RetrogeneDB ID: retro_cjac_917

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:59826304..59827098(-)
• Located in intron of: ENSCJAG00000014761

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZNF75D
• Ensembl ID: ENSCJAG00000014531
• Aliases: None
• Description: None

Sequence

>retro_cjac_917
CAGAAATTATGCTATCAGTGGCTGAGGCCAGAGAGCCACTCAAAAAATCAAATCTTGGAAATGGTAGTGCTAGAGCAGTT
CCTGACCATTCTGCCCAAAGAGACCCAGAACTGGGTGCAGAAGCATCATCCACAGCATGTCAAACAGGCTCTGGTCCTGG
TGGAACACTTGCAGAGAGAACCTGGTGAAACAAAGAATGGGGTTGCAGCCCATGAGCTGGGAAAGGAGGCAGTGCTCTTG
GGAGGAACAGCAGTGGGCCCCAGGCTTCAAGTGGAAGCCATCAGAGCCCCAACCAATGGGTCTGTTCCAAAAAGAATATT
GAAATACATACTGGGTACTACAAGAACAGCTGGGCTGGAATACTCTCAAAGAAACCCAGACTGTATATGAAAGAGCTATG
CATGTCCAACAGATTTTAGCCCTTTCTGGGCAGAAAAGCACCAAAGACTGGAAGATAGCATCTGAGCTCATCTGGCCTGA
GTCCCAGAGTTGGTTGACATTTGAAGATGTAGCTGTGTACTTTTCTGAGGAAGAATGGCAATTATTGGATCCTCCTGAGA
AGACTCTACAATGCTGTAATGCAGGATATATCTATGAGACTAGGGTTAAAGCTAAAAAATGACCTTGGAAATGATTATCC
TATGTCTGTTTCTGCATCTGAAATACAAACACCAGGATACAAAGTAACAAAAAAGACCAGAGTGAAAATTGCCCAGAAAA
CAATGGGCAGGGAAAATCATGGTGATACACACAGGGTATAGGAATGGCACCAAGCTTTTCCAAAGAAGAAAAAA

Alignment

ORF - retro_cjac_917 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.67 %
• Parental protein coverage: 52.55 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QKLCHQWLRPEIHSKEQILEMLVLEQFLSILPKETQNWVQKHHPQNVKQALVLVEFFQRKPDGTKNEVTV
          QKLC.QWLRPE.HSK.QILEM.VLEQFL.ILPKETQNWVQKHHPQ.VKQALVLVE..QR.P..TKN.V..
Retrocopy QKLCYQWLRPESHSKNQILEMVVLEQFLTILPKETQNWVQKHHPQHVKQALVLVEHLQREPGETKNGVAA

Parental  HELGKEAVLLGGTAV-APGFKWKPAEPQPTGVFQKEYWNTYWVLQEQLGWNTHKETQPVYERAVHDQQML
          HELGKEAVLLGGTAV.APGFKWKP.EPQP.G.FQKEY.NTYWVLQEQLGWNT.KETQ.VYERA.H.QQ.L
Retrocopy HELGKEAVLLGGTAV>APGFKWKPSEPQPMGLFQKEY*NTYWVLQEQLGWNTLKETQTVYERAMHVQQIL

Parental  ALSEQKSTKDWKMASEFILPASQSLLTFEDVAVYFSEEEWQLLDPPE-KTLYNDVMQDIYETVISLGLKL
          ALS.QKSTKDWK.ASE.I.P.SQS.LTFEDVAVYFS.EE...L..P....LYN.VMQDI......LGLKL
Retrocopy ALSGQKSTKDWKIASELIWPESQSWLTFEDVAVYFS-EEEWQLLDPP>RRLYNAVMQDIS---MRLGLKL

Parental  KSDTGNDHPVSVSTSEMQTPGCKVSENTRRKIAQKTMGRENHGDTHRVQKWHRAFPRKKR
          K.D.GND.P.SVS.SE.QTPG.KV...TR.KIAQKTMGRENHGDTHRV..WH.AFP.KK.
Retrocopy KNDLGNDYPMSVSASEIQTPGYKVTKKTRVKIAQKTMGRENHGDTHRV*EWHQAFPKKKK

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	1.60 RPM	0.51 RPM
SRP051959_heart	2.49 RPM	0.54 RPM
SRP051959_kidney	0.87 RPM	0.89 RPM
SRP051959_liver	1.19 RPM	0.56 RPM
SRP051959_lung	2.98 RPM	1.09 RPM
SRP051959_lymph_node	1.14 RPM	2.92 RPM
SRP051959_skeletal_muscle	0.63 RPM	0.22 RPM
SRP051959_spleen	6.95 RPM	1.37 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_917 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_917 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_917 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014531	2 retrocopies	retro_cjac_3200, retro_cjac_917 ,
Homo sapiens	ENSG00000186376	1 retrocopy	retro_hsap_797,
Otolemur garnettii	ENSOGAG00000032383	1 retrocopy	retro_ogar_1516,
Pongo abelii	ENSPPYG00000020747	1 retrocopy	retro_pabe_918,