RetrogeneDB ID: retro_chof_282

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_6156:26392..27007(-)
• Located in intron of: ENSCHOG00000001240

Retrocopy information

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

Parental gene information

• Parental gene symbol: PEX13
• Ensembl ID: ENSCHOG00000012871
• Aliases: None
• Description: peroxisomal biogenesis factor 13 [Source:HGNC Symbol;Acc:8855]

Sequence

>retro_chof_282
ATAGGATTAAGAAGAGGCTCAGAGAATGAGGACTTTTGGGAAGAGAGCGAAGGAACTGGAGCTTGCCTTGGTGCTGAGGA
CAGAGCAGCCAACTCAACAAAATCTTGGCCAATATTCTTGTTCTTTGCTGTTATCCTTGGTGGTCCTCAACTCATCTGGA
AACTGCTGTCTGCCCACAATGATGAAGTAGCAGACAATACCAACTAGGCAAGTGGTGAGGATGACCATGTAGTTGCTAGA
GCAGAATATGATTTTGCTGCCATACCTGAAGAAGAAATTTCTTTCCGTGATGGTGATATGCTAAACTTAGCTCTTAAAGA
ACAACAACCCAAAGTGCATGGTTGGCTTCTGGCTAGTCTTGATGGTCAAACAACAGGATTTGTACCTGCTAACTACATCA
AAATTCTTGGTAAAAGAAGAGGTAGGAAAACAGTGGAATCCAGTAAAATTTCCTAGCAGCAACAATCTTACACCAACACA
ACACTAATTAAAGGAGCCACTGCTGCTGATTCTTTGGATGAATAGGAAGCTGCCTTTGAATCTGTTTTTGTTGAAACTAG
TAAGGTTCCAGTTGCATCTGATTACACTGGGAAAAATGGAGATAAACAGGATCTT

Alignment

ORF - retro_chof_282 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.76 %
• Parental protein coverage: 50.87 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IGLRRGSENEDLWAESEGTVACLGAEDGAANSAKSWPIFLFFAVILGGPYLIWKLLSTHSDEVADNTNWA
          IGLRRGSENED.W.ESEGT.ACLGAED.AANS.KSWPIFLFFAVILGGP.LIWKLLS.H.DEVADNTN.A
Retrocopy IGLRRGSENEDFWEESEGTGACLGAEDRAANSTKSWPIFLFFAVILGGPQLIWKLLSAHNDEVADNTN*A

Parental  SGEDDHVVARAEYDFAAVSEEEISFRAGDMLNLALKEQQPKVRGWLLASLDGQTTGLVPANYVKILGKRR
          SGEDDHVVARAEYDFAA..EEEISFR.GDMLNLALKEQQPKV.GWLLASLDGQTTG.VPANY.KILGKRR
Retrocopy SGEDDHVVARAEYDFAAIPEEEISFRDGDMLNLALKEQQPKVHGWLLASLDGQTTGFVPANYIKILGKRR

Parental  GRKTMESSKISKQRQSYTNTTLIKGATAADSLDEQEAAFESVFVETNKVPVASDSTGKNGDKQDL
          GRKT.ESSKIS.Q.QSYTNTTLIKGATAADSLDE.EAAFESVFVET.KVPVASD.TGKNGDKQDL
Retrocopy GRKTVESSKIS*QQQSYTNTTLIKGATAADSLDE*EAAFESVFVETSKVPVASDYTGKNGDKQDL

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_282 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012871	1 retrocopy	retro_chof_282 ,
Equus caballus	ENSECAG00000019622	1 retrocopy	retro_ecab_403,
Felis catus	ENSFCAG00000028969	1 retrocopy	retro_fcat_1832,
Mus musculus	ENSMUSG00000020283	1 retrocopy	retro_mmus_1932,