RetrogeneDB ID: retro_cjac_4204

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:92393529..92393885(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNEP1R1
• Ensembl ID: ENSCJAG00000001997
• Aliases: None
• Description: CTD nuclear envelope phosphatase 1 regulatory subunit 1 [Source:HGNC Symbol;Acc:26759]

Sequence

>retro_cjac_4204
GAAGAGCTCAAGGGTTTTGAGAGGAGAATAACTGAATATATTCATTTTTTTGCAACCCACTACTGAACATTGGAAAATGT
TTCTTACAGTGGTATCTGTCCGTACAGCTACTGGTACCTGGAACTGCTTGATAGATCCTGATACACAAAAGGTGTCCCTT
CTTCCCATCATTATGGAATCATCCATTTTTCATCATTAACTGTATCACTCTAATAGGCTAGTTCTTTGCTGGAATACACA
AGACAGTAGTTGCACCATCGATTATAACTGCTCAATGCCAAACGGCATTAGCAGAATACAATACTTCTTGTAATGATGCA
GGAAAACTAATTTTGAAATGTAGGCCTCATGTTCAA

Alignment

ORF - retro_cjac_4204 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.0 %
• Parental protein coverage: 83.1 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QDLKAFERRLTEYIHC-LQPATGRWRMLLIVVSVCTATGAWNWLIDPETQKVS-FFTSLWNHPFFTISCI
          ..LK.FERR.TEYIH..LQP.T..W.M.L.VVSV.TATG.WN.LIDP.TQKVS.FF.SLWNHPFF.I.CI
Retrocopy EELKGFERRITEYIHF>LQPTTEHWKMFLTVVSVRTATGTWNCLIDPDTQKVS>FFPSLWNHPFFIINCI

Parental  TLIGLFFAGIHKRVVAPSIIAARCRTVLAEYNMSCDDTGKLILKPRPHVQ
          TLIG.FFAGIHK.VVAPSII.A.C.T.LAEYN.SC.D.GKLILK.RPHVQ
Retrocopy TLIG*FFAGIHKTVVAPSIITAQCQTALAEYNTSCNDAGKLILKCRPHVQ

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	0.00 RPM	5.84 RPM
SRP051959_heart	0.00 RPM	4.68 RPM
SRP051959_kidney	0.00 RPM	6.59 RPM
SRP051959_liver	0.00 RPM	3.81 RPM
SRP051959_lung	0.00 RPM	6.33 RPM
SRP051959_lymph_node	0.00 RPM	7.28 RPM
SRP051959_skeletal_muscle	0.00 RPM	4.87 RPM
SRP051959_spleen	0.00 RPM	6.20 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4204 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4204 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4204 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4886
Pan troglodytes	retro_ptro_3255
Gorilla gorilla	retro_ggor_3051
Pongo abelii	retro_pabe_3799
Macaca mulatta	retro_mmul_2624

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006491	1 retrocopy	retro_amel_732,
Callithrix jacchus	ENSCJAG00000001997	1 retrocopy	retro_cjac_4204 ,
Cavia porcellus	ENSCPOG00000012791	1 retrocopy	retro_cpor_669,
Erinaceus europaeus	ENSEEUG00000005737	1 retrocopy	retro_eeur_211,
Felis catus	ENSFCAG00000023936	1 retrocopy	retro_fcat_1713,
Homo sapiens	ENSG00000205423	1 retrocopy	retro_hsap_4886,
Gorilla gorilla	ENSGGOG00000025211	1 retrocopy	retro_ggor_3051,
Loxodonta africana	ENSLAFG00000012573	1 retrocopy	retro_lafr_907,
Myotis lucifugus	ENSMLUG00000006900	2 retrocopies	retro_mluc_1437, retro_mluc_2115,
Macaca mulatta	ENSMMUG00000008365	3 retrocopies	retro_mmul_1586, retro_mmul_1873, retro_mmul_2624,
Mustela putorius furo	ENSMPUG00000003109	1 retrocopy	retro_mputfur_453,
Nomascus leucogenys	ENSNLEG00000000727	2 retrocopies	retro_nleu_1341, retro_nleu_831,
Oryctolagus cuniculus	ENSOCUG00000005923	1 retrocopy	retro_ocun_1267,
Otolemur garnettii	ENSOGAG00000015665	1 retrocopy	retro_ogar_2835,
Pongo abelii	ENSPPYG00000007335	3 retrocopies	retro_pabe_1396, retro_pabe_2430, retro_pabe_3799,
Pan troglodytes	ENSPTRG00000041682	1 retrocopy	retro_ptro_3255,
Ictidomys tridecemlineatus	ENSSTOG00000001179	1 retrocopy	retro_itri_350,