RetrogeneDB ID: retro_chof_1082

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_19550:9905..10928(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KPNA4
• Ensembl ID: ENSCHOG00000008565
• Aliases: None
• Description: karyopherin alpha 4 (importin alpha 3) [Source:HGNC Symbol;Acc:6397]

Sequence

>retro_chof_1082
AACCCCGGCTTGGAGAACCGCTGCATCAAGAGCTTCAAGAGCAAGGGCCGCGATGTGGAGACAATGCGAAGACACTGAAA
TGAAGTAACAGTTGAACTGTGGAAGAACAAACAAGATGAACACTTACTAAAAAAGAGAAATGTTCCCCAAGAAGAAAGTT
TAGAAGATTCAGATGTTGATACTGACTTTGAAGCACAAAATGTAACACTAGACGCTATATTGCAGAATGCTGCAAGCGAT
AACCCAGTGGTCCAATTGAGTGCTGTCCAGGCTGCAAGAAAGCTATTATCCAGTGACAGAAACCCACTGATTGATGACCT
AATAAAATCTGGGATTTTACCAATTCTAGTCAAATGTCTAGAAAGGGATGATAATCCTTCGTTACAATTTGAAGCTGCTT
GGGCGCTAACTAATATAGTATCAGGAACTTCTGCACAGACTCAAGCTGTTGTACAGTCTAATGCAGTACCTCTTTTTCTA
AGACTTCTCCATTAACCACATCAGAATGTTTGTGAACAAGTATCATGGGCTTTGGGAAACATCATAGGTGATGGTCCTCC
ATGTAGAGATTATGTCATATCACTGGGTGTTGTCAAACCTCTTTTGTCCTTTATCAATCCTTCCATTCCCATCACCTTCC
TTTGGAATGTCATATGGGTCATTGTCAATCTCTGCAGGAATAAGGACCCCCCACTGCCTATGGAGACAGTTCAGGAGATT
TTGCCAGCATTATGTGTCCTCATATACCATACAGACATAAATATCCTTATAGACACTGTTTGAGCTCTGTTGTACCTGAC
AGATGGAGGTAATGAGCAGATTCAGATGGTTATTGATTCAGGGGTTGTGCCATTTCTTGTGCCCCATCTGAGCCACCAGG
AAGTGAAAGTTCAAACAGCAGCCCTCAGGGCAGTCAGCAGTATAGTGACCGGCACGGATGAGCAGACCCAGGCCGTTCTC
AACTGCGATGTCCTGTCCCACTTCCCAAATCTCCTATCACACCCAAAAGAGAAGATAAATAAG

Alignment

ORF - retro_chof_1082 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.59 %
• Parental protein coverage: 65.45 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NEKLDNQRLKNFKNKGRDLEXXXXXXXXXXXXXXXNKRDEHLLKRRNVPHEDICEDSDIDGDYRVQNTSL
          N..L.N...K.FK.KGRD.E...............NK.DEHLLK.RNVP.E...EDSD.D.D...QN..L
Retrocopy NPGLENRCIKSFKSKGRDVETMRRH*NEVTVELWKNKQDEHLLKKRNVPQEESLEDSDVDTDFEAQNVTL

Parental  EAIVQNASSDNQGIQLSAVQAARKLLSSDRNPPIDDLIKSGILPILVHCLERDDNPSLQFEAAWALTNIA
          .AI.QNA.SDN...QLSAVQAARKLLSSDRNP.IDDLIKSGILPILV.CLERDDNPSLQFEAAWALTNI.
Retrocopy DAILQNAASDNPVVQLSAVQAARKLLSSDRNPLIDDLIKSGILPILVKCLERDDNPSLQFEAAWALTNIV

Parental  SGTSEQTQAVVQSNAVPLFLRLLHSPHQNVCEQAVWALGNIIGDGPQCRDYVISLGVVKPLLSFISPSIP
          SGTS.QTQAVVQSNAVPLFLRLLH.PHQNVCEQ..WALGNIIGDGP.CRDYVISLGVVKPLLSFI.PSIP
Retrocopy SGTSAQTQAVVQSNAVPLFLRLLH*PHQNVCEQVSWALGNIIGDGPPCRDYVISLGVVKPLLSFINPSIP

Parental  ITFLRNVTWVMVNLCRHKDPPPPMETIQEILPALCVLIHHTDVNILVDTVWALSYLTDAGNEQIQMVIDS
          ITFL.NV.WV.VNLCR.KDPP.PMET.QEILPALCVLI.HTD.NIL.DTV.AL.YLTD.GNEQIQMVIDS
Retrocopy ITFLWNVIWVIVNLCRNKDPPLPMETVQEILPALCVLIYHTDINILIDTV*ALLYLTDGGNEQIQMVIDS

Parental  GIVPHLVPLLSHQEVKVQTAALRAVGNIVTGTDEQTQVVLNCDALSHFPALLTHPKEKINK
          G.VP.LVP.LSHQEVKVQTAALRAV..IVTGTDEQTQ.VLNCD.LSHFP.LL.HPKEKINK
Retrocopy GVVPFLVPHLSHQEVKVQTAALRAVSSIVTGTDEQTQAVLNCDVLSHFPNLLSHPKEKINK

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_1082 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004243	1 retrocopy	retro_chof_805,
Choloepus hoffmanni	ENSCHOG00000008565	2 retrocopies	retro_chof_1082 , retro_chof_823,
Echinops telfairi	ENSETEG00000019546	1 retrocopy	retro_etel_1695,
Rattus norvegicus	ENSRNOG00000010768	1 retrocopy	retro_rnor_592,