RetrogeneDB ID: retro_cjac_1981

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:186033800..186034375(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000011821
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: AURKAIP1
• Ensembl ID: ENSCJAG00000034618
• Aliases: None
• Description: None

Sequence

>retro_cjac_1981
ATACTCCGGGTGCGCCTGACTTCTCAGCTGCTCAAGGCTGTTTCCTGGGCAGGCTGCAGTCCGCCCTGGCCTGTCTCGGG
AGTGCTGGGCAGCCATACCTGCAGGCCCCCTTACAGCACACAGCCAGCTGGCACAGGTAGGGCTGCCTCCCTCCTTGGAA
AGGGGGCCCAGCTGGAGCTCGAGGAGATGCTGGTCCCCAGGAAGATGTCCACCAGCCCCCTGGAGAGCTGCCTTACAGCC
CGCTGCCTCCTGCTCAGACTGGATGCCCGGACTACGGGGACTGCGGCTCCAGCCCAATTCTATGAGTGTCCGCATAGCCC
AATGGGGGAAGGGGCCAAGCAGGGGGATGAAAAGGTCTGGGATGCACCTCAGATGCAGCGCAAACACGTGTTGAAGACTC
GCAGGCGGAAGATGAACCACCACAAGTACCGGAAGGGGCAGAGAGGCCCCCGGTTCCTGCAGCGGAAGTTCCGGGAAGGA
CTTAAGCAGATCACGTTCAAAAGAGACCAGAGGCGCGTCTGGCTGAAGGAAACCCCTGAGCCTGTCAGACCTCCCGGGTC
TACCTGAGGGGCAGA

Alignment

ORF - retro_cjac_1981 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLLVRLTSPLFRAVPWAGCRRLWPSSGELGGRACGHFYSTQPAGRGRTASLPRKGAQLELEEMLVPRKMS
          .L.VRLTS.L..AV.WAGC...WP.SG.LG...C...YSTQPAG.GR.ASL..KGAQLELEEMLVPRKMS
Retrocopy ILRVRLTSQLLKAVSWAGCSPPWPVSGVLGSHTCRPPYSTQPAGTGRAASLLGKGAQLELEEMLVPRKMS

Parental  ISPLESWLTARCLLPRLDSGTPGTVAPPQPHECPPCHTGEGAEQGDEGVGDAPVMQCKNVLKIRRRKMNH
          .SPLES.LTARCLL.RLD..T.GT.AP.Q..ECP....GEGA.QGDE.V.DAP.MQ.K.VLK.RRRKMNH
Retrocopy TSPLESCLTARCLLLRLDARTTGTAAPAQFYECPHSPMGEGAKQGDEKVWDAPQMQRKHVLKTRRRKMNH

Parental  HKYRKLVKRTRFLRRKIREGRLKRKQLKFERDLRRIWLKAGLKEAPE-GWQTPKIYQRGR
          HKYRK.....RFL.RK.REG....KQ..F.RD.RR.WLK....E.PE...QT...Y.RGR
Retrocopy HKYRKGQRGPRFLQRKFREG---LKQITFKRDQRRVWLK----ETPE<ACQTSRVYLRGR

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	2.91 RPM
SRP051959_heart	0.00 RPM	4.35 RPM
SRP051959_kidney	0.00 RPM	4.57 RPM
SRP051959_liver	0.00 RPM	6.93 RPM
SRP051959_lung	0.02 RPM	3.16 RPM
SRP051959_lymph_node	0.00 RPM	3.36 RPM
SRP051959_skeletal_muscle	0.00 RPM	10.96 RPM
SRP051959_spleen	0.00 RPM	2.46 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1981 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1981 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1981 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000034618	1 retrocopy	retro_cjac_1981 ,
Myotis lucifugus	ENSMLUG00000004317	1 retrocopy	retro_mluc_81,
Tursiops truncatus	ENSTTRG00000017044	1 retrocopy	retro_ttru_1186,