RetrogeneDB ID: retro_chof_285

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_6225:16657..17527(-)
• Located in intron of: ENSCHOG00000009368

Retrocopy information

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

Parental gene information

• Parental gene symbol: RFFL
• Ensembl ID: ENSCHOG00000001950
• Aliases: None
• Description: ring finger and FYVE-like domain containing E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:24821]

Sequence

>retro_chof_285
AAGAAAAATCTCTGCCTGACCTGTTCAAGGCAAGTGGGGACTGGGCTCCGCCTCTGTCACCTCTGCCAGTGGTTCCAAGC
TACTGCCGTTCAGGGGGAGGAGCTCATGAAGATGAAAGTGAAGGACCTGAGGGACTGTCTCAGCCCCCATGATATCTCTA
CTGAAATATGCTGGGAGGAGGAGGAGCTGGTGTTCTTGGTGGTTGGACAGCAGCCTCTTATCTCCCAGGAGGGCAGGACA
CATGCCCCCATCTTGGCCCTGCACTTCCCTGAGCAGCAGACCTTCTGACTCAGCCTCTAACCAGCACAACATCTCCTGCC
TCACCCACCCTCCCTTCTTCTACACAAGCTACTTCTGTTGGCCCAGACCAGGATCAGGAAAATCAGCAGGTTGATGGCCA
TGTGTCTCATGACCAAGAGGAACCGTCTACCTGGAGAACACAGCCAGAGTGACTGCTGAGGATGAAGCTGAATATATCGA
CTCAGAGGATAGGTTTGTGCCAGGCCAGAGGGCTTCTCTGTCTGACCTGATCAGTCTGGAAGACACTGAAGCACTGACTG
TGTGGCAGTTGAAGGAGATCCTGGCTTGCAACTTTGTCAATTACAAGGGCTGCTGTTAGAAGTGGGAGCTGATGGAAAGG
GTGATTTGGCTGTACAGGGATTAAAAAGGATCCAGTACCTGATATGTGGTGCTGAAGATCAAAATGGGGGTGCCAGCATA
GAAGAGAACCTGTGTAAGATCTGTACAGACTCACCCACTGACTGTGTTCTGCTGGAGTGTGGCCACATGGTTACCTGCAC
CAAGTTTGGCAAGCACATGAATGAATGTCCCATCTGCTGTCAGTATGTGATCTGAGCAATGCATGTCTTC

Alignment

ORF - retro_chof_285 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.17 %
• Parental protein coverage: 97.36 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KKNFCMTCASQVGTGPLLCLLCQRFRATAFQREELMKMKVKGLRDYLSLHDISTEMCREKEELVFLVLDQ
          KKN.C.TC..QVGTG..LC.LCQ.F.ATA.Q.EELMKMKVK.LRD.LS.HDISTE.C.E.EELVFLV..Q
Retrocopy KKNLCLTCSRQVGTGLRLCHLCQWFQATAVQGEELMKMKVKDLRDCLSPHDISTEICWEEEELVFLVVGQ

Parental  QPVISQEGRTCASHLSPDFPEQQAF-LTQPHTSTAPSTSSNLPSSPTQATSVGPAQAQENQQANGHVSQD
          QP.ISQEGRT.A..L...FPEQQ.F.LTQP.TST....S..LPSS.TQATSVGP.Q.QENQQ..GHVS.D
Retrocopy QPLISQEGRTHAPILALHFPEQQTF<LTQPLTSTTSPASPTLPSS-TQATSVGPDQDQENQQVDGHVSHD

Parental  QEEP-VYLESTARVPAEDETQSIDSEDSFVPGRRASLSDLTNLEDIEALTVRQLKEILARNFVNYKGCCE
          QEEP.VYLE.TARV.AEDE...IDSED.FVPG.RASLSDL..LED.EALTV.QLKEILA.NFVNYKGCC.
Retrocopy QEEP<VYLENTARVTAEDEAEYIDSEDRFVPGQRASLSDLISLEDTEALTVWQLKEILACNFVNYKGCC*

Parental  KWELMERVTRLYKDQKG-LQHLVCGAEDQNGGAVPPSMEENLCKICMDSPIDCVLLECGHMVTCTKCGKR
          KWELMERV..LY.D.KG..Q.L.CGAEDQNGGA...S.EENLCKIC.DSP.DCVLLECGHMVTCTK.GK.
Retrocopy KWELMERVIWLYRD*KG<IQYLICGAEDQNGGA---SIEENLCKICTDSPTDCVLLECGHMVTCTKFGKH

Parental  MNECPICRQYVIRAVHVF
          MNECPIC.QYVI.A.HVF
Retrocopy MNECPICCQYVI*AMHVF

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_285 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001950	2 retrocopies	retro_chof_1069, retro_chof_285 ,
Macropus eugenii	ENSMEUG00000012628	1 retrocopy	retro_meug_1745,
Otolemur garnettii	ENSOGAG00000024777	1 retrocopy	retro_ogar_621,
Ochotona princeps	ENSOPRG00000011769	1 retrocopy	retro_opri_385,
Tarsius syrichta	ENSTSYG00000008923	2 retrocopies	retro_tsyr_1749, retro_tsyr_2060,