RetrogeneDB ID: retro_chof_1486

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_30557:7347..7568(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000000940
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000013206
• Aliases: None
• Description: None

Sequence

>retro_chof_1486
TACAAGCCCAAGTATGTTCAGCTCAAGAAGAAGTTAGAAGATGAGTTCCCTGAATGCCTGGACATCAGCAGTGAGGGGAC
CTCCCCCAAACCACCAGGTTCTTTGAAGTGATGGTGGCTGGAAAGTTGGTTCACTCCAAGAAGAAAGGCAATGGCTTTGT
GGACACAGAGGGCAAATTTCTGAAGCCAGTAGCTGCTATCAAAGCCATCTTGGCTCAGGGG

Alignment

ORF - retro_chof_1486 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.33 %
• Parental protein coverage: 98.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YKPKYVQLKKKLEDEFPGCLDISGEGT-PQ-TTGFFEVMVAGKLVHSKKKGDGFVDTESKFLRLVAAIKA
          YKPKYVQLKKKLEDEFP.CLDIS.EGT.P..TT.FFEVMVAGKLVHSKKKG.GFVDTE.KFL..VAAIKA
Retrocopy YKPKYVQLKKKLEDEFPECLDISSEGTSPK<TTRFFEVMVAGKLVHSKKKGNGFVDTEGKFLKPVAAIKA

Parental  ALAQG
          .LAQG
Retrocopy ILAQG

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_1486 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 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015208	1 retrocopy	retro_amel_1135,
Bos taurus	ENSBTAG00000008203	2 retrocopies	retro_btau_1527, retro_btau_756,
Canis familiaris	ENSCAFG00000004074	1 retrocopy	retro_cfam_1368,
Choloepus hoffmanni	ENSCHOG00000013206	2 retrocopies	retro_chof_1486 , retro_chof_61,
Felis catus	ENSFCAG00000015176	2 retrocopies	retro_fcat_108, retro_fcat_186,
Mustela putorius furo	ENSMPUG00000004433	1 retrocopy	retro_mputfur_326,
Rattus norvegicus	ENSRNOG00000013548	2 retrocopies	retro_rnor_1819, retro_rnor_688,
Ictidomys tridecemlineatus	ENSSTOG00000001294	1 retrocopy	retro_itri_578,