RetrogeneDB ID: retro_chof_1811

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_391521:343..1098(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENO1
• Ensembl ID: ENSCHOG00000003483
• Aliases: None
• Description: enolase 1, (alpha) [Source:HGNC Symbol;Acc:3350]

Sequence

>retro_chof_1811
ATATCTATTCTCAAGATCATTGACACATAGGTCTTTGACATTTGTGGAAATCCCACCATTGAGGTTGGTTTCTTCACCCC
AAAAGTTCTCTTCATAGTTACCATGCCCAGCTGTGAAGGCCTAGCTCTGTGAGGCCTAGAGTTCTGGGACAATGACCAGA
TGTGATATATGGGAAAAGGTATCTCAGAGGTATTGAGCACATCAATAAAACTATTGCAGTTTCCTAGTTAGCAAGAAACT
GAACATTATGGGAGAAGAAAAGAATGACAAGCTGATGATAGAGATGGATGGAGCTGAAAATAAGTCTAAATTTGGTGCAG
ACACCACCGTGGGAGTATTCCTCCCTTGCTTTATACAAGGTGGAGTAATTCAGAAGGGGGCCCCCTGTACTGTCACATTG
CTGACCTGGCTGGCAAATTGGGAGTCATCCTGCCAGTTCCCGCTTTCAACGTGATCAATGGCGGCTCTCACACAGGCAAC
AAGTTGGACATGCAGGAATGCATGATCCTCCCTGTCAGCACAGCCTAGTTCAGAGAGGCCATGAGCATCAGAGCAGAGGT
TTACCACAACCTGAAGAATGTCATCAAGATGAAATACAGGAAAATATGCCACCCGACGTGGGGGGGATAAAGGCAGATTT
TCCCTCAACATCCTGGAGAACAAAGAAACCCTGGAGCTGATTAAATGTGCAGTTGGCAAATGTTACAGAGACAGGTTGTA
ATTGGCATGGATGTCCTGCCTCTGAATTCTTCAGG

Alignment

ORF - retro_chof_1811 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.98 %
• Parental protein coverage: 58.2 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MSILKIFAREIFDSRGNPTVEVDLFTQKGLFRAAVPSGASAGIYEALELRDNDKTRYMGKGVS-KAVEHI
          .SILKI.....FD..GNPT.EV..FT.K.LF....PS.........LE..DND...YMGKG.S....EHI
Retrocopy ISILKIIDT*VFDICGNPTIEVGFFTPKVLFIVTMPSCEGLAL*-GLEFWDNDQM*YMGKGIS<RGIEHI

Parental  NKTIAPA-LVSKKLNVVEQEKIDKLMIEMDGTENK-KFGANAILGVSL-AVCKAGAVEKGVP-LYRHIAD
          NKTIA...LVSKKLN....EK.DKLMIEMDG.ENK.KFGA....GV.L......G...KG.P.LY.HIAD
Retrocopy NKTIAVS<LVSKKLNIMGEEKNDKLMIEMDGAENKSKFGADTTVGVFLPCFIQGGVIQKGAP<LYCHIAD

Parental  LAGNSEVILPVPAFNVINGGSHAGNKLAMQEFMILPVGAANFREAMRIGAEVYHNLKNVIKEKY-GKDAT
          LAG...VILPVPAFNVINGGSH.GNKL.MQE.MILPV..A.FREAM.I.AEVYHNLKNVIK.KY.GK.AT
Retrocopy LAGKLGVILPVPAFNVINGGSHTGNKLDMQECMILPVSTA*FREAMSIRAEVYHNLKNVIKMKY>GKYAT

Parental  -NVGDEGGFAPNILENKEALELIKNAVGKAGYSDK-VVIGMDV-AASEFFK
          ...GD.G.F..NILENKE.LELIK.AVGK..Y.D..VVIGMDV..ASEFF.
Retrocopy RRGGDKGRFSLNILENKETLELIKCAVGKC-YRDR<VVIGMDV<PASEFFR

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_1811 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 17 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003483	2 retrocopies	retro_chof_1289, retro_chof_1811 ,
Callithrix jacchus	ENSCJAG00000000359	4 retrocopies	retro_cjac_1963, retro_cjac_2238, retro_cjac_3891, retro_cjac_438,
Erinaceus europaeus	ENSEEUG00000008602	2 retrocopies	retro_eeur_23, retro_eeur_243,
Homo sapiens	ENSG00000074800	1 retrocopy	retro_hsap_325,
Macropus eugenii	ENSMEUG00000005942	11 retrocopies	retro_meug_1445, retro_meug_1521, retro_meug_353, retro_meug_472, retro_meug_494, retro_meug_652, retro_meug_664, retro_meug_765, retro_meug_794, retro_meug_874, retro_meug_888,
Macropus eugenii	ENSMEUG00000007840	1 retrocopy	retro_meug_96,
Monodelphis domestica	ENSMODG00000009521	1 retrocopy	retro_mdom_1794,
Mustela putorius furo	ENSMPUG00000006382	2 retrocopies	retro_mputfur_1162, retro_mputfur_547,
Mus musculus	ENSMUSG00000063524	1 retrocopy	retro_mmus_109,
Oryctolagus cuniculus	ENSOCUG00000010086	1 retrocopy	retro_ocun_933,
Otolemur garnettii	ENSOGAG00000004001	1 retrocopy	retro_ogar_1059,
Ochotona princeps	ENSOPRG00000009492	1 retrocopy	retro_opri_969,
Pan troglodytes	ENSPTRG00000000109	1 retrocopy	retro_ptro_261,
Pteropus vampyrus	ENSPVAG00000005030	1 retrocopy	retro_pvam_317,
Rattus norvegicus	ENSRNOG00000017895	1 retrocopy	retro_rnor_112,
Sarcophilus harrisii	ENSSHAG00000005522	1 retrocopy	retro_shar_304,
Tarsius syrichta	ENSTSYG00000002509	1 retrocopy	retro_tsyr_2011,