RetrogeneDB ID: retro_cjac_641

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:182898587..182899104(-)
• Located in intron of: ENSCJAG00000017316

Retrocopy information

• Ensembl ID: ENSCJAG00000017291
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: POLR2G
• Ensembl ID: ENSCJAG00000018688
• Aliases: None
• Description: polymerase (RNA) II (DNA directed) polypeptide G [Source:HGNC Symbol;Acc:9194]

Sequence

>retro_cjac_641
GTGTTCTACCATATCTCTCCAGAGCACAAAATCCTGGTGTACCCACGCTACTTCGGCCCCAACTTGCTCAACATGGTGAA
GCAGAAGCTCTTCACCGAGGTGGAGGGGACCTGCACCGGGAAGTATGGTTTTGTAAACGCTATAACCACCATTGACAATA
TCGGTGCTGGTGTGATCCAGCCAGGCCGAGGCTTCCTCCTTTATCCAGTTAAGTACAAGGCTATTGTTTTCCGGCCCTTT
AAAAGCGAAGTGGTGGATGCTATTGTCACTCAGGTCAACAAAGTTGGACTCTTCACAGAAATTGGGCCTATGTCTTGCTT
CATCTCTCGACATTCCATCCCTTCAGAGATGGAGTTTGATCCTAACTCCAACCCACCATGTTACAAGACAACGGATGAGG
ATATTGTGATTCAGCAGGACGATGAGATCCGCTTAAAGACTGTGGGGACCCGTGTGGACAAGAATGACATTTTTGCTATT
GGCTCCCTGATGGATGATTACTTAAGGGCTTGTAAGC

Alignment

ORF - retro_cjac_641 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.91 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MFYHISLEHEILLHPRYFGPNLLNTVKQKLFTEVEGTCTGKYGFVIAVTTIDNIGAGVIQPGRGFVLYPV
          .FYHIS.EH.IL..PRYFGPNLLN.VKQKLFTEVEGTCTGKYGFV.A.TTIDNIGAGVIQPGRGF.LYPV
Retrocopy VFYHISPEHKILVYPRYFGPNLLNMVKQKLFTEVEGTCTGKYGFVNAITTIDNIGAGVIQPGRGFLLYPV

Parental  KYKAIVFRPFKGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQD
          KYKAIVFRPFK.EVVDA.VTQVNKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKT.DEDIVIQQD
Retrocopy KYKAIVFRPFKSEVVDAIVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTTDEDIVIQQD

Parental  DEIRLKIVGTRVDKNDIFAIGSLMDDYL-GLVS
          DEIRLK.VGTRVDKNDIFAIGSLMDDYL.GLVS
Retrocopy DEIRLKTVGTRVDKNDIFAIGSLMDDYL>GLVS

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	0.73 RPM	9.19 RPM
SRP051959_heart	0.32 RPM	9.66 RPM
SRP051959_kidney	0.71 RPM	9.32 RPM
SRP051959_liver	0.32 RPM	8.58 RPM
SRP051959_lung	0.78 RPM	12.27 RPM
SRP051959_lymph_node	0.46 RPM	17.62 RPM
SRP051959_skeletal_muscle	0.94 RPM	8.60 RPM
SRP051959_spleen	0.50 RPM	16.05 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_641 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_641 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_641 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018688	1 retrocopy	retro_cjac_641 ,
Dipodomys ordii	ENSDORG00000015696	1 retrocopy	retro_dord_574,
Macropus eugenii	ENSMEUG00000011547	1 retrocopy	retro_meug_139,
Myotis lucifugus	ENSMLUG00000011039	1 retrocopy	retro_mluc_261,
Pteropus vampyrus	ENSPVAG00000003481	1 retrocopy	retro_pvam_91,