RetrogeneDB ID: retro_chof_483

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_113487:2971..3955(-)
• 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_483
ATGCTTGACTGGATTAAGTGCTTAATTAGGATGGTTTTCAACAAGTTGGAGTGAGCATGTAATCAGTACTTTGGTCTAGG
AAGCCATATGGTTCATTTCAAAGTATTGTAAGGAAAATTGGTTCTAATTTGTCTCTGATTCAGTGTCCAAGAGTTCAGTT
CCAGCTTACCAGCCATACAACAGAATAGAGTCTAACCACCAAGGAGAGGATGCAGTGGCATCTTTTGCTGATATTGGATG
GGTAGCCAAAGAAGATGGAGAGTGTTCAACAAATTAAGGACAGAAGTCAGGTCAAGACAATCCCTTCAGAAAGAACTTCC
TTTCTTTGAGAAGCCCCCAAGCAGGCAGATTTCCTTACCAAACCTGTCTTAAGAAGAGTCTCAACTGAGGACACAACACT
GGCGAATGAGGAAGCACTACAGAAGATCAGTGCTCTTGAAATGACTCACACTCTCAGAGCTCAGACTGCCAAAAATTGTG
ACCCTGCAAGAGCAGCAGAATATCATTGCAGGTGAATTAGATTCTACCACATCTGTTACCACAGCACTACCCTCCATCCC
ACCACCTCCACCACCAACTGCCCTCCCTGCAACAGAGCTCTACCAAAATACATCTGCTATTGATCTGATTAAAAAGCAAA
GAGTGAAAAAAGCTAATTGCTGAAAAGACGAGTCCAAAGAAACCTGACATGCCAAATATGGGTAGAAATCCTTAAAGATA
GGAACAGTGTAAAACCTCAGTCCATTAAAAAGTCAGAGCAAGATGTAAAGCCCAAACTAGTGGACCCTACAGACCCCGCT
GCCCTCATTGCAGGAGCTCTGAAAATGAAAGTTGTTCATTGGTTCAAAGCAATAGCCAAAGTGAAGTTGAAAAGTAATTC
CAAAATCAGAATCAGAGACCAAATCAGGAATGGTATTGTTTGGGCCACACAGGTTGAAGTCTATAGGAAAAATGAAGTCT
TTAATTGAAAATGGTTCAACTTCC

Alignment

ORF - retro_chof_483 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.9 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 9

Retrocopy - Parental Gene Alignment:

Parental  MLDWIKRLIRMVF-QQVGVSMQSVLWSGKPYGSSRSIVRKIGTNLSLIQCPRVQFQLTSHATEWS-PDHQ
          MLDWIK.LIRMVF.QQVGVSM.SVLWS.KPYGS..SIVRKIG.NLSLIQCPRVQFQLTSH.TE.S...HQ
Retrocopy MLDWIKCLIRMVF<QQVGVSM*SVLWSRKPYGSFQSIVRKIGSNLSLIQCPRVQFQLTSHTTE*S<SNHQ

Parental  EEDRVASFADVGWVAKEGGECST-RLRTEVRSRQPLQEDLPFFEKPPSRRISLSNLSQEEPQLRT-TALA
          .ED.VASFAD.GWVAKE.GECST..LRTEVRSRQ.LQ..LPFFEKPPSR.ISL.NLS.EE.QLRT.T.LA
Retrocopy GEDAVASFADIGWVAKEDGECST<KLRTEVRSRQSLQKELPFFEKPPSRQISLPNLS*EESQLRT<TTLA

Parental  NEEALQKISALENELATLRAQIA-KIVTLQEQQNLIAGDLASTTSVTTALPCVPPPPPPPPPPLPATGLH
          NEEALQKISALE....TLRAQ.A.KIVTLQEQQN.IAG.L.STTSVTTALP....PPPPPP..LPAT.L.
Retrocopy NEEALQKISALE-MTHTLRAQTA>KIVTLQEQQNIIAGELDSTTSVTTALPSI--PPPPPPTALPATELY

Parental  QSTSAIDLIKERREKKAS-AGKINPKKPDMPNM-LEILKDMNSVKLRSVKRSEQDVKPKPVDPADPDSTT
          Q.TSAIDLIK..R.KKA..A.K..PKKPDMPNM..EILKD.NSVK..S.K.SEQDVKPK.VDP.DP....
Retrocopy QNTSAIDLIKKQRVKKAN>AEKTSPKKPDMPNM>VEILKDRNSVKPQSIKKSEQDVKPKLVDPTDPAALI

Parental  LEPLKKKFAHRY-LSDSQNEAE-KVVPKSESETTSGTMLFGPHMLKSTGRMKSLIENVSDS
          ...LK.K..H....S.SQ.E.E.KV.PKSESET.SG..LFGPH.LKS.G.MKSLIEN.S.S
Retrocopy AGALKMKVVHWF<QSNSQSEVE<KVIPKSESETKSGMVLFGPHRLKSIGKMKSLIENGSTS

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_483 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,