RetrogeneDB ID: retro_chof_2337

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_6707:38..838(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000003246
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TSPAN5
• Ensembl ID: ENSCHOG00000013549
• Aliases: None
• Description: tetraspanin 5 [Source:HGNC Symbol;Acc:17753]

Sequence

>retro_chof_2337
ATGTCCGGGAAGCACTACAAGGGTCCTGAAGTCAGTTGTTGCATCAAATATTTCATATTTGGCTTCAATGTCATATTTTG
GTTTTTGGGAATAGCATTTCTTGGAATTGGACTGTGGGCATGGAATGAAAAAGGCGTTCTGTCCAACATCTCTTCCATCA
CCGACCTCGGCGGCTTTGACCCAGTTTGGCTCTTCCTTGTGGTGGGAGGAGTGATGTTCATTTTGGGATTCGCAGGGTGC
ATTGGAGCTCTACGGGAAAACACTTTCCTTCTCAAGTTTTTTTCTGTGTTCCTGGGAATTATTTTCTTCCTGGAGCTCAC
TGCTGGGGTCCTGGCATTTGTTTTCAAAGACTGGATCAAAGACCAGCTGTATTTCTTTATAAACAACAACATCAGAGCGT
ACAGGGATGATATTGACTTGCAAAACCTCATATACTTCACCCAGGAATATTGGCAGTGCTGTGGGGCTTTTGGAGCTGAT
GATTGGAACCTAAATATTTACTTCAATTGCACAGATTCCAACGCAAGTCGAGAGCGATGTGGCGTGCCGTTCTCCTGCTG
TACTAAAGATCCTGCAGAAGATGTAATCAACACTCAGTGTGGCTATGATGCCAGGCAAAGCCAGAAGTTGATCAGCAGAT
TGTAATCTACACAAAAGGCTGTGTGCCCCAGTTTGAGAAGTGGCTGCAGGACAATTTAACTATCGTGTTTATTTTCATAG
GCATTGCTTTGCTGCAGATTTTTGGGATATGCCTGGCCCAGAATTTGGTTAGTGACATTGAAGCTGTCAGGGCTAGCTGG

Alignment

ORF - retro_chof_2337 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.91 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSGK-YKGSEISC-IKYFI-GFNIIFWFLGIAFLGIGLWAWNEKGVLSNISSITDLGGFDPVWLFLVVGG
          MSGK.YKG.E.SC.IKYFI.GFN.IFWFLGIAFLGIGLWAWNEKGVLSNISSITDLGGFDPVWLFLVVGG
Retrocopy MSGKHYKGPEVSCCIKYFIFGFNVIFWFLGIAFLGIGLWAWNEKGVLSNISSITDLGGFDPVWLFLVVGG

Parental  VMFILGFAGCIGALRENTFLLKFFSVFLGIIFFLELTAGVLAFVFKDWIKDQLYFFINNNIRAYRDDIDL
          VMFILGFAGCIGALRENTFLLKFFSVFLGIIFFLELTAGVLAFVFKDWIKDQLYFFINNNIRAYRDDIDL
Retrocopy VMFILGFAGCIGALRENTFLLKFFSVFLGIIFFLELTAGVLAFVFKDWIKDQLYFFINNNIRAYRDDIDL

Parental  QNLIDFTQEYWQCCGAFGADDWNLNIYFNCTDSNASRERCGVPFSCCTKDPAEDVINTQCGYDARQ-KPE
          QNLI.FTQEYWQCCGAFGADDWNLNIYFNCTDSNASRERCGVPFSCCTKDPAEDVINTQCGYDARQ.KPE
Retrocopy QNLIYFTQEYWQCCGAFGADDWNLNIYFNCTDSNASRERCGVPFSCCTKDPAEDVINTQCGYDARQ<KPE

Parental  VDQQIVIYTKGCVPQFEKWLQDNLTIVAGIFIGIALL-IFGICLAQNLVSDIEAVRASW
          VDQQIVIYTKGCVPQFEKWLQDNLTIV..IFIGIALL.IFGICLAQNLVSDIEAVRASW
Retrocopy VDQQIVIYTKGCVPQFEKWLQDNLTIVF-IFIGIALLQIFGICLAQNLVSDIEAVRASW

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_2337 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013851	1 retrocopy	retro_amel_742,
Canis familiaris	ENSCAFG00000010287	1 retrocopy	retro_cfam_314,
Choloepus hoffmanni	ENSCHOG00000013549	1 retrocopy	retro_chof_2337 ,
Dasypus novemcinctus	ENSDNOG00000012685	1 retrocopy	retro_dnov_91,
Echinops telfairi	ENSETEG00000007405	1 retrocopy	retro_etel_1985,
Pteropus vampyrus	ENSPVAG00000003024	1 retrocopy	retro_pvam_79,