RetrogeneDB ID: retro_chof_553

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_120894:3203..3970(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBA3
• Ensembl ID: ENSCHOG00000013626
• Aliases: None
• Description: ubiquitin-like modifier activating enzyme 3 [Source:HGNC Symbol;Acc:12470]

Sequence

>retro_chof_553
GTGGCTGTTGATGGTGGGTGTGGGGACACTGGAGACTGGGAAGGTCGCTGGAACCATGTAAAGAAGTTCTTTGAGCGACC
TGGACTCTTCACACACCCTGATTTCAAACCGAGCACTGAATCTCTGAAGTTTTTGTTAGATACAGGTAAAGCTCTAGTCA
TTGGAGATGGCGGCTTAGGATGTGAGCTCCTAAGAAATCTGGCATTGTCTGGTTTTAGACAGATTCATGTCATAGACATG
GACACTATAGATGTTTCCAATCTAAATGAGCAGTTTTTATTTAGGCCTAAAGATGTTGGAATTCCTAAAGCTGAAGTTGC
TGCTGAATTTCTAAATGCAAGAATTCCTAAATGCAATGTAGTTCCACATTTCAACAAGATTCAGGATTTTAATGGCACTT
TCTATTGACAATTTCATATTATTGTATGTGGACTGGACTCTATCACTGCCAGAAGATGGATAAATGGCATGCTGATATCT
CTTCTAAATTATGAAGATGGTGTGTTAGATCCAAGCTCCATTGTCCCTTTGATAGATGAGGAACAGAAGGTTTTAAAGGA
AATGCCAGGGTGATTCTACCAGGAATGACTGCTCGTATTAAATGTACACTGGAACTTTATCCACCACAGGTTAATTTTCC
CATGTGCACCATTGCATCTATGCCCAGGCTACCAGAACACTGTGTTGAGTATGTAAGAATATTGCAGTGGCCTAAGGAAC
AACCTTTTGGAGAAGGGGTGCCATTAGATGGAGATGATCCTGATCAT

Alignment

ORF - retro_chof_553 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.55 %
• Parental protein coverage: 58.18 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAVDGGCGDTGDWEGRWNHVKKFLERSGPFTHPDFEPSTESLQFLLDTCKVLVIGAGGLGCELLKNLALS
          .AVDGGCGDTGDWEGRWNHVKKF.ER.G.FTHPDF.PSTESL.FLLDT.K.LVIG.GGLGCELL.NLALS
Retrocopy VAVDGGCGDTGDWEGRWNHVKKFFERPGLFTHPDFKPSTESLKFLLDTGKALVIGDGGLGCELLRNLALS

Parental  GFRQIHVIDMDTIDVSNLNRQFLFRAKDVGRPKAEVAAEFLNDRIPNCNVVPHFNKIQDFNDTFYRQFHI
          GFRQIHVIDMDTIDVSNLN.QFLFR.KDVG.PKAEVAA...........VVPHFNKIQDFN.TFY.QFHI
Retrocopy GFRQIHVIDMDTIDVSNLNEQFLFRPKDVGIPKAEVAAXXXXXXXXXXXVVPHFNKIQDFNGTFY*QFHI

Parental  IVCGLDSIIARRWINGMLISLLNYEDGVLDPSSIVPLIDG-GTEGFKGNARVILPGMTACIECTLELYPP
          IVCGLDSI.ARRWINGMLISLLNYEDGVLDPSSIVPLID..GTEGFKGNARVILPGMTA.I.CTLELYPP
Retrocopy IVCGLDSITARRWINGMLISLLNYEDGVLDPSSIVPLIDE<GTEGFKGNARVILPGMTARIKCTLELYPP

Parental  QVNFPMCTIASMPRLPEHCIEYVRILQWPKEQPFGEGVPLDGDDPDH
          QVNFPMCTIASMPRLPEHC.EYVRILQWPKEQPFGEGVPLDGDDPDH
Retrocopy QVNFPMCTIASMPRLPEHCVEYVRILQWPKEQPFGEGVPLDGDDPDH

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_553 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 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010117	1 retrocopy	retro_amel_204,
Choloepus hoffmanni	ENSCHOG00000013626	2 retrocopies	retro_chof_1740, retro_chof_553 ,
Callithrix jacchus	ENSCJAG00000013395	2 retrocopies	retro_cjac_2827, retro_cjac_2986,
Erinaceus europaeus	ENSEEUG00000005430	2 retrocopies	retro_eeur_374, retro_eeur_663,
Otolemur garnettii	ENSOGAG00000007771	2 retrocopies	retro_ogar_1868, retro_ogar_2776,
Rattus norvegicus	ENSRNOG00000006221	1 retrocopy	retro_rnor_852,
Sus scrofa	ENSSSCG00000011506	1 retrocopy	retro_sscr_192,