RetrogeneDB ID: retro_chof_578

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_123211:3147..3691(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTEN
• Ensembl ID: ENSCHOG00000009252
• Aliases: None
• Description: phosphatase and tensin homolog [Source:HGNC Symbol;Acc:9588]

Sequence

>retro_chof_578
TATGGAGAAGTAAGGACCACAGTCAAAATGGGAGTAACTATTCCCAGTCAGAGACACTGTGTATTATCATAGATATTAAA
AATCATCTGCATTATAGACCAGTGTCACTGTTGTTTCACAAGATGATCTTCGAAACCATTCTGGTGTTCAGCGGCAGAAC
CTGCAATGCTCAGTTTGTGGTCTGCTAGCTAAATTCCTCAAATTCTGGCCCCACATGACAGGAAGATAAATTCATATACT
TTGAATTCTCTGAGCTATTGCCTGTGTGTGGTGACATCAAAGTAGAGTTATTCCACAAACAGAAAAAGATGCTAAAAAAG
GACAAAATGTTTCACTTTTGAGTAAGTATGTTCTTCATACCAGGGCCAGAGGAAACCTTTGAAAAAGTAGAAAATGGAAG
TCTATGTGGTCAAGAAATTGATAGTATTTGCAGTATAGAGCATGCAGACAATGACAAAGAATGTCTGGTACATACTTTAA
CAATAATTTATCTTGACAAAACAAATAAAGACAAGGCCAACTTGTCTTTTCTCCAAATTTTAAG

Alignment

ORF - retro_chof_578 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.6 %
• Parental protein coverage: 54.84 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YGEVRTRDKKGVTIPSQRRYVYYYSYLLK-NHLDYRPVALLFHKMMFETIPMFSGGTCNPQFVVCQLKVK
          YGEVRT..K.GVTIPSQR..V...S..LK.NHL.YRPV.LLFHKM.FETI..FSG.TCN.QFVVC.L...
Retrocopy YGEVRTTVKMGVTIPSQRHCV--LS*ILK<NHLHYRPVSLLFHKMIFETILVFSGRTCNAQFVVC*LN--

Parental  IYSSSGPTRREDKFMYFEFPQPLPVCGDIKVEFFHKQNKMLKKDKMFHFWVNTFFIPGPEETSEKVENGS
          ..S.SGPT..EDKF.YFEF...LPVCGDIKVE.FHKQ.KMLKKDKMFHF.V..FFIPGPEET.EKVENGS
Retrocopy -SSNSGPT*QEDKFIYFEFSELLPVCGDIKVELFHKQKKMLKKDKMFHF*VSMFFIPGPEETFEKVENGS

Parental  LCDQEIDSICSIERADNDKEYLVLTLTKNDLDKANKDKAN-RYFSPNFK
          LC.QEIDSICSIE.ADNDKE.LV.TLT...LDK.NKDKAN...FSPNFK
Retrocopy LCGQEIDSICSIEHADNDKECLVHTLTIIYLDKTNKDKAN<LVFSPNFK

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_578 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.

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009252	1 retrocopy	retro_chof_578 ,
Homo sapiens	ENSG00000171862	1 retrocopy	retro_hsap_4245,
Gorilla gorilla	ENSGGOG00000000893	1 retrocopy	retro_ggor_2846,
Nomascus leucogenys	ENSNLEG00000012141	1 retrocopy	retro_nleu_1280,
Pongo abelii	ENSPPYG00000002448	1 retrocopy	retro_pabe_3393,
Sarcophilus harrisii	ENSSHAG00000003709	1 retrocopy	retro_shar_828,
Sus scrofa	ENSSSCG00000010440	2 retrocopies	retro_sscr_236, retro_sscr_237,