RetrogeneDB ID: retro_cjac_4043

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:11744177..11745666(+)
• Located in intron of: ENSCJAG00000003979

Retrocopy information

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

Parental gene information

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

Sequence

>retro_cjac_4043
ATGAGCTTCGGCTCGGAGCACTATCTGTGCTGCTCCTCCTCCTACCGCAAGGTGTTCGGGGACGGCTCCCGCCTGTCCGC
GCACCTCTCCGGGGCCGGCGGTGCGGGCGGCTTCCGTTCACAGTCCCTGTCCCTGTCCAGCAGCAATGTGGCTTCCTCGA
CCGCCTGCTCCTTGGCCTTGTAGCTCGGCCTCGGCCTGGCCTATCGCCGGCATCCGATGGGCTGGACCTGAGCCAGGCGG
CGGCGTGCACCAACTAGTACAAGATCATCCGCACCAACGAGAAGGACCAGCTGCAGGGACTCAGCGACCGCTTTGCGGTG
TTCTTCGAGAAGGTGCATCAGCTGGAGACGCAGAACCACGCCTGGAGGCCGAGCTGGCTGCGCTGTGGCAGCGCCACGCT
GAGCGGTTGCGCGTCGGCGAGCTCTTCCAGCGCGAGCTGCGAGACCTGGGCGCGCAGCTGGAGGAGGCGACCTCGGCACA
CATGCAGGCCCTGCTGGAGCGCGACGGGCTGGCCGAGGAGGTGCAGCAGCTGCGGGCGCACTGTAAGGAGGAGAGCCGTG
GTCCTGAAGGTGCCGAGCACGCCCTGAAGGCGCAGCAGTGCGATGTGGACGGCGCCATGCTGGCCCGCCTGGACCTGGAG
AAGGTGGAGTTGCTGCTGGACGAGCTGGCTTTCGTGCGCCAGGTGCGCGACGAGGAGGTAGCCGAGCTGCTGGCCACGCA
GCAGGCGTCATCACAGGCCGCGGCCGAGGTGGACATGGCTTTGGCTAAACCAGACCTGAGCTCGGCGCTGAGGGAGATCC
GTGCCTAACATGAGTCCCTGGCTGCTAAGAACCTGCAGTCCGCGGAGGAATGGTACAAGTCCAAGTTCGCCAACCTGAAC
GAGCAGGCGGCGTGCAGCACCGAGGCCATCCGAGCCAGCCGCGAGGAGATCCACGAGTACCGGCGCCAGCTGCAGGCGCG
CACCATCGAGACCGAGGGCCTGTGCGGGGCCAGCGAGTCCTTGGAGAGGCAGATCCTGGAACTGGAGGAGCGGCACAATG
CCGAGGTGGCTGGCTACCAGGATAGCATTGGGCAGCTAGAGAATGATCTGAGGAACACCAAGAGTGAGATGGCACGCCAC
CTTCGGCAATACCAGGACTTGCTCAATGTCAAAATGGCTCTTGACATTGAGATAGCAGCTTACAGGAAACTGCTGGAAGG
CGAAGAGACACGTTTTAGCACCAGTGGGTTAAGCATTTCGGGACTGCATCCACTTCCCAATCCAAGTTATCTGCTCCCAT
CTAGAATCCTCAGTTCAACCTCCAAAGTCTCATCCACTGGGCTATCACTTAAGAAAGAGGAAGAGGAGGAGGAGGCATCT
AAGGTAGCCTCTAAGAAAACCTCCCAGATAGGGGAAAGTTTTGAAGACATATTAGAGGAGACAGTAATATCTACTAAGAA
AACTGAGAAATCAAATATAGAAGAAACTACCATTTTGAGCCAAAAAATA

Alignment

ORF - retro_cjac_4043 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.62 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSFGSEHYLCSSSSSYRKVFGDGSRLSARLAGAGGAGGFRSQSLSRSNVASSTACSSASSLGLGLAYRR-
          MSFGSEHYLC.SSS.YRKVFGDGSRLSA.L.GAGGAGGFRSQSLS.S.............L.LGL.....
Retrocopy MSFGSEHYLCCSSS-YRKVFGDGSRLSAHLSGAGGAGGFRSQSLSLSSSNVASSTACSLAL*LGLGLAY<

Parental  PPASDGLDLSQAAARTNEYKIIRTNEKEQLQGLNDRFAVFIEKVHQLETQNRA-LEAELAALRQRHAEPS
          .PASDGLDLSQAAA.TN.YKIIRTNEK.QLQGL.DRFAVF.EKVHQLETQN.A.LEAELAAL.QRHAE..
Retrocopy SPASDGLDLSQAAACTN*YKIIRTNEKDQLQGLSDRFAVFFEKVHQLETQNHA<LEAELAALWQRHAERL

Parental  RVGELFQRELRDLRAQLEEASSARAQALLERDGLAEEVQRLRARCEEESRGREGAERALKAQQRDVDGAT
          RVGELFQRELRDL.AQLEEA.SA..QALLERDGLAEEVQ.LRA.C.EESRG.EGAE.ALKAQQ.DVDGA.
Retrocopy RVGELFQRELRDLGAQLEEATSAHMQALLERDGLAEEVQQLRAHCKEESRGPEGAEHALKAQQCDVDGAM

Parental  LARLDLEKKVESLLDELAFVRQVHDEEVAELLATLQASSQAAAEVDVAVAKPDLSSALREIRAQYESLAA
          LARLDLEK.VE.LLDELAFVRQV.DEEVAELLAT.QASSQAAAEVD.A.AKPDLSSALREIRA..ESLAA
Retrocopy LARLDLEK-VELLLDELAFVRQVRDEEVAELLATQQASSQAAAEVDMALAKPDLSSALREIRA*HESLAA

Parental  KNLQSAEEWYKSKFANLNEQAARSTEAIRASREEIHEYRRQLQARTIEIEGLRGANESLERQILELEERH
          KNLQSAEEWYKSKFANLNEQAA.STEAIRASREEIHEYRRQLQARTIE.EGL.GA.ESLERQILELEERH
Retrocopy KNLQSAEEWYKSKFANLNEQAACSTEAIRASREEIHEYRRQLQARTIETEGLCGASESLERQILELEERH

Parental  NAEVAGYQDSIGQLENDLRNTKSEMARHLREYQDLLNVKMALDIEIAAYRKLLEGEETRFSTSGLSISGL
          NAEVAGYQDSIGQLENDLRNTKSEMARHLR.YQDLLNVKMALDIEIAAYRKLLEGEETRFSTSGLSISGL
Retrocopy NAEVAGYQDSIGQLENDLRNTKSEMARHLRQYQDLLNVKMALDIEIAAYRKLLEGEETRFSTSGLSISGL

Parental  NPLPNPSYLLPSRILSSTSKVSSTGLSLKKEEEEEEASKVASKKTSQIGESFEEILEETVISTKKTEKSN
          .PLPNPSYLLPSRILSSTSKVSSTGLSLKKEEEEEEASKVASKKTSQIGESFE.ILEETVISTKKTEKSN
Retrocopy HPLPNPSYLLPSRILSSTSKVSSTGLSLKKEEEEEEASKVASKKTSQIGESFEDILEETVISTKKTEKSN

Parental  IEETTISSQKI
          IEETTI.SQKI
Retrocopy IEETTILSQKI

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	0.58 RPM	0.51 RPM
SRP051959_heart	0.32 RPM	0.25 RPM
SRP051959_kidney	0.44 RPM	0.29 RPM
SRP051959_liver	0.13 RPM	0.17 RPM
SRP051959_lung	0.68 RPM	0.47 RPM
SRP051959_lymph_node	0.94 RPM	0.41 RPM
SRP051959_skeletal_muscle	0.50 RPM	0.28 RPM
SRP051959_spleen	0.42 RPM	0.32 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4043 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4043 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4043 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,