RetrogeneDB ID: retro_chof_1692

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_359362:541..1153(+)
• 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_1692
GCACCAGCGGAACAATATCCCAACCTTGTTGTGGAGAGAGTGACCGATTTCAGTTGGTACTTTGTAAGTCAGATCCAGGA
TGGCACTGGGTGTAGTGCTTTCATTGGCATTGGCTTCATAGATCAGGATGACGCCTTCCAAGTTAATGTTTCATTGAAAG
ATCATTTCAAGTGGGTAAAGCAGGAATTTGAGATTTTCAAAGACTCTCAGGAAAGGGATACTCGGACCAAGTTAGATCTG
GACTTCAAGGAAGGACAGACCATCAATGTGAGTATTGGGAACATGACAACCAAGAAAGGAGGTGCTTCTGAGCCCAGGAC
TTCAGGAGCTGGAGGCCTAAGTTTATTCCCATCCCCACCTGGAAGCAAAGTCATTATTTCCTAACCATCCTCCTAAGTTG
CCATCAGTAACCATGTCACTCCACCACTCACTCCAAAATCTAAACATGGAGGCAGTGAGACAGATATTCTTTCAGATTTG
GATTCTCCTGCTCCTGTCACAACACCAGCACCAGCTTCAGTTTCCACAGGAAATGACTTGTGGGGAGACTTTAGCATGCA
TCCCAGCTCTGTTTCAAACCAGGCACCACAACCATCCAACTGAGTCCAGTTC

Alignment

ORF - retro_chof_1692 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75. %
• Parental protein coverage: 74.18 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  APVEQYPGIAVETVTDSSRYFVIRIQDGTGRSAFIGIGFTDRGDAFDFNVSLQDHFKWVKQESEISKESQ
          AP.EQYP...VE.VTD.S.YFV..IQDGTG.SAFIGIGF.D..DAF..NVSL.DHFKWVKQE.EI.K.SQ
Retrocopy APAEQYPNLVVERVTDFSWYFVSQIQDGTGCSAFIGIGFIDQDDAFQVNVSLKDHFKWVKQEFEIFKDSQ

Parental  EMDTRPKLDLGFKEGQTIKLSIGNITTKKGGASKPRTSGAGGLSLLPPPPGGKVTIPPPSSSVAISNHVT
          E.DTR.KLDL.FKEGQTI..SIGN.TTKKGGAS.PRTSGAGGLSL.P.PPG.KV.I..PSS.VAISNHVT
Retrocopy ERDTRTKLDLDFKEGQTINVSIGNMTTKKGGASEPRTSGAGGLSLFPSPPGSKVIIS*PSS*VAISNHVT

Parental  PPPIPKSNHGGSDADILLDLDSPAPVTTPATAPVTAGNYLCGDFTTASNSVSNQAPQPSNWVQF
          PP..PKS.HGGS..DIL.DLDSPAPVTTPA.A.V..GN.L.GDF.....SVSNQAPQPSN.VQF
Retrocopy PPLTPKSKHGGSETDILSDLDSPAPVTTPAPASVSTGNDLWGDFSMHPSSVSNQAPQPSN*VQF

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_1692 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 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,