RetrogeneDB ID: retro_chof_233

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_5098:80177..80603(-)
• Located in intron of: ENSCHOG00000007245

Retrocopy information

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

Parental gene information

• Parental gene symbol: JOSD1
• Ensembl ID: ENSCHOG00000001723
• Aliases: None
• Description: Josephin domain containing 1 [Source:HGNC Symbol;Acc:28953]

Sequence

>retro_chof_233
AAGAGAGTTTCCAGAAATACCATGGTGACATCTCACAAGAAGAGCATGTAGGGAAACAGGAACTATGATGTGAACATCAT
CATGGCAGCACTTCAAACCAAGGGCTATGAAGCTGTTTAGTGGGACAAACACAGGGATGTCAGTGCCATTGTTCTCACTA
ATGTCATGGGCTTCATCATGAATCTGCCCTCCAGCCTGTGCTGGGGTCCGTTGAAGTTGCCTCTCAAAAGGCAGCACTGG
ATCTGCACTGGAGAGGTGGGAAATGCCTACTACAGCCTCAACTACAAACTCAAGGTGACTGAGTGGATTGGAGGTGAGAG
TGAGCTCAGGAAATTTCTAAAACATCATTTGCGAGGAAAGAACTGTGAACTCCTGCTGGTGGTACCAGAACAGGTGGAGG
CCCACCAGGGTTGGAGGGCTGCTGTG

Alignment

ORF - retro_chof_233 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.51 %
• Parental protein coverage: 70.3 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QRLSPNTMVTPHKKSMLGNGNYDVNVIMAALQTKGYEAVWWDKRRDVSVIALTNVMGFIMNLPSSLCWGP
          .R.S.NTMVT.HKKSM.GN.NYDVN.IMAALQTKGYEAV.WDK.RDVS.I.LTNVMGFIMNLPSSLCWGP
Retrocopy KRVSRNTMVTSHKKSM*GNRNYDVNIIMAALQTKGYEAV*WDKHRDVSAIVLTNVMGFIMNLPSSLCWGP

Parental  LKLPLKRQHWICVREVGGAYYNLDSKLKVPEWIGGESELRKFLKHHLRGKNCELLLVVSEEVEAHQSWRA
          LKLPLKRQHWIC..EVG.AYY.L..KLKV.EWIGGESELRKFLKHHLRGKNCELLLVV.E.VEAHQ.WRA
Retrocopy LKLPLKRQHWICTGEVGNAYYSLNYKLKVTEWIGGESELRKFLKHHLRGKNCELLLVVPEQVEAHQGWRA

Parental  DV
          .V
Retrocopy AV

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_233 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 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010171	1 retrocopy	retro_btau_1508,
Canis familiaris	ENSCAFG00000001379	1 retrocopy	retro_cfam_1500,
Choloepus hoffmanni	ENSCHOG00000001723	2 retrocopies	retro_chof_1576, retro_chof_233 ,
Equus caballus	ENSECAG00000015546	1 retrocopy	retro_ecab_251,
Felis catus	ENSFCAG00000002821	1 retrocopy	retro_fcat_565,
Macropus eugenii	ENSMEUG00000002899	2 retrocopies	retro_meug_1507, retro_meug_531,
Microcebus murinus	ENSMICG00000011798	1 retrocopy	retro_mmur_1202,
Myotis lucifugus	ENSMLUG00000003764	1 retrocopy	retro_mluc_1868,
Mus musculus	ENSMUSG00000022426	1 retrocopy	retro_mmus_3014,
Otolemur garnettii	ENSOGAG00000007520	3 retrocopies	retro_ogar_1462, retro_ogar_2911, retro_ogar_3487,
Pteropus vampyrus	ENSPVAG00000010148	1 retrocopy	retro_pvam_181,
Rattus norvegicus	ENSRNOG00000014440	2 retrocopies	retro_rnor_2954, retro_rnor_906,
Sarcophilus harrisii	ENSSHAG00000015931	1 retrocopy	retro_shar_643,
Ictidomys tridecemlineatus	ENSSTOG00000024999	1 retrocopy	retro_itri_193,
Tarsius syrichta	ENSTSYG00000008846	1 retrocopy	retro_tsyr_1076,