RetrogeneDB ID: retro_chof_1806

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_389622:462..837(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000003323
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000012823
• Aliases: None
• Description: None

Sequence

>retro_chof_1806
TATTTGTTTTCTGCACGAGTACAACTGTCAAAATATAGGGTTCCAAATCTTTTGGGCTTCTACCAGCAGTATCATCACCA
TCCAATCCCAGATGGAGGGACTCCTGACGTAGCCAGCTGCTGTGAAATAATGGAAGAGCTTGCAATCTGCCTTAAAAATA
ACCGGAAAACCTTAATACACTGTTATGGAGGACTTGGGAGATCTTGTCTTGTAGCTGCTTGTCTCCTGCTATACCTATCT
GACACAGTATCACCACAGCAAGCCATAGACAGCCTAAGAGACTTAAGAGGATCTGGGGCAAAACAGACCATAAAGCAATA
TAATTATCTCCATGAGTTCAGTGACAAACTAACTGCACATTTATCATCAAGAGAT

Alignment

ORF - retro_chof_1806 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.6 %
• Parental protein coverage: 71.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FVFCTRGELSKYRVPNLLGFYQQYGITTHHHPIRDGGTPDIASCCEIMEELAICLKNNRKTLIHCYGGLG
          ..F..R..LSKYRVPNLLGFYQQY....HHHPI.DGGTPD.ASCCEIMEELAICLKNNRKTLIHCYGGLG
Retrocopy YLFSARVQLSKYRVPNLLGFYQQY----HHHPIPDGGTPDVASCCEIMEELAICLKNNRKTLIHCYGGLG

Parental  RSCLVAACLLLYLSDTVSPQQAIDSLRNVRGSGAIQTIKQYNYLHEFRDKLTAHLSSRD
          RSCLVAACLLLYLSDTVSPQQAIDSLR..RGSGA.QTIKQYNYLHEF.DKLTAHLSSRD
Retrocopy RSCLVAACLLLYLSDTVSPQQAIDSLRDLRGSGAKQTIKQYNYLHEFSDKLTAHLSSRD

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_1806 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
Choloepus hoffmanni	ENSCHOG00000012823	1 retrocopy	retro_chof_1806 ,
Echinops telfairi	ENSETEG00000018617	1 retrocopy	retro_etel_1763,
Felis catus	ENSFCAG00000015089	2 retrocopies	retro_fcat_135, retro_fcat_626,
Loxodonta africana	ENSLAFG00000014833	1 retrocopy	retro_lafr_637,
Macropus eugenii	ENSMEUG00000002497	3 retrocopies	retro_meug_1255, retro_meug_1768, retro_meug_1849,
Procavia capensis	ENSPCAG00000015559	1 retrocopy	retro_pcap_104,
Sarcophilus harrisii	ENSSHAG00000008977	1 retrocopy	retro_shar_502,
Tupaia belangeri	ENSTBEG00000010203	2 retrocopies	retro_tbel_1809, retro_tbel_4700,