RetrogeneDB ID: retro_chof_2580

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_87557:12..840(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM175A
• Ensembl ID: ENSCHOG00000013241
• Aliases: None
• Description: family with sequence similarity 175, member A [Source:HGNC Symbol;Acc:25829]

Sequence

>retro_chof_2580
CTAATATTAACACCAAATATAACAACAGAAAGCCGCTCTATCCATGGTTGGAGCATGCTTTACAAAAACCTCAAGAACTT
TTTCATAGGGTACTTTACTGGTTGCTAAACTGGGCATAACTGAACAACTGGGTTATAAAACTGCATCAGGTTCCTGTGTG
TCCATTGGTTTTAGCCGAGCAGTAAAACACACAGTCCTGGATTTTTTTAAAAGATGATGGATCTTTAAAGGAGGTACAGA
AGATAAATGAAATGTAGCCTTCATTATAAGAGGAATTAAAGAGCATATGCAAAAAAGTGAAACATGGTGAGAGAGCAAAC
AGAAACTACTAGAGGATGTAAACAGACTAAAACAAGAAAGTAAAAAAAGAAAATGGGCACAGATCCAAGCAGCAGCAGGA
GAGAAGAATGTTCCACAAGACCCACTGGAGAATGCTTTTCTTTGTCCAGCTTTACAGACCTTATTTCCAGATTGTGAGCT
TCTTCATTCATGTGTTATCTCCTTGAAACATAAGCATATTTATAAAATTCCTGTAATACTAGCCACCATTTCAATGTGGT
AGACAAACTGACTTTTAATGGTAGAATACACTGACATTCTTGAAGCTAATCAAGCTAGTGGACAGCAAATGATTAAGCGA
AAGTTTTGGACGTGGATAATGGATGGCAAGTCAAGAAATAACGGCTGTTGGAGGTACAAAAAAGACCATCCAAAACAGAT
ACTGATAGTAGTAACCAAGAGGAAGCATCCACAATTAGCAGTCCAGAAACAGATGAAGAGATTGTGAAAGTGAAGGGTTC
TTGTGACTAACCACAGTCTCCCACATTT

Alignment

ORF - retro_chof_2580 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.14 %
• Parental protein coverage: 67.73 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  LLLTPSITTESCSTHR-LEHALHKPQDGLFHRV-PLVVANLGMTEQLGYKTVSSSCTSSGFGRAVK-THS
          L.LTP.ITTES.S.H..LEHAL.KPQ..LFHRV..L.VA.LG.TEQLGYKT.S.SC.S.GF.RAVK.T.S
Retrocopy LILTPNITTESRSIHG<LEHALQKPQE-LFHRV<TLLVAKLGITEQLGYKTASGSCVSIGFSRAVK>TQS

Parental  SEFFKEDGSLKEVHKINEMYASLQKELKSICKKVEHSERA-VEKLLEDVNRLKQEIKKRKQAQIQAAR-E
          ..F.K.DGSLKEV.KINEM..SL..ELKSICKKV.H.ERA...KLLEDVNRLKQE.KKRK.AQIQAA..E
Retrocopy WIFLKDDGSLKEVQKINEM*PSL*EELKSICKKVKHGERA<KQKLLEDVNRLKQESKKRKWAQIQAAAGE

Parental  NNVPEVPQENAFLCEALRTFFPDCELLHSCVISLKNKHISK-SCCNTNHHLNVVDKLT-LMVEYNDILEA
          .NVP..P.ENAFLC.AL.T.FPDCELLHSCVISLK.KHI.K...CNT.HH.NVVDKLT.LMVEY.DILEA
Retrocopy KNVPQDPLENAFLCPALQTLFPDCELLHSCVISLKHKHIYK<NSCNTSHHFNVVDKLT>LMVEYTDILEA

Parental  NQAHGQQMIKRK-ALDMDDGWQIKKSRLLEMQKRPSKTDTESSNQEKASTISSPETDEEIVKMKGSGDYP
          NQA.GQQMIKRK..LD.D.GWQ.KK.RLLE.QKRPSKTDT.SSNQE.ASTISSPETDEEIVK.KGS.D.P
Retrocopy NQASGQQMIKRK<VLDVDNGWQVKK*RLLEVQKRPSKTDTDSSNQEEASTISSPETDEEIVKVKGSCD*P

Parental  QSPTF
          QSPTF
Retrocopy QSPTF

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_2580 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 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007635	3 retrocopies	retro_chof_1691, retro_chof_2426, retro_chof_2563,
Choloepus hoffmanni	ENSCHOG00000013241	1 retrocopy	retro_chof_2580 ,
Homo sapiens	ENSG00000163322	1 retrocopy	retro_hsap_4024,
Gorilla gorilla	ENSGGOG00000005818	1 retrocopy	retro_ggor_2701,
Macaca mulatta	ENSMMUG00000015357	2 retrocopies	retro_mmul_1499, retro_mmul_2320,
Nomascus leucogenys	ENSNLEG00000009133	2 retrocopies	retro_nleu_1198, retro_nleu_661,
Pongo abelii	ENSPPYG00000014898	2 retrocopies	retro_pabe_2208, retro_pabe_3301,
Pan troglodytes	ENSPTRG00000023645	2 retrocopies	retro_ptro_1911, retro_ptro_2728,