RetrogeneDB ID: retro_cjac_1466

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 16:37049558..37050032(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IGJ
• Ensembl ID: ENSCJAG00000014618
• Aliases: None
• Description: None

Sequence

>retro_cjac_1466
ATGAAGAACTATCTTCTTTTCTAAACAGTCCAGGCCATTTTTGTTAAGTCTGTTCTTGTGACAGCCCAAGATGAAGATGA
GAGGATCATTCTTGTTGACAACAAATGTAAGTAGACCCAGGTTATTTTCAGCATCATCTCTTCTACCAACGATCCTGATG
AGAACCTTGTGGAGAGAAATATCCAAATTACTGTTCTTCTGAACAAGAAGAATATCTCTGGTCCCATCTCAAGGTTGAGA
ACCAAATTTGTGTACCATTTGTCAGACCTCTGTAAAATATGTGATCCTACAGAAGTGGAACTGGATAATCAGAGCTCCTG
CTACTCAAACAATATCTGTGATGAAGACAGTGCTACAGAGACATGGCATGCTGATGATAGAAGCAAGTTCTACATAACTA
TGGTCCCACTTACATATGGTGGTGAGACCAAAATGGTGAAAATAGGCTTGGCCCCAGGTTCCTGCCACCCTGAC

Alignment

ORF - retro_cjac_1466 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.38 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKNHLLFWGVLAIFVTAGHVKAQ-EDERIVLVDNKCKCARITSRIIRSSNDPNEDIVERNIRIIVPLNNR
          MKN.LLF..V.AIFV....V.AQ.EDERI.LVDNKCK.......II.S.NDP.E..VERNI.I.V.LN..
Retrocopy MKNYLLF*TVQAIFVKSVLVTAQDEDERIILVDNKCK*TQVIFSIISSTNDPDENLVERNIQITVLLN-K

Parental  ENISDPTSPLRTKFVYHLSDLCKKCDPTEVELDNQIVTATQSNICDEDSATETCYTYDRNKCYTAVVPLV
          .NIS.P.S.LRTKFVYHLSDLCK.CDPTEVELDNQ.......NICDEDSATET....DR.K.Y...VPL.
Retrocopy KNISGPISRLRTKFVYHLSDLCKICDPTEVELDNQS-SCYSNNICDEDSATETWHADDRSKFYITMVPLT

Parental  FGGETKMVESALTPDSCYPD
          .GGETKMV...L.P.SC.PD
Retrocopy YGGETKMVKIGLAPGSCHPD

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	820.51 RPM
SRP051959_heart	0.00 RPM	6.91 RPM
SRP051959_kidney	0.00 RPM	146.25 RPM
SRP051959_liver	0.00 RPM	87.73 RPM
SRP051959_lung	0.00 RPM	79.47 RPM
SRP051959_lymph_node	0.00 RPM	406.03 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.16 RPM
SRP051959_spleen	0.00 RPM	862.97 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1466 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1466 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1466 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014618	1 retrocopy	retro_cjac_1466 ,
Homo sapiens	ENSG00000132465	1 retrocopy	retro_hsap_4086,
Macaca mulatta	ENSMMUG00000022096	1 retrocopy	retro_mmul_2300,
Nomascus leucogenys	ENSNLEG00000007714	1 retrocopy	retro_nleu_3069,
Pongo abelii	ENSPPYG00000014809	1 retrocopy	retro_pabe_3272,
Pan troglodytes	ENSPTRG00000016134	1 retrocopy	retro_ptro_2771,