RetrogeneDB ID: retro_chof_1350

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_269973:206..624(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MXI1
• Ensembl ID: ENSCHOG00000006556
• Aliases: None
• Description: MAX interactor 1, dimerization protein [Source:HGNC Symbol;Acc:7534]

Sequence

>retro_chof_1350
GAATACTTAGAAGTTCTGATTCCGCTGGAATCAGACTGCACCAGACACAGACAAGGTTTCCTCTACGAAGCCAAAGCGCA
CTTCAAGAGACTTGACGAAGCTGAAAGAAGAGCCAACACCAGCTCGAGAACTTGGAATGAGAACAGAGATTTTTGAAGCA
GTGATTGGAACAGCTGCAGGGTCCTCAGGAGATGGAACGAATTCCAGTGGACAGCACTGGATCGACTGTGTCTTCAGATC
GTTCTGATTGGGAGCGAGAGGAAACGGCGGTGGATGTTGAAAGCGCAGGGCTCTCCCGTGGAGACGTGGACAGTATCAGT
CCCGCCAGCAGCGGTGACAGTGAGGACAGCAGTAGCGGGCAGCGTGTTGGGAGCGAGGAGGGTTAATCCAGTCCAGTGTC
AAACTTTTCTCCACTTCC

Alignment

ORF - retro_chof_1350 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.13 %
• Parental protein coverage: 71.21 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ERLKVLIPLGPDCTRHTTLGLLNKAKAHIKKLEEVER-KSQHQLENLEREQRFLKRRLEQLQGPQEMERI
          E.L.VLIPL..DCTRH...G.L..AKAH.K.L.E.ER.KSQHQLENLE.EQRFLK..LEQLQGPQEMERI
Retrocopy EYLEVLIPLESDCTRHRQ-GFLYEAKAHFKRLDEAER<KSQHQLENLE*EQRFLKQ*LEQLQGPQEMERI

Parental  RMDSIGSTISSDRSDSEREEIEVDVESTEFSHGEVDNISTTSISDIDDHSSLQSIGSDEGYSS-ASVKLS
          ..DS.GST.SSDRSD.EREE..VDVES...S.G.VD.IS..S..D..D.SS.Q..GS.EG.SS..SVKL.
Retrocopy PVDSTGSTVSSDRSDWEREETAVDVESAGLSRGDVDSISPASSGDSEDSSSGQRVGSEEG*SS<SSVKLF

Parental  FTS
          .TS
Retrocopy STS

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_1350 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 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003047	1 retrocopy	retro_chof_1224,
Choloepus hoffmanni	ENSCHOG00000006556	2 retrocopies	retro_chof_1350 , retro_chof_1817,
Cavia porcellus	ENSCPOG00000022901	1 retrocopy	retro_cpor_574,
Dasypus novemcinctus	ENSDNOG00000002479	2 retrocopies	retro_dnov_1336, retro_dnov_668,
Mus musculus	ENSMUSG00000025025	1 retrocopy	retro_mmus_1948,
Sus scrofa	ENSSSCG00000022128	1 retrocopy	retro_sscr_947,
Vicugna pacos	ENSVPAG00000003400	2 retrocopies	retro_vpac_483, retro_vpac_595,