATGCTTCCAATGAGAGAACATCCTAAAACAGAGGAAGATATTCTTTTTGCA
GTACTTAAGTGTAGCAGCAAGAAAACTGGAAATAATTCTAACTCAGCCTCTGATGATTCCAGTGGGCTGGAGTGGGAGAA
TGACTCTGTTAGTGCTAAAATGGATGATAAGGGCAATTCTTAGTGTTCTGGATTTATAAATCCTGTATTAGAACTGTCGG
ATTCTGGCATAAAGCAATCTGATACAGATCAA

Alignment

ORF - retro_chof_1995 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.88 %
• Parental protein coverage: 56.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EKQRFVQRYHPSNKGEYQSSGPEDDFESCLRNVKSQYEVFRNSRLSSDATVLTPNTESSCDLMTKTK-ST
          E.QR.VQRYHP.N.GEYQSSG.EDDFESCLRNVKSQYEV.R.SRLSSDATVLTPN.E.SCDLMTKTK..T
Retrocopy ERQRVVQRYHPANQGEYQSSGLEDDFESCLRNVKSQYEVCRSSRLSSDATVLTPNKERSCDLMTKTK<TT

Parental  SGNDDSTSLDLEWEDEEGINRLLPMREHPKTEEDILFAVLKCSSKKTGNNSNSASDDSNGLEWENDFVSA
          S.NDDSTSLDLEWE.E.G.NR.LPMREHPKTEEDILFAVLKCSSKKTGNNSNSASDDS.GLEWEND.VSA
Retrocopy SRNDDSTSLDLEWEGEDGMNRMLPMREHPKTEEDILFAVLKCSSKKTGNNSNSASDDSSGLEWENDSVSA

Parental  EMDN-GNSEYSGFVNPVLELSDSGIKQPGTDQ
          .MD..GNS..SGF.NPVLELSDSGIKQ..TDQ
Retrocopy KMDDKGNS*CSGFINPVLELSDSGIKQSDTDQ

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_1995 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007262	2 retrocopies	retro_chof_1995 , retro_chof_8,
Monodelphis domestica	ENSMODG00000005746	1 retrocopy	retro_mdom_160,
Oryctolagus cuniculus	ENSOCUG00000004413	1 retrocopy	retro_ocun_91,
Otolemur garnettii	ENSOGAG00000001631	1 retrocopy	retro_ogar_1054,
Sus scrofa	ENSSSCG00000009128	1 retrocopy	retro_sscr_245,