RetrogeneDB ID: retro_chof_1347

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_26895:8359..8958(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP4R2
• Ensembl ID: ENSCHOG00000007954
• Aliases: None
• Description: protein phosphatase 4, regulatory subunit 2 [Source:HGNC Symbol;Acc:18296]

Sequence

>retro_chof_1347
GAAACAATGATTCAGTGTCCCAATTTAAAGGTTATTTTATTTTCAGACTGGAGAAAGTTACAGGTGATTTCAGAACTTCA
GCTCCTGAACCAAGAGGTTCTCCCAACCCTAATGTCGAATATATTCCCTTTGATGAAATGAAGGAAAGAATACTGAAAAT
TGCCACTGGATTTAATGATATCCCTTTTACTATTCAGCGACTGTGTGAATTGCTAACAGATCCAAGGAGAAACTATACAG
GAACAGACAAATTTCTCAGAGGAGTAGAAAAGAATGTGATGGTTGTTAGCTGTGTTTATCCTTCTTCAGAGAAAAACAAT
TCTAGGAGTTTGAATTGAATGAACAGTGTTATGTTTCCTGGAAATTCACCAAGTTATGCTGAGAGGTCTAGTATAAATGG
GCCTAGTATAAATCTACCAAAGGTTTCTTTGTCAGCCCCAATGACAACAAATAGCTTACCAGAGAGCACAGATAGCAAAG
AGTCAAACTTAAGCAAAATGAGGACAAAAATCACAGTGACTCCCTGACATCTGGATCAGAAAGTTCCTCAGTGAGCCCTA
TAAAAAACAACAGCCAGATGAGATGCTGTGAAAGCTGAA

Alignment

ORF - retro_chof_1347 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.12 %
• Parental protein coverage: 63.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ETMIQW-SQFKGYFIFKLEKVMDDFRTSSPEPRGPPNPNVEYIPFDEMKERILKIVTGFNGIPFTIQRLC
          ETMIQ..SQFKGYFIF.LEKV..DFRTS.PEPRG.PNPNVEYIPFDEMKERILKI.TGFN.IPFTIQRLC
Retrocopy ETMIQC<SQFKGYFIFRLEKVTGDFRTSAPEPRGSPNPNVEYIPFDEMKERILKIATGFNDIPFTIQRLC

Parental  ELLTDPRRNYTGTDKFLRGVEKNVMVVSCVYPSSEKNNSSSLNRMNGVMFPGNSPSYTERSNINGPGTPR
          ELLTDPRRNYTGTDKFLRGVEKNVMVVSCVYPSSEKNNS.SLN.MN.VMFPGNSPSY.ERS.INGP....
Retrocopy ELLTDPRRNYTGTDKFLRGVEKNVMVVSCVYPSSEKNNSRSLN*MNSVMFPGNSPSYAERSSINGPS---

Parental  PLNRPKVSLSAPMTTNGLPESTDSKESN-LQQNEDKNHSDSLTSGSESSSVSPIKN-KHPDE-DAVEAE
          ..N.PKVSLSAPMTTN.LPESTDSKESN.L.QNEDKNHSDSLTSGSESSSVSPIKN...PDE.DAV.AE
Retrocopy -INLPKVSLSAPMTTNSLPESTDSKESN<LKQNEDKNHSDSLTSGSESSSVSPIKN<QQPDE<DAVKAE

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_1347 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 8 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007954	3 retrocopies	retro_chof_1347 , retro_chof_1914, retro_chof_2285,
Echinops telfairi	ENSETEG00000019946	2 retrocopies	retro_etel_1238, retro_etel_148,
Homo sapiens	ENSG00000163605	6 retrocopies	retro_hsap_2744, retro_hsap_2745, retro_hsap_2746, retro_hsap_2904, retro_hsap_3138, retro_hsap_3283,
Loxodonta africana	ENSLAFG00000000513	1 retrocopy	retro_lafr_603,
Macaca mulatta	ENSMMUG00000016959	1 retrocopy	retro_mmul_1224,
Mus musculus	ENSMUSG00000052144	3 retrocopies	retro_mmus_1068, retro_mmus_1157, retro_mmus_3474,
Oryctolagus cuniculus	ENSOCUG00000006235	1 retrocopy	retro_ocun_292,
Pan troglodytes	ENSPTRG00000015108	5 retrocopies	retro_ptro_1855, retro_ptro_1856, retro_ptro_2121, retro_ptro_2220, retro_ptro_2974,