RetrogeneDB ID: retro_chof_1894

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_41720:3556..4598(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RIOK2
• Ensembl ID: ENSCHOG00000003803
• Aliases: None
• Description: RIO kinase 2 [Source:HGNC Symbol;Acc:18999]

Sequence

>retro_chof_1894
GCATTAGTATATGAAGAAAGCGATGGAATTAATTGTCAAACTTACAAATTATGGGCTAGTTCATGGAGATTTCAATAAAT
TCAATCTCATGGGGGATAAAGATGACCACATCATCTTGATTGATTTTCCAAAATGGTTTCAACTTTCTCTTTCCAATGCT
GAATGGTATTTTGACAGAGGTGTTAAATGCACTAGCTATTTCTTCCTGTAACATTTCAGCTATGAAAGTGAACTTTATCC
AGCATTTAGTGATATCAGGAGGATGGACTGTCTTGATGGAGAGGTCTCAGCCAGTAGAACACAAAGGAAATTCAGGCAGA
TAATAAACTGCTTCATCTGGTAGGTCCAGATGATAAAAATGTTGAAACTGAAGAAGGATCTAAAATTCTCATTTTCTGAT
GAAGACATGTCAGGAAAAGCAAAGGTCTGTAGGTCAGAAACTGAAAGTGAACAAAGCTCTCTAGGTGAGTCAGATGGCTG
CCGCCGCAGGTTATCTGGAGACTTTAAACAAATAAAGGAAGATTATCTACCAAAGGAGACTGCTGATGCACAAAGTTTTG
AAATGACTGAATTCAACCAAGCTGTAGAGGAAACAAAAGGACAGGTTGTTGAAAACAATTCTGAAATTGAGTTTTCTAAG
GAGCAAAACAAAACTGAAAATGACACTAAGCAAGATGGTCAGTTGGGTCAAGGAGGAATCCCTGCTGGCTCTGAGTAGTA
AGATGAATGCCCTCATCTGATTGCCGTGTCATCATTCAATAAAGAATTCAGGCCATTTGGAGATGAAGAAAGTATGAGAG
ATATTAGAAATCAATATAGAACAAGAACTCTGAGTGCTACTTCTGCAGGCAGTGCTGTAAGCTGTTCAACAATTCCTCTG
GAACTGGTAAAACAGAAGGTGAAATGTCTGCTGACAAAACAGCAGTAGGCAATAGTCAGACGTCAACTGCAGAAAGTAAA
AGCAAATATATTTACCAAACAATGGAGGGAAAACATGCAAAATATTAAATCAAGCTTCGAAGCAGCTAGCTTTTGGGGAG
AA

Alignment

ORF - retro_chof_1894 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.07 %
• Parental protein coverage: 63.14 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ALVYDE-AMELIVKLANHGLIHGDFNEFNLILDKDDHITMIDFPQMVSTSHPNAEWYFDRDVKCIRDFFM
          ALVY.E.AMELIVKL.N.GL.HGDFN.FNL..DKDDHI..IDFP.....S..NAEWYFDR.VKC...FF.
Retrocopy ALVYEE>AMELIVKLTNYGLVHGDFNKFNLMGDKDDHIILIDFPKWFQLSLSNAEWYFDRGVKCTSYFFL

Parental  KRFSYESELYPTFSDIRRTNSLEVEVSASG-YTKEMQADDELLHPVGPDDKNVETEEGS-EFSFSDEEMS
          ..FSYESELYP.FSDIRR...L..EVSAS...TKE.QAD..LLH.VGPDDKNVETEEGS..FSFSDE.MS
Retrocopy *HFSYESELYPAFSDIRRMDCLDGEVSASR<NTKEIQADNKLLHLVGPDDKNVETEEGS>KFSFSDEDMS

Parental  GKAKVCRSETESEQSSLGESDGCCYRSSGDLEQIKEDDL-SENADRHNFEMTEFNQPLEEIKGHVVENSS
          GKAKVCRSETESEQSSLGESDGC..R.SGD..QIKED.L..E.AD...FEMTEFNQ..EE.KG.VVEN.S
Retrocopy GKAKVCRSETESEQSSLGESDGCRRRLSGDFKQIKEDYLPKETADAQSFEMTEFNQAVEETKGQVVENNS

Parental  ETEFSEEQNRTESVTKEDGQTDQGRIYTGSEEYEDECPHLIALSSLNKEFRPFRDEENLRDI-IQYRTRT
          E.EFS.EQN.TE..TK.DGQ..QG.I..GSE....ECPHLIA.SS.NKEFRPF.DEE..RDI..QYRTRT
Retrocopy EIEFSKEQNKTENDTKQDGQLGQGGIPAGSE**D-ECPHLIAVSSFNKEFRPFGDEESMRDIRNQYRTRT

Parental  LSVTSAGSAVSCSTIPPELVKQKVKRQLTKQQKAAVRRRLQKGEANIFTKQRRENMQNIKSSLEAASFWG
          LS.TSAGSAVSCSTIP.ELVKQKVK..LTKQQ.A.VRR.LQK..ANIFTKQ.RENMQNIKSS.EAASFWG
Retrocopy LSATSAGSAVSCSTIPLELVKQKVKCLLTKQQ*AIVRRQLQKVKANIFTKQWRENMQNIKSSFEAASFWG

Parental  D
          .
Retrocopy E

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_1894 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	ENSCHOG00000003803	1 retrocopy	retro_chof_1894 ,
Felis catus	ENSFCAG00000024077	1 retrocopy	retro_fcat_170,