RetrogeneDB ID: retro_chof_2419

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_73828:4735..5093(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDPN
• Ensembl ID: ENSCHOG00000007003
• Aliases: None
• Description: podoplanin [Source:HGNC Symbol;Acc:29602]

Sequence

>retro_chof_2419
CAGCATGGTCTGACCATTTTTCCAGGTGTGGAAAAATGGCATGGTGACTCCAGGTGCCAGTGAAGAGCCCAGTAATTCTG
CTGGCTTGACAATTCTGGGGCCAAAAAGGGCAAAGAGAGTGACAGTCATTCTCATGAAGGGTTGGTCATCTATAGAAAGC
ACATTCCATGCCCAAGAAGAAAGTCAGAACACCACAGCCCCAAATGCAGTGAGTGGTCACTCTGGGAAACTGGGTAGAGA
GGCACCATCAAGAGTTGAGAACAATGGTTTGGCAATAGTAACCCTGATTGGAATCATAGTTGGGGTCTTACTAGCCATTG
GTTTCATTGGTGCAGTCATCATTGTGGTTGTGCAAAAA

Alignment

ORF - retro_chof_2419 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.83 %
• Parental protein coverage: 84.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EDGAAVSPGVE-DGVVTPGASEQPDKSAGLTTQGLTTTKSVTVIRVTDRTPLEST----EESQKTTASNV
          ..G....PGVE..G.VTPGASE.P..SAGLT..G....K.VTVI........EST....EESQ.TTA.N.
Retrocopy QHGLTIFPGVE>NGMVTPGASEEPSNSAGLTILGPKRAKRVTVILMKGWSSIESTFHAQEESQNTTAPNA

Parental  GTGHSEKVGGEALPTVENDGLTTVTLVGIIVGVSLATAFIGGVIYMVVRK
          ..GHS.K.G.EA...VEN.GL..VTL.GIIVGV.LA..FIG.VI..VV.K
Retrocopy VSGHSGKLGREAPSRVENNGLAIVTLIGIIVGVLLAIGFIGAVIIVVVQK

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_2419 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	ENSCHOG00000007003	3 retrocopies	retro_chof_1612, retro_chof_2419 , retro_chof_583,
Callithrix jacchus	ENSCJAG00000013772	1 retrocopy	retro_cjac_1300,
Mus musculus	ENSMUSG00000028583	1 retrocopy	retro_mmus_774,
Pteropus vampyrus	ENSPVAG00000011180	1 retrocopy	retro_pvam_1402,
Tarsius syrichta	ENSTSYG00000005667	1 retrocopy	retro_tsyr_1571,