RetrogeneDB ID: retro_cjac_402

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:66884828..66885411(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000009344
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NANOG
• Ensembl ID: ENSCJAG00000018999
• Aliases: None
• Description: Nanog homeobox [Source:HGNC Symbol;Acc:20857]

Sequence

>retro_cjac_402
ATGAATATGGATCCTTCTTATCCACAAAGCCTGCCTTGCTCCAAAGCATCTGACTGTAAAGAATCTTCACCTATGCCTGT
GATTTCTGGGGCTGAAGAAAATTATCCATCCTTGCAAATGTCTTCTGCTGAGATGCCTCACACAGAGACTGTCTCCCCTC
TTCCTTCCTCCATGGATCTGCTTATTCAGGACAGCCCTGATTCTTCCTCCAGTCCCAAAGGCAAACAACCCACTGCTGCA
GAGAGTAGTGCCACAATAAAGGAAGACAAAGTCCCGGTCAAGAAACAGAAGACCAGAACTGTATTCACTTCCACCCAGCT
GTGTGTACTCAATGACAGTTCAGAGACAGAAATACCTCAGTATCCAGCAGATGCAAGAACGTTCCAACATCCTGAATGTT
AGCTACAAACAGATGAAGACCTGTTTCCAGAACCAGAGAATGAAATCTAAGAGGTGGCAGAAAAACAACTGGCCAAAGAA
TAGCAATGATGTGATGGAGAAGGCCTCAGCGCCCGCCTATCCCAGCCTCTACTCTTCCTACCACCAGGGATGCCTGATGA
ACACAACTGGGAACCTTCCAGTG

Alignment

ORF - retro_cjac_402 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.37 %
• Parental protein coverage: 63.93 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSMDPVCSQSLPCSEASDCGESSPTPVICEPEENYPSLQMCSAEMPHTETVSPLPSSMDLLTQDSPDSST
          M.MDP...QSLPCS.ASDC.ESSP.PVI...EENYPSLQM.SAEMPHTETVSPLPSSMDLL.QDSPDSS.
Retrocopy MNMDPSYPQSLPCSKASDCKESSPMPVISGAEENYPSLQMSSAEMPHTETVSPLPSSMDLLIQDSPDSSS

Parental  SP-KGKRPTAAESSPAVKEDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQV
          SP.K...P......P.....K............S....CV.....QRQKYLS.QQMQE.SNILN.SYKQ.
Retrocopy SP>KANNPLLQRVVPQ*RKTKSRSRNRRPE-LYSLPPSCVYSMTVQRQKYLSIQQMQERSNILNVSYKQM

Parental  KTWFQNQRMKSKRWQKNNWPRNTSDVTQKASAPTYPSLYSSYHQGCLVNTAGNLPV
          KT.FQNQRMKSKRWQKNNWP.N..DV..KASAP.YPSLYSSYHQGCL.NT.GNLPV
Retrocopy KTCFQNQRMKSKRWQKNNWPKNSNDVMEKASAPAYPSLYSSYHQGCLMNTTGNLPV

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	0.00 RPM
SRP051959_heart	0.00 RPM	0.02 RPM
SRP051959_kidney	0.00 RPM	0.02 RPM
SRP051959_liver	0.00 RPM	0.00 RPM
SRP051959_lung	0.05 RPM	0.18 RPM
SRP051959_lymph_node	0.09 RPM	0.00 RPM
SRP051959_skeletal_muscle	0.04 RPM	0.00 RPM
SRP051959_spleen	0.08 RPM	0.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_402 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_402 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_402 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017064	1 retrocopy	retro_amel_354,
Canis familiaris	ENSCAFG00000013914	1 retrocopy	retro_cfam_724,
Choloepus hoffmanni	ENSCHOG00000000972	4 retrocopies	retro_chof_1267, retro_chof_264, retro_chof_794, retro_chof_987,
Callithrix jacchus	ENSCJAG00000018999	8 retrocopies	retro_cjac_1732, retro_cjac_2234, retro_cjac_2441, retro_cjac_402 , retro_cjac_4153, retro_cjac_4177, retro_cjac_880, retro_cjac_989,
Cavia porcellus	ENSCPOG00000002621	1 retrocopy	retro_cpor_1132,
Echinops telfairi	ENSETEG00000004648	8 retrocopies	retro_etel_1155, retro_etel_1334, retro_etel_134, retro_etel_1434, retro_etel_1935, retro_etel_630, retro_etel_818, retro_etel_963,
Felis catus	ENSFCAG00000001621	1 retrocopy	retro_fcat_932,
Macropus eugenii	ENSMEUG00000009949	2 retrocopies	retro_meug_266, retro_meug_940,
Microcebus murinus	ENSMICG00000002228	1 retrocopy	retro_mmur_575,
Myotis lucifugus	ENSMLUG00000029325	2 retrocopies	retro_mluc_1562, retro_mluc_2054,
Myotis lucifugus	ENSMLUG00000030580	1 retrocopy	retro_mluc_169,
Monodelphis domestica	ENSMODG00000017979	2 retrocopies	retro_mdom_1293, retro_mdom_1938,
Mustela putorius furo	ENSMPUG00000016731	5 retrocopies	retro_mputfur_1140, retro_mputfur_1553, retro_mputfur_261, retro_mputfur_553, retro_mputfur_691,
Oryctolagus cuniculus	ENSOCUG00000013783	1 retrocopy	retro_ocun_971,
Otolemur garnettii	ENSOGAG00000026339	1 retrocopy	retro_ogar_568,
Procavia capensis	ENSPCAG00000015460	2 retrocopies	retro_pcap_143, retro_pcap_429,
Pteropus vampyrus	ENSPVAG00000006989	1 retrocopy	retro_pvam_1251,