RetrogeneDB ID: retro_cjac_760

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:15736164..15737154(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022593
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: INA
• Ensembl ID: ENSCJAG00000018178
• Aliases: None
• Description: None

Sequence

>retro_cjac_760
GGGCTAGCAGAGGAGGTGCAGCGGCTGCGGGCGCGCTGTGAGGAGGAGAGCCGCGGACGCGAAGGTGCGGAGCGCGCCCT
GAAGGCGCAGCAGCTCGACGTGGACGGCGCCACGCTGGCCCGCTTGGACCTGGAGAAGAAGGTGGAGTCGCTGCTGGACG
AGCTGGCCTTCGTGCGCTAGGTGCCCCACGAGGAGGTAGCCGAGCTGCTGGCCATGCTCCTGGCGTCGTCACAGGCCGCG
GCTGAGGTGAACGTGGCTGTGGCTAAACCAGATCTGAGCTCGGTGCTGAGGGAGATCCGCGCCCAATATGAGTCCTTGGC
TGCTAAGAACCTGCAGTCCGCGGAGGAATGGTACAAGTCCAAGTTCGCCAACCTGAAGGAGCAGGCGGTGCGCAGCACCG
AGGCCATCCGAGCCAGCCGCGAGGGGATCCACGAGTACCGGCGCCAGCTGCAGGCGCACAGCATCAAGATCGAGGGCCTG
CGCAGGGCCAACGCGTCCTTGGAGAGGCAGATCCTGGAACTGGAGGAGGGGCACAATGCCGAGGTGGCTGGCTACCAGGA
TGACATTGGGCAGCTAGAGAATGATCTGAGGAACACCAAGAGTGAGATGGCATGCCACCTTCGGGAATACCAGGACTTGC
TCAATGTTAAAATGGCTCTTGACATTGAGACAGCAGCTTACAGGAGACTGCTGGAAGGCGAAGAGACACGTTTTAGCACC
AGTGGGTTAAGCATTTCGGAGCTGAATCCACTTCTCAATCCAAGTTATCTGCTTACATCTAGAATCCTCAGTTCTACAAC
CTCCAAAGTCTCATCCACTGGGCTATCACTTAAGAAAGAGGAAGAGGAGGAGGAGGCATCTAAGGTAGCCTCTAAGAAAA
CCTCTGAGATACGGGAAAGTTTTGAAGAAATATTAGAGGAGACAGTAATATCTACTAAGAAAACCGAGAAATCAAATATA
GAAGAAACCACCATTTCGAGCCAAAAAATA

Alignment

ORF - retro_cjac_760 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.82 %
• Parental protein coverage: 65.93 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GLAEEVQRLRARCEEESRGREGAERALKAQQRDVDGATLARLDLEKKVESLLDELAFVRQVHDEEVAELL
          GLAEEVQRLRARCEEESRGREGAERALKAQQ.DVDGATLARLDLEKKVESLLDELAFVR.V..EEVAELL
Retrocopy GLAEEVQRLRARCEEESRGREGAERALKAQQLDVDGATLARLDLEKKVESLLDELAFVR*VPHEEVAELL

Parental  ATLQASSQAAAEVDVAVAKPDLSSALREIRAQYESLAAKNLQSAEEWYKSKFANLNEQAARSTEAIRASR
          A.L.ASSQAAAEV.VAVAKPDLSS.LREIRAQYESLAAKNLQSAEEWYKSKFANL.EQA.RSTEAIRASR
Retrocopy AMLLASSQAAAEVNVAVAKPDLSSVLREIRAQYESLAAKNLQSAEEWYKSKFANLKEQAVRSTEAIRASR

Parental  EEIHEYRRQLQARTIEIEGLRGANESLERQILELEERHNAEVAGYQDSIGQLENDLRNTKSEMARHLREY
          E.IHEYRRQLQA..I.IEGLR.AN.SLERQILELEE.HNAEVAGYQD.IGQLENDLRNTKSEMA.HLREY
Retrocopy EGIHEYRRQLQAHSIKIEGLRRANASLERQILELEEGHNAEVAGYQDDIGQLENDLRNTKSEMACHLREY

Parental  QDLLNVKMALDIEIAAYRKLLEGEETRFSTSGLSISGLNPLPNPSYLLPSRILSS-TSKVSSTGLSLKKE
          QDLLNVKMALDIE.AAYR.LLEGEETRFSTSGLSIS.LNPL.NPSYLL.SRILSS.TSKVSSTGLSLKKE
Retrocopy QDLLNVKMALDIETAAYRRLLEGEETRFSTSGLSISELNPLLNPSYLLTSRILSSTTSKVSSTGLSLKKE

Parental  EEEEEASKVASKKTSQIGESFEEILEETVISTKKTEKSNIEETTISSQKI
          EEEEEASKVASKKTS.I.ESFEEILEETVISTKKTEKSNIEETTISSQKI
Retrocopy EEEEEASKVASKKTSEIRESFEEILEETVISTKKTEKSNIEETTISSQKI

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	0.51 RPM
SRP051959_heart	0.05 RPM	0.25 RPM
SRP051959_kidney	0.00 RPM	0.29 RPM
SRP051959_liver	0.00 RPM	0.17 RPM
SRP051959_lung	0.00 RPM	0.47 RPM
SRP051959_lymph_node	0.00 RPM	0.41 RPM
SRP051959_skeletal_muscle	0.02 RPM	0.28 RPM
SRP051959_spleen	0.00 RPM	0.32 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_760 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_760 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_760 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008688	2 retrocopies	retro_cjac_1026, retro_cjac_1456,
Callithrix jacchus	ENSCJAG00000018178	4 retrocopies	retro_cjac_1685, retro_cjac_394, retro_cjac_4043, retro_cjac_760 ,
Macaca mulatta	ENSMMUG00000008872	1 retrocopy	retro_mmul_936,
Nomascus leucogenys	ENSNLEG00000015236	1 retrocopy	retro_nleu_795,