RetrogeneDB ID: retro_chof_387

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_102867:263..1135(+)
• 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_387
CTGCTGTAGTCCCTAGCCCGTTGCTCGCTGCTTGAGCCTGGAGATCCAGTGGTTTCAGCGCTCAGCCCCTACTTCGGCAC
CAAGATGTGCTACGAGGATGCCAATCCCGGGCTGATGCCTGACCCTGAGGCACCACGGCGGGACCCCGAGCTGCTGGAGG
GGACTTTCACCCCCGTGCAGCTGGTCGCTCTCATCCGTCATGGAACCGGCTACCCCACGGCCAAACAAATTCCTCAAGCT
GCGACAGCTACACGGGCTGCTGCAGGCTCGCGGTCCAGGTGGTAGCAGAGCCAGAGCTGCCGGCGGACGCGACCTGAGTG
GCACGCTGGCAGATTGGCCGCTGTGGGAGCGGACTGGATGGATGGGCAGCTGCTGGCAAAGGGCGGCAGGACATGCGACA
GCTGGCGCTGCATCTGGCCTCGTTCTTCCCTTCTCTCTTCAGCCGCGAGAACTACGGTCGCCCGCGGCTCATCACCAGCT
CCAAGCACCGCAGCGTGGATTGTGGCACCGCTTTCCTGGAAGGGCTTCAGCAGCACTACCACCTGGGTCTGCCACCACCA
GACGTTGCAGAAAAGGAGTGTGGATTTCCAAGAATTAATAGTAAACTAATGAGGTTCTTTTATCATTGTGAGAAGTTTTT
AACTGAAGTAGAAAGGAATGCTATGGCTCTTTACGATGTAGAAGCCTTCAAAACTGGGCCAGAAATGCAGAACGTTTTTT
AAAAAGTTGAAGCTACTTTGCAAATACCAGTAAGAGAATTAAATGCAGATTTAATTCTGGTAGCTTTTTTCACCTGTTCA
TTTGGCCTGGCAATGAAAGGTGTTAAATCTCCATAGTGTGATGTTTTTGACATGGATGATGCAAAGATATTA

Alignment

ORF - retro_chof_387 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.97 %
• Parental protein coverage: 59.88 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VLLSLVRCSLLEPGDPVVSALSPYFGTKTRYEDANPGPTPDPAAPRRDPELLEGTCTPVQLVALIRHGTR
          .L.SL.RCSLLEPGDPVVSALSPYFGTK..YEDANPG..PDP.APRRDPELLEGT.TPVQLVALIRHGT.
Retrocopy LL*SLARCSLLEPGDPVVSALSPYFGTKMCYEDANPGLMPDPEAPRRDPELLEGTFTPVQLVALIRHGTG

Parental  YPTAKQIR-KLRQLHGLLQARGPSGNSGSAAGGRDLSAALADWPLWY-ADWMDGQLVEKG-RQDMRQLAL
          YPTAKQI..KLRQLHGLLQARGP.G....AAGGRDLS..LADWPLW..ADWMDGQL..KG.RQDMRQLAL
Retrocopy YPTAKQIP>KLRQLHGLLQARGPGGSRARAAGGRDLSGTLADWPLWE<ADWMDGQLLAKG<RQDMRQLAL

Parental  RLASLFPSLFSRENYGRLRLVTSSKHRCVDSGAAFLEGLWQHYHPGLPPPDVAEMECGLPRINDKLMRFF
          .LAS.FPSLFSRENYGR.RL.TSSKHR.VD.G.AFLEGL.QHYH.GLPPPDVAE.ECG.PRIN.KLMRFF
Retrocopy HLASFFPSLFSRENYGRPRLITSSKHRSVDCGTAFLEGLQQHYHLGLPPPDVAEKECGFPRINSKLMRFF

Parental  DHCEKFLTEVERNATALYHVDAFKTGPEMQNILKKVAATLQVPVSDLNADLIQVAFFTCSFDLAIKGVKS
          .HCEKFLTEVERNA.ALY.V.AFKTGPEMQN...KV.ATLQ.PV..LNADLI.VAFFTCSF.LA.KGVKS
Retrocopy YHCEKFLTEVERNAMALYDVEAFKTGPEMQNVF*KVEATLQIPVRELNADLILVAFFTCSFGLAMKGVKS

Parental  PWCDVFDIDDAKVL
          P.CDVFD.DDAK.L
Retrocopy P*CDVFDMDDAKIL

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_387 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,