RetrogeneDB ID: retro_chof_1086

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_196613:211..1037(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000013305
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: AZIN1
• Ensembl ID: ENSCHOG00000005164
• Aliases: None
• Description: antizyme inhibitor 1 [Source:HGNC Symbol;Acc:16432]

Sequence

>retro_chof_1086
ACTACATCAGAGAATTGTAGGCATCTCTTGGAATGTGCTAAGGAACTTGATGTCCAAATAACTGGGGTTAAATTTCACAT
TTCAAGTGCTTGCAAGGTATCTCAAGTATTTGTACATGCTCTGTCTGATGTGCGATGTGTGTTTGACAGTGCTGGAGAAT
TTTGTTTCAAGATGAACATTTTAGACATTGGTGGAGGCTTCACAGGAACTGAATTTCAGTTGGAAGAGGTTAATCATGTT
ATCAGCCCTTTATTGGATATCTACTTTCCTGAAGTGTCTGGCATTGAGATTATTTCAGAACCTGGAAGCTACTATGTGTC
TTCTGCATTTACACTTGCAGTTAATATCATTGCAAAGAAAGTTGTTGAAAATGATAAATTTTCCTCTGGAGTAGGAAAAA
ATGTAAGTGATGAACCAGCATTTATGTATTACATGAATGATGGTGTCTATGGTTCTTTTGCAAGTAAACTGTCAGAGGAC
TTAATATCATTTCAGAGGTTCACAAGAAATACAAGGAAGATGAGCCTTTGTTTACAAGCAGCCTTTGGGGTCCATCCTGT
GATGAGCTTGATCAGATTGTAGAAAGCTGTCTTCTTCCTGAGCAGAATGTAGGAGATTGGCTTATCTTTGATAATACGGG
AGCAGATTCTTTCCTGGGCCATCTACTTTTAATGATTTTCAGAGACCAACTATTTATTACATGATGTCATTTAGTGATTG
GTATGAGATGCAAGATGTTGGAATTACTTCAGACACAGTGATGAAGAACTTCTTTGTGCCTTCTTGCATTCAACTGAACC
AAGAAGACAGCTTTTCCATTGAAGCT

Alignment

ORF - retro_chof_1086 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.46 %
• Parental protein coverage: 61.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TTLKNCRHLLECAKELDVQIIGVKFHVSSACKISQVYVHALSDARCVFDMAGEFGFKMNILDIGGGFTGT
          TT..NCRHLLECAKELDVQI.GVKFH.SSACK.SQV.VHALSD.RCVFD.AGEF.FKMNILDIGGGFTGT
Retrocopy TTSENCRHLLECAKELDVQITGVKFHISSACKVSQVFVHALSDVRCVFDSAGEFCFKMNILDIGGGFTGT

Parental  EYQFEAVNHVISPLLDIYFPEGSGIKIISEPGSYYVSSAFTLAVNIIAKKVVQNDKFSSGVGKNGSDEPA
          E.Q.E.VNHVISPLLDIYFPE.SGI.IISEPGSYYVSSAFTLAVNIIAKKVV.NDKFSSGVGKN.SDEPA
Retrocopy EFQLEEVNHVISPLLDIYFPEVSGIEIISEPGSYYVSSAFTLAVNIIAKKVVENDKFSSGVGKNVSDEPA

Parental  FMYYVNDGVYGSFASKLSED-LNTIPEVHKKYKEDEPLFTSSLWGPSCDELDQIVESCLLPELNVGDWLI
          FMYY.NDGVYGSFASKLSED.LN.I.EVHKKYKEDEPLFTSSLWGPSCDELDQIVESCLLPE.NVGDWLI
Retrocopy FMYYMNDGVYGSFASKLSED<LNIISEVHKKYKEDEPLFTSSLWGPSCDELDQIVESCLLPEQNVGDWLI

Parental  FDNMGADS-FHDPSAFNDFQRPAIYYMMSFSDXXEMQDAGITSDTVMKNFFFVPSCIQLSQEDSFPTDA
          FDN.GADS.F..PS.FNDFQRP.IYYMMSFSD..EMQD.GITSDTVMKN.FFVPSCIQL.QEDSF...A
Retrocopy FDNTGADS<FPGPSTFNDFQRPTIYYMMSFSDWYEMQDVGITSDTVMKN-FFVPSCIQLNQEDSFSIEA

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_1086 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005164	2 retrocopies	retro_chof_1086 , retro_chof_1522,
Choloepus hoffmanni	ENSCHOG00000010898	2 retrocopies	retro_chof_1618, retro_chof_2111,
Equus caballus	ENSECAG00000016922	1 retrocopy	retro_ecab_1096,
Oryctolagus cuniculus	ENSOCUG00000015196	1 retrocopy	retro_ocun_1439,
Tursiops truncatus	ENSTTRG00000000140	1 retrocopy	retro_ttru_1210,