RetrogeneDB ID: retro_chof_2357

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_68004:7710..8658(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MKRN1
• Ensembl ID: ENSCHOG00000011015
• Aliases: None
• Description: makorin ring finger protein 1 [Source:HGNC Symbol;Acc:7112]

Sequence

>retro_chof_2357
ACAGCCACAACATCAGGCGCAGGAGCGGCAGCGGCGGCAGCAGTCTCCCCCACCCCTGTCCCCACAGTCACCTCCCCGTC
CCTGGGGGGAGGGGGAGGCGGCAGCGACAGTAGTGGCTGCGGCTGGACTAAACAAGTCACCTACAGGTATTTTATGCATG
GGGTTTGTAAGGAAGGAGATAACTGTCGCTACTCACATGAGCTCTCTGACAGTCCATATGGTGTAGTGTGCAAGTATTTT
CAGCGAGGAGACTGTATTTACGGAGACCGCTGCAGATACGAACATAGCAAGCCATTGAAACAGGAAGAAGCAACTGCTGC
AGATCTGACTGCAAAATCATCCCTTGCTGCTTCCTCAAGTCTCTCATCAGTAGTTGGACCACTTGTTGAAATGAGTGCGG
GTGAAGCTGAGTCAAGAAATTCAAACTTTGCAACTATAGGAGCAGGCACAGAAGACTGGGTGAATGCCATTGAGTTTGTT
CCTGGGCAACCCTACTGTGACCGTACTGCCCCTTCCTGCACTGAAGCACCCCTGCAGGGCTCAGTGACCAAGGAAGAATC
AGAGAAAGAGCAAACCGCTGTGGAAACAAAGAAGCAGCTTTGCCCCTAGGCTGCAGCGGGAGAGTGCCGATATGGGGAGA
ACTGTGTGTTATCTCCATGGAGACTCATGTGATATGTGTGGGCTGCAGGTCCTACATGCAATGGATGCTGCCCAGAGATC
ACAACATATAAAATCTTGCATTCAGGCCCATGAGAAGGACATGGAGCTCTCATTTGCTGTCCAGCGCAGTAAGGACATGG
TTTGTGGGCTCTGCATGGAGGTTGTCTAAGAGAAAGCCAACCCCAGTGAGCACCGCTTTGGAATTCTCTCCAACTGCAAC
CACACCTACTGTCTCAAGTGTATTTGCAAGTGGAGGAGTGCTAAGCAATTTGGAGGAAGATCATAAAG

Alignment

ORF - retro_chof_2357 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.93 %
• Parental protein coverage: 66.39 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TATTSGAGAAAAAVAAASPTPIPTVTSPSLGAGGGGGGSDGSGGGWTKQVTCRYFMHGVCKEGDNCRYSH
          TATTSGAGAAAAA..A.SPTP.PTVTSPSLG..GGGGGSD.SG.GWTKQVT.RYFMHGVCKEGDNCRYSH
Retrocopy TATTSGAGAAAAA--AVSPTPVPTVTSPSLG--GGGGGSDSSGCGWTKQVTYRYFMHGVCKEGDNCRYSH

Parental  DLSDSPYGVVCKYFQRGYCIYGDRCRYEHSKPLNQEEATAADLTAKSSLAASSSVSSVVGPLVEMSAGEA
          .LSDSPYGVVCKYFQRG.CIYGDRCRYEHSKPL.QEEATAADLTAKSSLAASSS.SSVVGPLVEMSAGEA
Retrocopy ELSDSPYGVVCKYFQRGDCIYGDRCRYEHSKPLKQEEATAADLTAKSSLAASSSLSSVVGPLVEMSAGEA

Parental  ESRNSNFATIGAGTEDWVNAIEFVPGQPYCGRTAPSCTEAPLQGSVTKEESEKEQTAVETKKQLCPYAAV
          ESRNSNFATIGAGTEDWVNAIEFVPGQPYC.RTAPSCTEAPLQGSVTKEESEKEQTAVETKKQLCP.AA.
Retrocopy ESRNSNFATIGAGTEDWVNAIEFVPGQPYCDRTAPSCTEAPLQGSVTKEESEKEQTAVETKKQLCP*AAA

Parental  GECRYGENCV-YLHGDSCDMCGLQVLHPMDAAQRSQHIKSCIEAHEKDMELSFAVQRSKDMVCGICMEVV
          GECRYGENCV.YLHGDSCDMCGLQVLH.MDAAQRSQHIKSCI.AHEKDMELSFAVQRSKDMVCG.CMEVV
Retrocopy GECRYGENCV>YLHGDSCDMCGLQVLHAMDAAQRSQHIKSCIQAHEKDMELSFAVQRSKDMVCGLCMEVV

Parental  YEKANPSERRFGILSNCNHTYCLKCIRKWRSAKQFES-KIIK
          .EKANPSE.RFGILSNCNHTYCLKCI.KWRSAKQF...KIIK
Retrocopy *EKANPSEHRFGILSNCNHTYCLKCICKWRSAKQFGG<KIIK

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_2357 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 19 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008306	2 retrocopies	retro_btau_401, retro_btau_943,
Canis familiaris	ENSCAFG00000003953	2 retrocopies	retro_cfam_2157, retro_cfam_253,
Choloepus hoffmanni	ENSCHOG00000011015	3 retrocopies	retro_chof_173, retro_chof_2357 , retro_chof_89,
Callithrix jacchus	ENSCJAG00000013474	2 retrocopies	retro_cjac_210, retro_cjac_2991,
Cavia porcellus	ENSCPOG00000000948	1 retrocopy	retro_cpor_109,
Dasypus novemcinctus	ENSDNOG00000019564	2 retrocopies	retro_dnov_1011, retro_dnov_388,
Felis catus	ENSFCAG00000024942	1 retrocopy	retro_fcat_67,
Homo sapiens	ENSG00000133606	4 retrocopies	retro_hsap_1140, retro_hsap_4197, retro_hsap_4676, retro_hsap_4859,
Gorilla gorilla	ENSGGOG00000023977	4 retrocopies	retro_ggor_119, retro_ggor_2813, retro_ggor_3031, retro_ggor_381,
Microcebus murinus	ENSMICG00000002114	1 retrocopy	retro_mmur_1184,
Macaca mulatta	ENSMMUG00000010420	3 retrocopies	retro_mmul_191, retro_mmul_2597, retro_mmul_76,
Mus musculus	ENSMUSG00000029922	1 retrocopy	retro_mmus_2663,
Nomascus leucogenys	ENSNLEG00000001921	4 retrocopies	retro_nleu_1027, retro_nleu_2167, retro_nleu_33, retro_nleu_939,
Otolemur garnettii	ENSOGAG00000009877	2 retrocopies	retro_ogar_3468, retro_ogar_424,
Pongo abelii	ENSPPYG00000018057	3 retrocopies	retro_pabe_3435, retro_pabe_3776, retro_pabe_947,
Pan troglodytes	ENSPTRG00000019766	5 retrocopies	retro_ptro_2849, retro_ptro_3106, retro_ptro_3234, retro_ptro_75, retro_ptro_776,
Sus scrofa	ENSSSCG00000016498	2 retrocopies	retro_sscr_43, retro_sscr_637,
Tarsius syrichta	ENSTSYG00000009996	3 retrocopies	retro_tsyr_1256, retro_tsyr_1525, retro_tsyr_508,
Tursiops truncatus	ENSTTRG00000009528	2 retrocopies	retro_ttru_1064, retro_ttru_1128,