RetrogeneDB ID: retro_cjac_1498

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 16:14016984..14017306(-)
• Located in intron of: ENSCJAG00000009122

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFV3
• Ensembl ID: ENSCJAG00000015786
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) flavoprotein 3, 10kDa [Source:HGNC Symbol;Acc:7719]

Sequence

>retro_cjac_1498
GTAGTGGCTCCGCTTTTGCTGTGACAAAGACGAGTCGAGGCACTGAAGACCATCCTCCTCAAAGCCCATGTGTTTCAAGG
ACTTTCTTCCACAGTTTCTTTGTCTGCGGCATCAGGGAAGAGTGAAAAGGCTCAGCCACAGAATCCCAAGAAAAAGTTCA
CCAAAAAAGCCAGTCCCAGTGCCTGCTAAGTCATTTCACAACACTACCTACAAGAACCTCCAGCATCATGACTGCACCAC
GTACACCTCCTTAGACCTAAAAATCGGCCTCTCAAACTTCAGGGTGCCTCAGCCCTCCTTAGGCCAGGAGTCAGCTCGAC
AC

Alignment

ORF - retro_cjac_1498 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.97 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAPLLLQQGRAGALKTLLQEAHVFRGLASTVSLSAESGRSEKGQPQN-PKKQSTPKNPASAPTEPFDNT
          ..APLLL.Q.R..ALKT.L..AHVF.GL.STVSLSA.SG.SEK.QPQN.P.K.S.PK.P...P...F.NT
Retrocopy VVAPLLL*QRRVEALKTILLKAHVFQGLSSTVSLSAASGKSEKAQPQN>PRK-SSPKKPVPVPAKSFHNT

Parental  TYKNLQHHDYTTYTFLDLNLDLSKFRMPQPSSGRESPRH
          TYKNLQHHD.TTYT.LDL...LS.FR.PQPS.G.ES.RH
Retrocopy TYKNLQHHDCTTYTSLDLKIGLSNFRVPQPSLGQESARH

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	0.22 RPM	5.44 RPM
SRP051959_heart	0.30 RPM	12.02 RPM
SRP051959_kidney	0.20 RPM	12.65 RPM
SRP051959_liver	0.26 RPM	10.85 RPM
SRP051959_lung	0.21 RPM	7.42 RPM
SRP051959_lymph_node	0.00 RPM	6.28 RPM
SRP051959_skeletal_muscle	0.07 RPM	14.98 RPM
SRP051959_spleen	0.23 RPM	10.25 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1498 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1498 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1498 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021491	10 retrocopies	retro_btau_445, retro_btau_769, retro_btau_770, retro_btau_772, retro_btau_773, retro_btau_774, retro_btau_803, retro_btau_804, retro_btau_805, retro_btau_806,
Canis familiaris	ENSCAFG00000010508	1 retrocopy	retro_cfam_1001,
Callithrix jacchus	ENSCJAG00000015786	1 retrocopy	retro_cjac_1498 ,