RetrogeneDB ID: retro_cjac_2125

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:26424007..26424530(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFB9
• Ensembl ID: ENSCJAG00000012818
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 9, 22kDa [Source:HGNC Symbol;Acc:7704]

Sequence

>retro_cjac_2125
TTCTCTGCGCCGGCGGCCTACCTGATTCGTCAGCAGAAGGTGTTGTGGTTTTATAAGCAGGCGCTGAGCCACCTCGAGTA
GTGGTGTGTCCACAGGGACAAATACTGCTACTTCACTTGTTTGATGAGTGCCCAGTTTGAAGAACATAAGAATGAAAAGG
ATATGATGAAGGCCACCCAGCTGCTGAGGGAGACTGAGGAAGATTTCTGGTACCGTCAGCATCCACAGCCATACATCTTT
CCTGACTCTCCTGGGGGTACCTCCTATGAGAGATACGAGTGTTACAAGGTTCCAGAAAACTGCTTGAATGCCTGGCATCC
TTGCCAGAAGGCAATGTATCCTGATTACTTTGCCAAGAGAGAAAAGGGGAAGAAACGGTGGGGAGAAAGCTGGGAATGAG
AGATTAAACAGCTGGAGGAGGAAACGCCACCTGGTGGTCCTCTGACTGGTTTTGCCTCTTGCCCTAAAAGAAGGTGATTT
GCCCCCACTGTGGTGGCATATTGTGACCAGACCCTGGGAGCGC

Alignment

ORF - retro_cjac_2125 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.41 %
• Parental protein coverage: 97.77 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FSAPVAYLTHQQKVLRLYKRALRHLESWCVHRDKYRYFACLMRARFEEHKNEKDMVKATLLLKEAEEEFW
          FSAP.AYL..QQKVL..YK.AL.HLE.WCVHRDKY.YF.CLM.A.FEEHKNEKDM.KAT.LL.E.EE.FW
Retrocopy FSAPAAYLIRQQKVLWFYKQALSHLE*WCVHRDKYCYFTCLMSAQFEEHKNEKDMMKATQLLRETEEDFW

Parental  YRQHPQPYIFPDSPGGTSYERYECYKLPENCLDAWHPSEKAMYPDYFAKREKWKKLRRESWEREIKQLEE
          YRQHPQPYIFPDSPGGTSYERYECYK.PENCL.AWHP..KAMYPDYFAKREK.KK...ESWE.EIKQLE.
Retrocopy YRQHPQPYIFPDSPGGTSYERYECYKVPENCLNAWHPCQKAMYPDYFAKREKGKKRWGESWE*EIKQLE-

Parental  ETPPGGP-LTEALPPARKEGDLPPLWWHIVTRPRER
          E..P.G..L...LP.A.KEGDLPPLWWHIVTRP.ER
Retrocopy EETPPGG>L*LVLPLALKEGDLPPLWWHIVTRPWER

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	24.43 RPM
SRP051959_heart	0.00 RPM	65.51 RPM
SRP051959_kidney	0.00 RPM	46.88 RPM
SRP051959_liver	0.00 RPM	54.52 RPM
SRP051959_lung	0.00 RPM	18.22 RPM
SRP051959_lymph_node	0.00 RPM	16.60 RPM
SRP051959_skeletal_muscle	0.00 RPM	124.24 RPM
SRP051959_spleen	0.00 RPM	18.87 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2125 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2125 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2125 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 18 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000010022	1 retrocopy	retro_acar_132,
Ailuropoda melanoleuca	ENSAMEG00000015852	2 retrocopies	retro_amel_1680, retro_amel_553,
Callithrix jacchus	ENSCJAG00000012818	1 retrocopy	retro_cjac_2125 ,
Equus caballus	ENSECAG00000018238	1 retrocopy	retro_ecab_541,
Felis catus	ENSFCAG00000004678	1 retrocopy	retro_fcat_689,
Homo sapiens	ENSG00000147684	2 retrocopies	retro_hsap_3905, retro_hsap_4112,
Gorilla gorilla	ENSGGOG00000015883	2 retrocopies	retro_ggor_2632, retro_ggor_2759,
Microcebus murinus	ENSMICG00000017481	1 retrocopy	retro_mmur_1494,
Myotis lucifugus	ENSMLUG00000003765	1 retrocopy	retro_mluc_1339,
Macaca mulatta	ENSMMUG00000015493	1 retrocopy	retro_mmul_1736,
Monodelphis domestica	ENSMODG00000001831	3 retrocopies	retro_mdom_1176, retro_mdom_1193, retro_mdom_1582,
Nomascus leucogenys	ENSNLEG00000005484	2 retrocopies	retro_nleu_1141, retro_nleu_578,
Otolemur garnettii	ENSOGAG00000030772	2 retrocopies	retro_ogar_1654, retro_ogar_925,
Pongo abelii	ENSPPYG00000018869	3 retrocopies	retro_pabe_2643, retro_pabe_3182, retro_pabe_3366,
Pan troglodytes	ENSPTRG00000020569	2 retrocopies	retro_ptro_2656, retro_ptro_2791,
Pteropus vampyrus	ENSPVAG00000009153	1 retrocopy	retro_pvam_243,
Ictidomys tridecemlineatus	ENSSTOG00000021955	1 retrocopy	retro_itri_611,
Tupaia belangeri	ENSTBEG00000006895	3 retrocopies	retro_tbel_1901, retro_tbel_2663, retro_tbel_610,