RetrogeneDB ID: retro_cjac_2168

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:110026871..110027448(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNF4A
• Ensembl ID: ENSCJAG00000017746
• Aliases: None
• Description: None

Sequence

>retro_cjac_2168
TTTTGTGAGCTCCCCCTGGATGACCAGGTGGCCCTGCTCAGAGCCCATGCTGGTGACCACCTGCTGCTCAGAGCCACCAA
GGATCCAGGAAAGATCAAGCAGCTGTGTTCCCAGGGGCAGGTGAGCTTGGAGGACTACTTCAACGACGGCCAGTATGACT
CACGTGGCCGCTTTGGCCAGCTGCTGCTGCTGCCCACCCTGCAGAGCATCACCTGGCAGATGATCAAGGAGATCCAGTTC
ATCAAGCTCTTGGCATGGCCAAGATTGACAACCTGCTGCAGGAGATGCTGTTGGGAGGGTCTTCCAGTGATGCACCCCAT
GCCCACCACCCCCTGCACCATCACCTGATGCAGGAACACATGGGAACCAACGTCACTGTTGCCAACACGATGCCCACTCA
CCTCAGCAACAGACAGATGTGTGGGCGGCCCCGGCCCAGGGGGCAGGCAGCCACCCCTGAGACCCCACAGCTCTCACCAC
CAGGTGGTCCAGGTCTGAGCCTTATAAACTCCTGCCAGGAGCCGTCACGACAATGGTCAAGCCCCCCTCTGCCATCCCCC
AGCCGACCATCACCAAG

Alignment

ORF - retro_cjac_2168 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.17 %
• Parental protein coverage: 55.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FQELQIDDNEYAYLKAIIFFDPDAKGLSDPGKIKRLRSQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQ
          F.EL..DD...A.L.A............DPGKIK.L.SQ.QVSLEDY.ND.QYDSRGRFG.LLLL.PTLQ
Retrocopy FCELPLDD-QVALLRAHAGDHLLLRATKDPGKIKQLCSQGQVSLEDYFNDGQYDSRGRFGQLLLL-PTLQ

Parental  SITWQMIEQIQFIKLF-GMAKIDNLLQEMLLGGSSSDAPHAHHPLHPHLMQEHMGTNVIVANTMPTHLSN
          SITWQMI..IQFIKL..GMAKIDNLLQEMLLGGSSSDAPHAHHPLH.HLMQEHMGTNV.VANTMPTHLSN
Retrocopy SITWQMIKEIQFIKLL<GMAKIDNLLQEMLLGGSSSDAPHAHHPLHHHLMQEHMGTNVTVANTMPTHLSN

Parental  GQMCEWPRPRGQAATRETPQPSPPGGSG-SEPYKLLPGAVATIVKPLSAIPQPTITK
          .QMC..PRPRGQAAT.ETPQ.SPPGG.G.SEPYKLLPGAV.T.VKP.SAIPQPTITK
Retrocopy RQMCGRPRPRGQAATPETPQLSPPGGPG<SEPYKLLPGAVTTMVKPPSAIPQPTITK

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	59.60 RPM
SRP051959_heart	0.00 RPM	0.07 RPM
SRP051959_kidney	0.00 RPM	108.62 RPM
SRP051959_liver	0.00 RPM	116.64 RPM
SRP051959_lung	0.00 RPM	0.05 RPM
SRP051959_lymph_node	0.00 RPM	0.00 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.02 RPM
SRP051959_spleen	0.00 RPM	0.02 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2168 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2168 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2168 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017746	1 retrocopy	retro_cjac_2168 ,