RetrogeneDB ID: retro_chof_1913

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_421101:8..439(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NECAP1
• Ensembl ID: ENSCHOG00000008087
• Aliases: None
• Description: NECAP endocytosis associated 1 [Source:HGNC Symbol;Acc:24539]

Sequence

>retro_chof_1913
GTAAAGCAGGAATCTGAGATTTCCAAAGAATCTCAGGAAATGGACACTCATCCCAAGTTAGATCTGGGTTTCAAGGAAGG
ACAGACCATCAAGTTGAGTACTGGGAACATTACAACCAAGAAAGGAGGTGCTTCTAAGCCCAGGACCTCAGGAGCTGGGG
GCCTAAGCTTACTCCAACCCCCACCTGGAGGCAAATTCACTATTCCCCCACCATCCCCCTCAGTTGCCATCAGTAACCAT
GTCGCCCCACCAGCCATTCCAAAATCTAATCACGAAGGTAGTGATACAGATACTCTTTTAGATTTGGATTCTCCTACTCC
TGTCACAACACCAGCAACAGCTCCAATTTTGGCAGGCATGACTTGTGGGGAGACATTAGCACTGCATCCAGCTCCTTTTC
AACCAGCACACAGAGATCCAACTGGGTCCAG

Alignment

ORF - retro_chof_1913 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.19 %
• Parental protein coverage: 52.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VKQESEISKESQEMDTRPKLDLGFKEGQTIKLSIGNITTKKGGASKPRTSGAGGLSLLPPPPGGKVTIPP
          VKQESEISKESQEMDT.PKLDLGFKEGQTIKLS.GNITTKKGGASKPRTSGAGGLSLL.PPPGGK.TIPP
Retrocopy VKQESEISKESQEMDTHPKLDLGFKEGQTIKLSTGNITTKKGGASKPRTSGAGGLSLLQPPPGGKFTIPP

Parental  PSSSVAISNHVTPPPIPKSNHGGSDADILLDLDSPAPVTTPATAPVTAG-NYLCGDFTTASNSVSNQAPQ
          PS.SVAISNHV.PP.IPKSNH.GSD.D.LLDLDSP.PVTTPATAP..AG...L.GD..TAS.S.S....Q
Retrocopy PSPSVAISNHVAPPAIPKSNHEGSDTDTLLDLDSPTPVTTPATAPILAG<HDLWGDISTASSSFST-STQ

Parental  PSNWVQ
          .SNWVQ
Retrocopy RSNWVQ

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_1913 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.

---

Parental genes homology:

Parental genes homology involve 16 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016989	1 retrocopy	retro_amel_1016,
Canis familiaris	ENSCAFG00000013930	1 retrocopy	retro_cfam_780,
Choloepus hoffmanni	ENSCHOG00000008087	3 retrocopies	retro_chof_1692, retro_chof_1818, retro_chof_1913 ,
Dasypus novemcinctus	ENSDNOG00000014778	2 retrocopies	retro_dnov_613, retro_dnov_986,
Homo sapiens	ENSG00000089818	1 retrocopy	retro_hsap_3839,
Gorilla gorilla	ENSGGOG00000010233	1 retrocopy	retro_ggor_2585,
Loxodonta africana	ENSLAFG00000002979	1 retrocopy	retro_lafr_632,
Mustela putorius furo	ENSMPUG00000016742	1 retrocopy	retro_mputfur_361,
Nomascus leucogenys	ENSNLEG00000001743	1 retrocopy	retro_nleu_1974,
Oryctolagus cuniculus	ENSOCUG00000004309	1 retrocopy	retro_ocun_606,
Otolemur garnettii	ENSOGAG00000006358	1 retrocopy	retro_ogar_3442,
Pongo abelii	ENSPPYG00000004238	1 retrocopy	retro_pabe_3059,
Pan troglodytes	ENSPTRG00000023277	1 retrocopy	retro_ptro_2615,
Rattus norvegicus	ENSRNOG00000009236	1 retrocopy	retro_rnor_1806,
Ictidomys tridecemlineatus	ENSSTOG00000010153	2 retrocopies	retro_itri_1107, retro_itri_740,
Tursiops truncatus	ENSTTRG00000014260	1 retrocopy	retro_ttru_1035,