RetrogeneDB ID: retro_chof_203

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_4431:9469..10653(+)
• Located in intron of: ENSCHOG00000008857

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLS1
• Ensembl ID: ENSCHOG00000011426
• Aliases: None
• Description: plastin 1 [Source:HGNC Symbol;Acc:9090]

Sequence

>retro_chof_203
ATAGACAGCAGTGGGTATGTCAGTGACTATGAACTTCAGGACCTGTTTAAGAAGCAAGCCTTCCTATGCCTGGCTACAAA
GTGTGCGAGAATGTGGAGAAAATTCTAGCAGTTGCTGACAACAACAAAGATGGCAAAATCAGCTTTGAAGAGTTTGTGTT
ACTAATGCAGGAGCTAAAAAGCAAGGACATCAGCAAAACATTCTGCAAAATAATTAACAAGAGGGAAGGGATTACCGCTA
TTGGATGAACTTCAGCCATTTCCAGTGAGGGTACACAGCATTCTTATTCAGAGGAAGAAAAAGTGGCTTTTGTTAACTGG
ATAAACAAAGCCCTAGAGAATGACCCTGACTGTAAGCATCTCATACCCATGAATCCCAATGACGGCAGTATTTTCAAATC
ACTTGCAGATGGCATCCTTCTTTGCAAAATGATCAACTTATCAGAACCAGATACAATTGATGAAAGAGCCATCAATAAGA
AAAAGCTCACCCCTTTCACTATTTCCAAAAATTTAAACCTAGCCCTGAATTCTGCCTCTGCCATTGGTTGCACAGTGGTC
AACATTGGCACACAGGATCTCAAAGAAGGAAAACCTCACTTGGTCTTGGGACTTCTGTGGCAGATCATCAAAGTTGGTCT
TTTTGCTGATATTGAGATTTCCAGGAATGAAGCTCTGATTACATTGCTGAGAGAAGGTGAGGAACTAGAGGAGCTAATGA
AGCTTTCTCCTGAGGAATTACTGCTGCGATGGGTGAACTACCATCTGACCAATGCAGGATGGCGTATTGTCAATAACTTC
AGCCAAGACATTAAGGATTCAAGAGCCTATTTTCATCTGCTTAATCAGATTGCCCCTAAGGGTGACAGGGATGATGGACC
TGCCATTGTCATTGACCTTTCAGGATTTAATGAGCAAAATGACCTGAAGCCTGCTGGATTCATGCTTCAAGAAGCAGATA
AATTGGGCTGTAAACGGTTTGTTACTCCTGCAGATGTGGTTTCAGGCAATCCTAAACTCAATTTAGCTTTTGTAGCTAAT
CTCTTTAACACATATCCATGCTTACGTAAACCTAATAATAATGACATCAATATGAATTTATTGGAAGGAGAGAGCAAGGA
AGAGAGGACATTTCAGAATTGGATGAATTCCTTTGGGGTCAACCCATACATTAATCATTTGTAC

Alignment

ORF - retro_chof_203 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.94 %
• Parental protein coverage: 65.12 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IDNSGYVSDYELQDLFK-EASLPLPGYKVREIVEKILAVADNNKDGKISFEEFVSLMQELKSKDISKTFR
          ID.SGYVSDYELQDLFK.EASLP.PGYKV.E.VEKILAVADNNKDGKISFEEFV.LMQELKSKDISKTF.
Retrocopy IDSSGYVSDYELQDLFK<EASLPMPGYKVCENVEKILAVADNNKDGKISFEEFVLLMQELKSKDISKTFC

Parental  KIINKREGITAIGGTSAISSEGTQHSYSEEEKVAFVNWINKALENDPDCKHLIPMNPNDGSLFKSLADGI
          KIINKREGITAIG.TSAISSEGTQHSYSEEEKVAFVNWINKALENDPDCKHLIPMNPNDGS.FKSLADGI
Retrocopy KIINKREGITAIG*TSAISSEGTQHSYSEEEKVAFVNWINKALENDPDCKHLIPMNPNDGSIFKSLADGI

Parental  LLCKMIN-SEPDTIDERAINTKKLTPFTISENLNLALNSASAIGCTVVNIGAQDLKEGKPHLVLGLLWQI
          LLCKMIN.SEPDTIDERAIN.KKLTPFTIS.NLNLALNSASAIGCTVVNIG.QDLKEGKPHLVLGLLWQI
Retrocopy LLCKMINLSEPDTIDERAINKKKLTPFTISKNLNLALNSASAIGCTVVNIGTQDLKEGKPHLVLGLLWQI

Parental  IKVGLFADIEISRNEALITLLSEGEELEELMKLSPEELLLRWVNYHLTNAGWRTINNFSQDIKDSRAYFH
          IKVGLFADIEISRNEALITLL.EGEELEELMKLSPEELLLRWVNYHLTNAGWR..NNFSQDIKDSRAYFH
Retrocopy IKVGLFADIEISRNEALITLLREGEELEELMKLSPEELLLRWVNYHLTNAGWRIVNNFSQDIKDSRAYFH

Parental  LLNQIAPKGDRDDGPAIVIDLSGFNEQNDLKRAGFMLQEADKLGCKQFVTPADVVSGNPKLNLAFVANLF
          LLNQIAPKGDRDDGPAIVIDLSGFNEQNDLK.AGFMLQEADKLGCK.FVTPADVVSGNPKLNLAFVANLF
Retrocopy LLNQIAPKGDRDDGPAIVIDLSGFNEQNDLKPAGFMLQEADKLGCKRFVTPADVVSGNPKLNLAFVANLF

Parental  NTYPCLHKPDNNDIDVNLLEGESKEERTFRNWMNSLGVNPYINHLY
          NTYPCL.KP.NNDI..NLLEGESKEERTF.NWMNS.GVNPYINHLY
Retrocopy NTYPCLRKPNNNDINMNLLEGESKEERTFQNWMNSFGVNPYINHLY

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_203 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011426	1 retrocopy	retro_chof_203 ,
Choloepus hoffmanni	ENSCHOG00000012037	1 retrocopy	retro_chof_1057,
Nomascus leucogenys	ENSNLEG00000004830	1 retrocopy	retro_nleu_285,