RetrogeneDB ID: retro_chof_589

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_124479:1259..2596(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSPA4
• Ensembl ID: ENSCHOG00000004852
• Aliases: None
• Description: heat shock 70kDa protein 4 [Source:HGNC Symbol;Acc:5237]

Sequence

>retro_chof_589
TGTTTCTATACTGAGGGGGAAAGACGATCAGTGATGGATGCAACACAGATTGCTGGTCTCAGTTGTCTTCGATTAACGAA
TGAAGCTACTGCAGTTACTCTTGCATATGGAATTTATAAACAAGATCTTACTAACTTAGAAGAGAAACCAAGAAGTGTGT
TTTTTGTAGACATGGGGCATTCTGCTTATCAGGTTTCTGTATGTGCATTTAATAGACGAAAACTGAAAGTTATGACCACT
GCTTTTGACACAACACTGGGAGGCAGAAAATTTGATGAAGTGTTAGTAAATCATTTATGCAAAGAATTTGGGAATAAATA
CAAACTAGACATAAAGTCCAAAATCCATGCATTATTAAGACTGTCTCAAGAATGTGAGAATCTCAAGAAATTGATGAGTG
CAAATGCTTCAGACCTCCCTTTGAACATGGAATATTTTATGAATGGTGTTGATGTATCTGGAACTATGAATAGAGGCAAA
TTTCTGGAGATGTCTCATGATCTCTTAGCTAGAGTGGATCCACCACTTTGTAGTGTTTTGGAACAAGCCAAGTTAAAGAA
AGAAGATATTTATGCAGTAGAGATAGTAGGTGGTGCTACATGAATCCCTACAGTAGAAGAGAAAATCAGCAAATTTTTGG
TAAAGAACTTAGTACAACATTAAATGCTGATGAAGCTGTCACTGGAGGCTGTGCATTGCTGTGTGCCATCTTGTCACCTG
CCTTCAAAGTCAGAGAATTTTCCATCACTGATGTTAGTACCATATCCAGTATCTCTGAGATGGAATTCTCCAGCTGAAGA
AGGGTTAAGTGACTGTGAAGTCTTTCCAAAAAAATCATGCTGCTCCCTTCTCTAAAGTCCTCGCATCTTATAGAAAGGAA
CCTTGCACTCTTGAGGCCTGTTGCAGCTCTTTTCAGGAATTGCCCTATCCAGATCCTGCTGTTGCTCAGTTTCAGTTCAG
AAAGTCACCCCCAGTCTAATGGCTCCACTTCAAAAGTGAAAGTAAAGGTTCCAGTAAATGTGCATGGCATTTTCAGTGTG
TCCAGTGCATCCCTAGTGGAAGTGCACAAGTCTGAGGAAAATAAGGAACCTGTGGAAACGGATCGGAATGCAAAGGAGGA
AGAGAAGTTGCAAGTGGACCAGGAGGAACCACATGTTGAAGAGCAACAGCAGCAGACTCCAGCAGAAAATAAGGCAGAGT
ATGAAGAAATGCAGACCTCTCAAGCTGGATCAAAAGACAAAAAAATGGACCAACCACCTTAAGCCAAGAAGGCCGAAGTA
AAGACCAGTACAGTAGACCTGCCAATTGAGAATCAGCTATTATGGCAGATAGAGAGA

Alignment

ORF - retro_chof_589 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.14 %
• Parental protein coverage: 53.41 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  CFYTDAERRSVMDATQIAGLNCLRLMNETTAVALAYGIYKQDLPALEEKPRNVVFVDMGHSAYQVSVCAF
          CFYT..ERRSVMDATQIAGL.CLRL.NE.TAV.LAYGIYKQDL..LEEKPR.V.FVDMGHSAYQVSVCAF
Retrocopy CFYTEGERRSVMDATQIAGLSCLRLTNEATAVTLAYGIYKQDLTNLEEKPRSVFFVDMGHSAYQVSVCAF

Parental  NRGKLKVLATAFDTTLGGRKFDEVLVNHFCEEFGKKYKLDIKSKIRALLRLSQECEKLKKLMSANASDLP
          NR.KLKV..TAFDTTLGGRKFDEVLVNH.C.EFG.KYKLDIKSKI.ALLRLSQECE.LKKLMSANASDLP
Retrocopy NRRKLKVMTTAFDTTLGGRKFDEVLVNHLCKEFGNKYKLDIKSKIHALLRLSQECENLKKLMSANASDLP

Parental  LNIECFMNDVDVSGTMNRGKFLEMCDDILARVEPPLRSVLEQAKLKKEDIYAVEIVGGATRIPAVKEKIS
          LN.E.FMN.VDVSGTMNRGKFLEM..D.LARV.PPL.SVLEQAKLKKEDIYAVEIVGGAT.IP.V.EKIS
Retrocopy LNMEYFMNGVDVSGTMNRGKFLEMSHDLLARVDPPLCSVLEQAKLKKEDIYAVEIVGGAT*IPTVEEKIS

Parental  KF-FGKELSTTLNADEAVTRGCALQCAILSPAFKVREFSITDV-VPYPISLRWNSPAEEGSSDCEVFP-K
          KF.FGKELSTTLNADEAVT.GCAL.CAILSPAFKVREFSITDV.VPYP.SLRWNSPAEEG.SDCEVFP.K
Retrocopy KF<FGKELSTTLNADEAVTGGCALLCAILSPAFKVREFSITDV>VPYPVSLRWNSPAEEGLSDCEVFP>K

Parental  NHAAPFSKVLTFYRKEPFTLEAYYSSPQELPYPDPAVAQF-SVQKVT-PQSDGSSSKVKVKVRINVHGIF
          NHAAPFSKVL..YRKEP.TLEA..SS.QELPYPDPAVAQF.SVQKVT.PQS.GS.SKVKVKV..NVHGIF
Retrocopy NHAAPFSKVLASYRKEPCTLEACCSSFQELPYPDPAVAQF<SVQKVT<PQSNGSTSKVKVKVPVNVHGIF

Parental  SVSSASLVEVHKSEENEEPMETDQNAKEEEKMQVDQEEPHVEEQQQQTPAENKAESEEMETSQAGSKDKK
          SVSSASLVEVHKSEEN.EP.ETD.NAKEEEK.QVDQEEPHVEEQQQQTPAENKAE.EEM.TSQAGSKDKK
Retrocopy SVSSASLVEVHKSEENKEPVETDRNAKEEEKLQVDQEEPHVEEQQQQTPAENKAEYEEMQTSQAGSKDKK

Parental  MDQPPQAKKAKVKTSTVDLPIENHLLWQIDR
          MDQPP.AKKA.VKTSTVDLPIEN.LLWQI.R
Retrocopy MDQPP*AKKAEVKTSTVDLPIENQLLWQIER

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_589 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004852	1 retrocopy	retro_chof_589 ,
Choloepus hoffmanni	ENSCHOG00000013998	1 retrocopy	retro_chof_1873,