RetrogeneDB ID: retro_chof_1750

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_375408:31..1167(+)
• 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_1750
CAAATTCTCAAGCTGCGACAGCTACACGGGCTGCTGCACGCTCGCGGTCCACGTGGTAGCACAGCCAGCGCTGCCGGCGG
ACGCGACCTGAGTGCCACGCTGGCACATTGGCCGCTGTGGTAACGGACTGGATGGACGGGCAGCTGCTGGAGAAAGGGCG
GCAGGACATGCGACAGCTGGCGCTGCATCTGGCCTCGCTCTTCCCTTCTCTCTTCAGCCGCGAGAACTACGGTCGCCTGC
GGCTCATCATCAGCTCCAAGCACCGCAGCGTGGATTGTGCCACCGCTTTCCTGGAGGTGCTTCGGCAGCACTACCACCCG
GGACTGCCACCACCAGACATTGCAAAAAAGGAGTGTGGACTTGCAAGGATTAATGATAAACTAATGAGGTTCTTTTATCA
TTGTGAGAAGTTTTTAACTGAAGTAGAAAGGAATGCTATGGCTCTTTACGATGTAGAAGCCTTCAAAACTGGACCAGAAA
AGCAGAACATTTTTTAAAAAGTTGAAGCTACTTTGCAAGTGCCAGGAAGGGAATTAAATGCAGGTTTAATTCTGGTAGCT
TTTTTCACCTGTTCATTTGACCTGGCAATTAAAGGTGTTAAATCTCCTTGGTGCAGTGTTTTTGACATGGATGATGCAAA
GGTATTAAAGTGTTTAAATGATCTGAAACAATATTGGAAAAGAGGATATAACTATACTATTAATAGTCAATCCAGCTGCA
CTCTTTCAGGATATCGTTCAGCACTTGGACAAAGCAATTGAACAGAAACAAAGGTCTCAGCCAATTTCTTCTCCACTCAT
CCTCCAGTTTGTTCAGGCAGAAACCCTTCTTCCACTGCTTTCTCTCATGGGCTACTTCAAAGATAAAGAGCTCCTAACAG
CTTACAATTACAAGGAAAAAATGCATCAGATATTCTGTAGTGGTCATATCGTACCCTATGCCTCAAACTTGATATTTGTG
CTTTACCATTGTGAAAATGCTAAGAATCCTAAAGAAGAATTCCAAGTGCAAATGTTGTTGAATGAAAAGGTGTTACCCTT
TGCTTACTCCCAAGAGACTGTTCTTTGTATGAGGATCTGAAAGACCATTACAAGGACATCCTTCAGAATTGTCATACCAG
TGAGGAATGTGAATTA

Alignment

ORF - retro_chof_1750 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.77 %
• Parental protein coverage: 78.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QIRKLRQLHGLLQARGPSGNSGSAAGGRDLSAALADWPLW-YADWMDGQLVEKGRQDMRQLALRLASLFP
          QI.KLRQLHGLL.ARGP.G...SAAGGRDLSA.LA.WPLW...DWMDGQL.EKGRQDMRQLAL.LASLFP
Retrocopy QILKLRQLHGLLHARGPRGSTASAAGGRDLSATLAHWPLW<VTDWMDGQLLEKGRQDMRQLALHLASLFP

Parental  SLFSRENYGRLRLVTSSKHRCVDSGAAFLEGLWQHYHPGLPPPDVAEMECGLPRINDKLMRFFDHCEKFL
          SLFSRENYGRLRL..SSKHR.VD...AFLE.L.QHYHPGLPPPD.A..ECGL.RINDKLMRFF.HCEKFL
Retrocopy SLFSRENYGRLRLIISSKHRSVDCATAFLEVLRQHYHPGLPPPDIAKKECGLARINDKLMRFFYHCEKFL

Parental  TEVERNATALYHVDAFKTGPEMQNILKKVAATLQVPVSDLNADLIQVAFFTCSFDLAIKGVKSPWCDVFD
          TEVERNA.ALY.V.AFKTGPE.QNI..KV.ATLQVP...LNA.LI.VAFFTCSFDLAIKGVKSPWC.VFD
Retrocopy TEVERNAMALYDVEAFKTGPEKQNIF*KVEATLQVPGRELNAGLILVAFFTCSFDLAIKGVKSPWCSVFD

Parental  IDDAKVLEYLNDLKQYWKRGYGYTINSRSSCTL-FQDIFRHLDKAIEQKQ-RSQPISSPLILQFVQAETL
          .DDAKVL..LNDLKQYWKRGY.YTINS.SSCTL.F...F....K.......RSQPISSPLILQFVQAETL
Retrocopy MDDAKVLKCLNDLKQYWKRGYNYTINSQSSCTL<FRISFSTWTKQLNRNK<RSQPISSPLILQFVQAETL

Parental  LPLFSFMGYFKDKELLRAYNYKEKIHRLFHSGHIVPYASNLMFVLYHCENAKNPKEEFQVQMLLNEKVLP
          LPL.S.MGYFKDKELL.AYNYKEK.H..F.SGHIVPYASNL.FVLYHCENAKNPKEEFQVQMLLNEKVLP
Retrocopy LPLLSLMGYFKDKELLTAYNYKEKMHQIFCSGHIVPYASNLIFVLYHCENAKNPKEEFQVQMLLNEKVLP

Parental  FAHSQETV-SLYEDLKDHYKDILQSCHTSEECEL
          FA.SQETV.SLYEDLKDHYKDILQ.CHTSEECEL
Retrocopy FAYSQETV<SLYEDLKDHYKDILQNCHTSEECEL

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_1750 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,