RetrogeneDB ID: retro_cjac_1262

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:16604944..16605459(-)
• Located in intron of: ENSCJAG00000016540

Retrocopy information

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

Parental gene information

• Parental gene symbol: C14orf166
• Ensembl ID: ENSCJAG00000006926
• Aliases: None
• Description: chromosome 14 open reading frame 166 [Source:HGNC Symbol;Acc:23169]

Sequence

>retro_cjac_1262
ATTCAAGATTGACAACAAGCTATTGACTGGCTTCTTGGTTTACCTATTAGACTTGAATATGGAAATAACTCTGAAAAATA
CAAGGAATTAGTATCTGATAGTGCAAAAACTGCTGACAATGCAACTAATATGCAGAACCATTGATCAATTTGGATGTAAA
TAATCCTGATTTTAAGCCTGGTATGATGGCTTTGACTAACCTGCTTCAGATTCAACGTCATGATGATTACCTGCTAATGC
TTAAGGCAATTCGAATTTTGGTTTAGGAGTGCCTGACACACAATGCAGTTGCTGAGGCAAATCAAACAAAAGAAGGCTTG
CCTGTTGTTTTAGACAAACATGCTCTTGGTTTTGACACAGGAGATGCAGTTCTTAATGAAGCTGCTCAAATTCTGTGATT
ACTGCATATAGAGGAGCTCAGAAAGCTACAGACAAAAATTAATGAAGCCATAGTAGCTGTTCAGACAATTATTGCTGATC
CAAGGACAGAGCACAGACTTGGAAAAGCTGGAAGA

Alignment

ORF - retro_cjac_1262 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.66 %
• Parental protein coverage: 69.92 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IQERQEAIDWLLGLAVRLEYGDNAEKYKDLVPDNAKTADNATKN-AEPLINLDVNNPDFKAGVMALANLL
          IQ..Q.AIDWLLGL..RLEYG.N.EKYK.LV.D.AKTADNAT...AEPLINLDVNNPDFK.G.MAL.NLL
Retrocopy IQD*QQAIDWLLGLPIRLEYGNNSEKYKELVSDSAKTADNATNM<AEPLINLDVNNPDFKPGMMALTNLL

Parental  QIQRHDDYLVMLKAIRILVQERLTQDAVAKANQTKEGLPVALDKHILGFDTGDAVLNEAAQILRLLHIEE
          QIQRHDDYL.MLKAIRILV.E.LT..AVA.ANQTKEGLPV.LDKH.LGFDTGDAVLNEAAQIL.LLHIEE
Retrocopy QIQRHDDYLLMLKAIRILV*ECLTHNAVAEANQTKEGLPVVLDKHALGFDTGDAVLNEAAQIL*LLHIEE

Parental  LRELQTKINEAIVAVQAIIADPKTDHRLGKVGR
          LR.LQTKINEAIVAVQ.IIADP.T.HRLGK.GR
Retrocopy LRKLQTKINEAIVAVQTIIADPRTEHRLGKAGR

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	0.27 RPM	24.36 RPM
SRP051959_heart	0.30 RPM	30.06 RPM
SRP051959_kidney	0.91 RPM	29.71 RPM
SRP051959_liver	0.17 RPM	27.27 RPM
SRP051959_lung	0.28 RPM	24.45 RPM
SRP051959_lymph_node	0.16 RPM	24.15 RPM
SRP051959_skeletal_muscle	0.04 RPM	41.69 RPM
SRP051959_spleen	1.39 RPM	28.89 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1262 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1262 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1262 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 29 parental genes, and 70 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002083	2 retrocopies	retro_amel_224, retro_amel_302,
Canis familiaris	ENSCAFG00000014648	4 retrocopies	retro_cfam_1025, retro_cfam_2042, retro_cfam_237, retro_cfam_734,
Callithrix jacchus	ENSCJAG00000006926	3 retrocopies	retro_cjac_1262 , retro_cjac_1947, retro_cjac_3207,
Cavia porcellus	ENSCPOG00000001317	6 retrocopies	retro_cpor_1041, retro_cpor_1177, retro_cpor_1239, retro_cpor_1247, retro_cpor_517, retro_cpor_541,
Dasypus novemcinctus	ENSDNOG00000003248	3 retrocopies	retro_dnov_458, retro_dnov_572, retro_dnov_609,
Dipodomys ordii	ENSDORG00000012335	1 retrocopy	retro_dord_619,
Equus caballus	ENSECAG00000012600	1 retrocopy	retro_ecab_483,
Erinaceus europaeus	ENSEEUG00000015583	1 retrocopy	retro_eeur_366,
Felis catus	ENSFCAG00000002663	3 retrocopies	retro_fcat_1160, retro_fcat_1415, retro_fcat_948,
Homo sapiens	ENSG00000087302	1 retrocopy	retro_hsap_2307,
Loxodonta africana	ENSLAFG00000003162	1 retrocopy	retro_lafr_301,
Microcebus murinus	ENSMICG00000008720	1 retrocopy	retro_mmur_857,
Myotis lucifugus	ENSMLUG00000008643	6 retrocopies	retro_mluc_1228, retro_mluc_1518, retro_mluc_1834, retro_mluc_2610, retro_mluc_456, retro_mluc_676,
Macaca mulatta	ENSMMUG00000018200	2 retrocopies	retro_mmul_1045, retro_mmul_2025,
Monodelphis domestica	ENSMODG00000013211	1 retrocopy	retro_mdom_1296,
Mustela putorius furo	ENSMPUG00000005253	6 retrocopies	retro_mputfur_1333, retro_mputfur_1421, retro_mputfur_203, retro_mputfur_328, retro_mputfur_655, retro_mputfur_797,
Mus musculus	ENSMUSG00000021807	2 retrocopies	retro_mmus_140, retro_mmus_3203,
Nomascus leucogenys	ENSNLEG00000012406	1 retrocopy	retro_nleu_2749,
Oryctolagus cuniculus	ENSOCUG00000014681	1 retrocopy	retro_ocun_221,
Otolemur garnettii	ENSOGAG00000013232	5 retrocopies	retro_ogar_1060, retro_ogar_1856, retro_ogar_2351, retro_ogar_2976, retro_ogar_3192,
Ochotona princeps	ENSOPRG00000016352	2 retrocopies	retro_opri_257, retro_opri_884,
Pongo abelii	ENSPPYG00000005814	1 retrocopy	retro_pabe_1980,
Pan troglodytes	ENSPTRG00000006344	1 retrocopy	retro_ptro_1631,
Pteropus vampyrus	ENSPVAG00000013392	1 retrocopy	retro_pvam_1088,
Sus scrofa	ENSSSCG00000005029	1 retrocopy	retro_sscr_1093,
Tupaia belangeri	ENSTBEG00000013898	5 retrocopies	retro_tbel_2579, retro_tbel_4337, retro_tbel_683, retro_tbel_880, retro_tbel_881,
Tarsius syrichta	ENSTSYG00000004528	6 retrocopies	retro_tsyr_1183, retro_tsyr_1289, retro_tsyr_1353, retro_tsyr_157, retro_tsyr_541, retro_tsyr_939,
Tursiops truncatus	ENSTTRG00000005721	1 retrocopy	retro_ttru_83,
Vicugna pacos	ENSVPAG00000011443	1 retrocopy	retro_vpac_142,