RetrogeneDB ID: retro_chof_796

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_149253:1377..2139(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MINPP1
• Ensembl ID: ENSCHOG00000013275
• Aliases: None
• Description: multiple inositol-polyphosphate phosphatase 1 [Source:HGNC Symbol;Acc:7102]

Sequence

>retro_chof_796
TGTGAGAAGTTTTAACTGAAGTAGAAAGGAATCCTATGGCCCTTTACGATGTAGAAGCCTTCAAAACTGGACCAGAAATG
CAGAACATTTTTTAAAAAGTTGAAGCTACTTTGCAAGTGCCAGTAAGAGATTTAAATGCAGACTTAATTCAGGTAGCTTT
TTTCACCTGTTCATTTGACCTGGCAATTAAAGGTGCTAAATCTCCTTGGTGCAATATTTTTGACATAGCCGATGCAAAGG
TATTAAAGTATTTAAATGATCTGAAACAATACTGGAAAAGAGGATATAGCTATACTATTAATAGTCAATCCAGCTGCACT
CTATTTCAGGATATCCTTCAACACTTGGACAAAGCAATTGAACAGAAACAAAGGTCTCAGCCAATTTCTTCTTCAGTCAT
CCTCCAGTTTGGTCAGACAGAAATCCTTCTTCCACTGCTTTCTCTCATGGGCTACTTCAAAGATAAGGAGCCCCTAATAG
CTTACAATTACAAGGAACAAATGCATCGGATGTTCCGGAGTGGTCACATTGTGCCCTATGCCTCAAACTTGATATTTGTG
ATTTACCATTTTGAAAATGCTAAGAATTGTAAAGAATTCCAAGTTCAGATGTTGTTGAATGAAAAGGTGTTACCCTTTGC
TCACTCCCAAGAGACTGTTCCTTGTATGAGGACCTGAAAGACATTACAAGGACATCCTTCACAGTTATCATACCAGTGAA
GAATGTGAATTACCAAAGGTAAATAGCGTATCTGATGAGCTG

Alignment

ORF - retro_chof_796 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.78 %
• Parental protein coverage: 52.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  CEKF-LTEVERNATALYHVDAFKTGPEMQNILKKVAATLQVPVSDLNADLIQVAFFTCSFDLAIKGVKSP
          CEKF.LTEVERN..ALY.V.AFKTGPEMQNI..KV.ATLQVPV.DLNADLIQVAFFTCSFDLAIKG.KSP
Retrocopy CEKF<LTEVERNPMALYDVEAFKTGPEMQNIF*KVEATLQVPVRDLNADLIQVAFFTCSFDLAIKGAKSP

Parental  WCDVFDIDDAKVLEYLNDLKQYWKRGYGYTINSRSSCTLFQDIFRHLDKAIEQKQRSQPISSPLILQFVQ
          WC..FDI.DAKVL.YLNDLKQYWKRGY.YTINS.SSCTLFQDI..HLDKAIEQKQRSQPISS..ILQF.Q
Retrocopy WCNIFDIADAKVLKYLNDLKQYWKRGYSYTINSQSSCTLFQDILQHLDKAIEQKQRSQPISSSVILQFGQ

Parental  AETLLPLFSFMGYFKDKELLRAYNYKEKIHRLFHSGHIVPYASNLMFVLYHCENAKNPKEEFQVQMLLNE
          .E.LLPL.S.MGYFKDKE.L.AYNYKE..HR.F.SGHIVPYASNL.FV.YH.ENAKN.K.EFQVQMLLNE
Retrocopy TEILLPLLSLMGYFKDKEPLIAYNYKEQMHRMFRSGHIVPYASNLIFVIYHFENAKNCK-EFQVQMLLNE

Parental  KVLPFAHSQETV-SLYEDLKD-HYKDILQSCHTSEECELQKVNSTSDEL
          KVLPFAHSQETV.SLYEDLKD.HYKDIL.S.HTSEECEL.KVNS.SDEL
Retrocopy KVLPFAHSQETV<SLYEDLKD<HYKDILHSYHTSEECELPKVNSVSDEL

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_796 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013275	4 retrocopies	retro_chof_1750, retro_chof_387, retro_chof_786, retro_chof_796 ,
Mus musculus	ENSMUSG00000024896	1 retrocopy	retro_mmus_2502,
Oryctolagus cuniculus	ENSOCUG00000002908	1 retrocopy	retro_ocun_1283,
Rattus norvegicus	ENSRNOG00000011287	1 retrocopy	retro_rnor_32,