RetrogeneDB ID: retro_chof_466

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_112486:848..1670(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTIF3
• Ensembl ID: ENSCHOG00000004404
• Aliases: None
• Description: mitochondrial translational initiation factor 3 [Source:HGNC Symbol;Acc:29788]

Sequence

>retro_chof_466
ATGGCTGCACTTTTTCTAAAGAAGTTAATCCTGCAAACTGTGAAGACTGAAATGAACTGCTTTGGAAGATGTTTTGGTAA
ACACGTGCAAAACACAGCACCAGCACCATTGTCCGTTATTGCTTCCGCCCCCAGACTCTTCTCCCTAACCCATGCAAAAT
TTTATAGTACTGTAGAAGAAAGCCAGGATGAAAGAAAAAAGAAAGTAAAAAGTGAAACAGCTTTTAGTAATACTGGAAGA
AAAATTAGTGAGCGAATTATTCGCATAATCGATGAGCACCGCAACGATTTAGGCAGCATGCACCGAGCAGACGTGATTAA
GCTCCTGGACGCGCGAGACCCGTGCTGTGAAAAGGAGCAGCAGCTCCGAGCCTCCAGAATACCGGCTCTTGAGGAGACTC
CTGTCCCCCGAAGAACTGCTCAGGCTCCGAGAAAGGGAAAAAGCCTTCCAAAACTGGACTGACACAGATAAAGGAATGGA
TTATTTTCTTCAATATGACAACATGATTTGGACACAAGAGTAAACAGATCAGAAATGGATTGACAAAAAATATCGAGTTC
AAATTACTGTAAAGAAAGGGAAGAGTGTAGAAGAGCCAGAAAATAAAGTGGAAGAGCTATTTAATCAGATCCTCCAGACC
ATGCTTGGAGTGGCCACCTTCTGAACCAGGCCACAAGCCATCAAAGGAGGAAAAGCTGCAATGTGTGTTCTTCCTCATTT
GAGCAAAAAAGGAGGAGGATGAGTACAGGGAAACTCAGGGGACCCAGAAAGGAGACAAAAGAAAATGTAAATGAAAATGA
TAGAAATTCAGTTGTTCTACAG

Alignment

ORF - retro_chof_466 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.44 %
• Parental protein coverage: 99.64 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  MAALFLKRLILQTVKTETNCFGRCFGKHIVQKTAPAPLSIIASAPRLSFLTHAKFYSTVEDSQDERKKKQ
          MAALFLK.LILQTVKTE.NCFGRCFGKH.VQ.TAPAPLS.IASAPRL..LTHAKFYSTVE.SQD......
Retrocopy MAALFLKKLILQTVKTEMNCFGRCFGKH-VQNTAPAPLSVIASAPRLFSLTHAKFYSTVEESQDXXXXXX

Parental  KTETAFSNTGRKISERIIRVIDEHGNDLGSMHRANVIKLLDARD-LRLVKRSSSSEPPEYQLMTGLQIHE
          ....AFSNTGRKISERIIR.IDEH.NDLGSMHRA.VIKLLDARD.......SSS.EPPEY.L...L...E
Retrocopy XXXXAFSNTGRKISERIIRIIDEHRNDLGSMHRADVIKLLDARD>RAVKRSSSS-EPPEYRLLRRLLSPE

Parental  ERLRLREREKA-KPK-TGPTQIKEL-TFSSNIGQHDLDT-KSKQ-TQKWIEKKYRVQITIKKGKYVEEPE
          E.LRLREREKA..PK.TG.TQIKE...FSS.I.QHDLDT.KSKQ..QKWI.KKYRVQIT.KKGK.VEEPE
Retrocopy ELLRLREREKA<LPK<TGLTQIKEW>LFSS-I*QHDLDT<KSKQ<DQKWIDKKYRVQITVKKGKSVEEPE

Parental  NKMEELFNQILQTMPGMATFSTRPQAIKGGKATMCVLRHLS-KKEEDEYRETQGTQKGDLTK-ENGNEKE
          NK.EELFNQILQTM.G.ATF.TRPQAIKGGKA.MCVL.HLS.KKEEDEYRETQGTQKGD..K..N.N...
Retrocopy NKVEELFNQILQTMLGVATF*TRPQAIKGGKAAMCVLPHLS>KKEEDEYRETQGTQKGDKRK>VNENDRN

Parental  LSCLQ
          ...LQ
Retrocopy SVVLQ

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_466 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004404	1 retrocopy	retro_chof_466 ,
Homo sapiens	ENSG00000122033	1 retrocopy	retro_hsap_3284,
Gorilla gorilla	ENSGGOG00000008409	1 retrocopy	retro_ggor_1318,
Nomascus leucogenys	ENSNLEG00000000343	1 retrocopy	retro_nleu_1350,
Oryctolagus cuniculus	ENSOCUG00000011721	1 retrocopy	retro_ocun_533,
Pongo abelii	ENSPPYG00000005236	1 retrocopy	retro_pabe_2713,
Pan troglodytes	ENSPTRG00000005732	1 retrocopy	retro_ptro_2221,
Tupaia belangeri	ENSTBEG00000012276	3 retrocopies	retro_tbel_4048, retro_tbel_4602, retro_tbel_760,