RetrogeneDB ID: retro_cjac_210

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:347351..348875(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022162
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MKRN1
• Ensembl ID: ENSCJAG00000013474
• Aliases: None
• Description: makorin ring finger protein 1 [Source:HGNC Symbol;Acc:7112]

Sequence

>retro_cjac_210
ATGGAAGAGCCTGCAGCTCCCTCAGAAGCCCACGAGGCAGCCGGGGCCCAGGCAGGTGCTGAGGCAGCAGGGGAGGGTGT
GTCTGGGCCCGACCTTCCCGCGTGTGAGCCCTCCGGGGAATCTGCTGCTCCAGATTCAGCACTGCCACATGTGGCCGTGG
GCTGGGCCCCCTTCCCTGTAGCTCCAGTCCCTGCCCACCTCCGCACGGGAGGCCTGAGGCCTGCCCCAGCCTCCGGAGGA
GGAGCCTGGCCCAGCCCCTTGCCAAGCCGAAGCAGTGGCATTTGGACAAAGCAGATCGCCTGCAGGTATTATATACATGG
GCAGTGCAAGGAGGGGGAGAACTGTCGCTATTCCCACGACCTTTCTTGTCGGAAGATGGCCACCGAGGGCCGCGTTTCGC
CGTCTGGGGCCTCTGCAAGTGGAGGCCCTAGCACGGCTGCGCACATCGAGCCCCCGACTCAGGAAGTGGCGGAAGCCCCC
CCGGCTGCATCCTCGCAGTCCTTGCCTGTGATTGGCTCGGCTGCTGAAAGGGGTTTCTTTGAAGCCGAGAGAGACAATGC
AGACCGTGGAGCTGCTGGAGAAGCAGGTGTAGAAAGCTGGGCGGATGCCATTGAGTTTGTTCCAGGGCAGCCCTACCGGG
GCCGCCGGGTTGCATCTGCTCCTGAGGCTCCTCTACAGAGCTCAGAGACTGAGAGGAAGCAGATGGCTGTGGGCAGGGGT
GAGCGGTTTTGCTATTATGCTTCCAGGGGAGTTTGCTTTCGTGGGGAGAGCTGTATGTACCTCCATGGAGACATATGCGA
CATGTGTGGGCTGCAGGCCTTGCACCCCATGGATGCTGCCCAAAGGGAAGACCATATAAGGGCCTGCATTGAAGCACACG
AGAAAGATATGGAACTCTCGTTTGCTGTGCAGCGTGGTATGGACAAGGTGTGTGGCATCTGCATGGAGGTTGTCTATGAG
AAAGCCAACCCCAATGACCGCCGATTTGGCATTCTTTCCAATTGCAACCATACCTTCTGTATTAGGTGTATCCGCAGGTG
GAGAAGTGCCAGACAGTTTGATAACAGGATCATCAAGTCTTGTCCACAGTGCAGGGTCACCTCCGACTTGGTCATTCCCA
GTGAGTTCTGGGTGGAGGAGGAGGAAGAGAAGCAGAAACTTATTCAGCAATACAAAGAGGCAATGAGCAACAAGGCCTGC
AGGTATTTTGCGGAAGGCAGGGGTAACTGCCCATTTGGAGACACATGCTTTTACAAGCATGAATACCCTGAGGGCTGGGG
AGATGAGCCTCCTGGGCCGGGTGGTGGGTCATTCAGTGCATACTGGCATCAACTTGTGGAGCCTGTGCGAATGGGAGAGG
GCAACGCGCTCTATAAAAGCAGTAAGAAGGAGCTTGTCGTGCTTCGGCTGGCCAGTCTGTTGTTTAAGCAGTTTCTTTCA
CTGAGAGATGAGTTCCCCTTCTCTGAGGAGCAGTGGGACTTGCTTCATTATGAGCTGGAAGAATATTTCAATTTGAATCT
GTAG

Alignment

ORF - retro_cjac_210 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.8 %
• Parental protein coverage: 77.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TELTTKSSLATSSSLSSVVGPLVEMNTSDAESRNSNFATVG-AGSEDWVNAIEFVPGQPYCGRTAPSCTE
          T........A.SS....V.G...E.....AE..N......G.AG.E.W..AIEFVPGQPY.GR...S..E
Retrocopy TQEVAEAPPAASSQSLPVIGSAAERGFFEAERDNADRGAAGEAGVESWADAIEFVPGQPYRGRRVASAPE

Parental  APLQGSVTKEESEKEQTTVETKKQLCPYAAVGECRYGENCVYLHGDSCDMCGLQVLHPMDAAQRSEHIKS
          APLQ.S....E.E..Q..V......C.YA..G.C..GE.C.YLHGD.CDMCGLQ.LHPMDAAQR..HI..
Retrocopy APLQSS----ETERKQMAVGRGERFCYYASRGVCFRGESCMYLHGDICDMCGLQALHPMDAAQREDHIRA

Parental  CIEAHEKDMELSFAVQRSKDMVCGICMEVVYEKANPSERRFGILSNCNHTYCLKCIRKWRSAKQFESKII
          CIEAHEKDMELSFAVQR..D.VCGICMEVVYEKANP..RRFGILSNCNHT.C..CIR.WRSA.QF...II
Retrocopy CIEAHEKDMELSFAVQRGMDKVCGICMEVVYEKANPNDRRFGILSNCNHTFCIRCIRRWRSARQFDNRII

Parental  KSCPECRITSNFVIPSEYWVEEKEEKQKLILKYKEAMSNKACRYFDEGRGSCPFGGNCFYKHAYPDGRRE
          KSCP.CR.TS..VIPSE.WVEE.EEKQKLI..YKEAMSNKACRYF.EGRG.CPFG..CFYKH.YP.G...
Retrocopy KSCPQCRVTSDLVIPSEFWVEEEEEKQKLIQQYKEAMSNKACRYFAEGRGNCPFGDTCFYKHEYPEGWGD

Parental  EPQRQKVGTSSRY
          EP.....G..S.Y
Retrocopy EPPGPGGGSFSAY

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP051959_colon	0.04 RPM	35.41 RPM
SRP051959_heart	0.09 RPM	25.40 RPM
SRP051959_kidney	0.00 RPM	45.59 RPM
SRP051959_liver	0.02 RPM	25.00 RPM
SRP051959_lung	0.20 RPM	42.44 RPM
SRP051959_lymph_node	0.05 RPM	27.26 RPM
SRP051959_skeletal_muscle	0.00 RPM	31.14 RPM
SRP051959_spleen	0.21 RPM	35.92 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_210 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_210 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_210 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 54 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,
Callithrix jacchus	ENSCJAG00000016733	1 retrocopy	retro_cjac_2362,
Cavia porcellus	ENSCPOG00000000948	1 retrocopy	retro_cpor_109,
Dasypus novemcinctus	ENSDNOG00000019564	2 retrocopies	retro_dnov_1011, retro_dnov_388,
Erinaceus europaeus	ENSEEUG00000001133	1 retrocopy	retro_eeur_643,
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,
Macropus eugenii	ENSMEUG00000007399	1 retrocopy	retro_meug_1659,
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,
Ochotona princeps	ENSOPRG00000010353	1 retrocopy	retro_opri_1073,
Procavia capensis	ENSPCAG00000014683	1 retrocopy	retro_pcap_19,
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,
Tupaia belangeri	ENSTBEG00000004564	2 retrocopies	retro_tbel_1410, retro_tbel_71,
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,