RetrogeneDB ID: retro_chof_2700

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_98770:1..618(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTFR1
• Ensembl ID: ENSCHOG00000006664
• Aliases: None
• Description: mitochondrial fission regulator 1 [Source:HGNC Symbol;Acc:29510]

Sequence

>retro_chof_2700
CCAATCACACAGATTTCTTTACCAAACGATTGTTAAGGAGTGTTTCAACTGGTATCAGCAACACGTTTGATGAAGGAAGC
CCTACGGAAGCTCAATTCTCTTGAATTTGTAATAGCCACTTTCAGAGTTCATATTGCCAATAATGGTGGCTATGCAAGAC
CATCAGTTCTCTCTGCTGGGATTTGGTTTCTACCGCATCTGTTACCACAGCACTACCACCACTACCTCCCATCCCCACCA
ACTGCCCTCCCTGCAACAGAGCTCTACCAAAATGATCTGATTAAAGAGCAAATAAAAGCAAAGAGTGAAAAAAGCTAATT
GCTGAAAAGACGAGTCCAAAGAAACCTGACATGCCAAATATGTTAAAAATCCTTAAACATATTCACAGTGTAAAATTTTG
GTCTGTTAAAAGGTCAGAGCAAGATGTAAAGCCCAAACTAGTGGACCCTACTGACCCCGCTGCCCTCATTGCAGAGGCTC
TGAAAAAGAAATTTGCTCATCGGTATCGAAGCAATAGCCAAAATGAAGTTGAAAAAGTAATTCCAAAGTCAGAATTAGAG
ACCACCTCAGGAACAGTGTTGTTTGGGCCACATGTATTGAAGTCAACTGGAAAAATA

Alignment

ORF - retro_chof_2700 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.08 %
• Parental protein coverage: 62.95 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PSRRISLSNLSQEEPQLRTTALANEEALQKISALENELATLRAQIAKIVTLQEQQNLIAG-DLASTTSVT
          P...ISL.N......QL........EAL.K...LE...AT.R..IA..........L.AG.DL.ST.SVT
Retrocopy PITQISLPNDC*GVFQLVSATRLMKEALRKLNSLEFVIATFRVHIANNGGYARPSVLSAG<DLVSTASVT

Parental  TALPCVPPPP-PPPPPPLPATGLHQSTSAIDLIKERRE-KKASAGKINPKKPDMPNMLEILKDMNSVKLR
          TAL...PP.P.P.PP..LPAT.L.Q.......IK...E.KK..A.K..PKKPDMPNML.ILK...SVK..
Retrocopy TAL---PPLP>PSPPTALPATELYQNDLIKEQIKAKSE<KKLIAEKTSPKKPDMPNMLKILKHIHSVKFW

Parental  SVKRSEQDVKPKPVDPADPDSTTLEPLKKKFAHRYLSDSQNEAEKVVPKSESETTSGTMLFGPHMLKSTG
          SVKRSEQDVKPK.VDP.DP.....E.LKKKFAHRY.S.SQNE.EKV.PKSE.ETTSGT.LFGPH.LKSTG
Retrocopy SVKRSEQDVKPKLVDPTDPAALIAEALKKKFAHRYRSNSQNEVEKVIPKSELETTSGTVLFGPHVLKSTG

Parental  RM
          ..
Retrocopy KI

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_2700 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 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012281	1 retrocopy	retro_amel_1640,
Choloepus hoffmanni	ENSCHOG00000006664	3 retrocopies	retro_chof_1268, retro_chof_2700 , retro_chof_483,
Dipodomys ordii	ENSDORG00000016322	1 retrocopy	retro_dord_293,
Homo sapiens	ENSG00000066855	1 retrocopy	retro_hsap_4849,
Macaca mulatta	ENSMMUG00000011263	1 retrocopy	retro_mmul_2590,
Mustela putorius furo	ENSMPUG00000009909	2 retrocopies	retro_mputfur_1244, retro_mputfur_894,
Oryctolagus cuniculus	ENSOCUG00000008165	1 retrocopy	retro_ocun_1594,
Pongo abelii	ENSPPYG00000018631	1 retrocopy	retro_pabe_3769,
Rattus norvegicus	ENSRNOG00000021359	1 retrocopy	retro_rnor_1821,
Tarsius syrichta	ENSTSYG00000010102	1 retrocopy	retro_tsyr_1899,