RetrogeneDB ID: retro_cjac_1685

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 18:35396257..35397322(-)
• Located in intron of: None

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_1685
GAGGCCGAGCTGCCCGCGCTGAGGCAGCGCCACGCCGAGGCTTCGCGCATTGGCGAACTCTTCCAGCGCGAGCTGCGCAC
GCAACTGGAGGAGGCGAGCCCGGCGCGTGCTCAGGCCCTGCTGGAGCGCCACGGGCTGGCCTAGGAGGTCCAGCGGCTGC
GGGCGCGCTGCAAGGAGGAGAGCCGCGGATGCAAAGCTGCCGGGCGTGCCCCGAAGGCGCAGTAGCGCCACGTGGATGGC
GCCAAGCTGGCCCGCCTGGACCTGGAGAAGAAAGTAGCTGAGCTGCTGGCCACGCTGCAGGCGTCGTCACAGGCCGCGGC
GGAGGTGGACGTGGCTGTGGCTAACCAGACCTGAGCTCGGCCCTGAGGGAGATCCACACCCAGTGTGAGTCCCTGGCTGC
TAAGAACCTGCAGTCTGCAGAGGAATGGTACAAGTCCAAGTTCGCCAACCTGAACGAGCAGGCGGCATGCAGCACCGAGG
CCATGCGAGCCAGCCGCGAGGAGATCCACGAGTACCAGGGCCAGCTGCAGACGTGCACCATCGAGATCGAGGGCCTGCGC
AGGGCCAACGAGCCCTTGGAGAGGCCGATCCTGGAGCTGGAGGAGCGGCGCAATGCCGAGGTGGCTGGCTACCAGGATAA
CATTGGGCAGCTAGAGAATGATCTGAGGAACACCAAGAGTGAGATGGCATGCCACCTTTGGGAATACCAGGACTTGCTCA
ATGTCAAAATGGCTCTTGACATTGAGATAGCAGCTTACAGGAAACTGCTGGAAGGTGAAGAGACACGTTTTAGCACCAGT
GGGTTAAGCATTTCGGGGCTGAATCCACTTCCCAATCCAAGTTATCCGCTCCCACCTAGAATCCTCAGTTCTAACAACCT
CCAAAATCTCATCCACTGGGCTATCACTTAAGAAAGAGGAGGAGGAGGAGGCATCTAAGGTAGCCTCTAAGAAAACCTCC
CAGATAGGGGAAAGTTTTGAAGACATATTAGAGGAGACAGTAATATCTACTAAGAAAACCGAGAAATCAAATACAGAAGA
AACCACCATTTCAAGCCAAAAAATA

Alignment

ORF - retro_cjac_1685 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.79 %
• Parental protein coverage: 71.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QRELRDLRAQLEEASSARAQALLERDGLAEEVQRLRARCEEESRGREGAERALKAQQRDVDGATLARLDL
          ..EL..LR....EAS........E.....EE....RA....E..G.......L.A..........A....
Retrocopy EAELPALRQRHAEASRIGELFQRELRTQLEEASPARAQALLERHGLA*EVQRLRARCKEESRGCKAAGRA

Parental  EKKVESLLDELAFVRQVHDEEVAELLATLQASSQAAAEVDVAVAK-PDLSSALREIRAQYESLAAKNLQS
          .K......D.....R......VAELLATLQASSQAAAEVDVAVA..PDLSSALREI..Q.ESLAAKNLQS
Retrocopy PKAQ*RHVDGAKLARLDLEKKVAELLATLQASSQAAAEVDVAVAN<PDLSSALREIHTQCESLAAKNLQS

Parental  AEEWYKSKFANLNEQAARSTEAIRASREEIHEYRRQLQARTIEIEGLRGANESLERQILELEERHNAEVA
          AEEWYKSKFANLNEQAA.STEA.RASREEIHEY..QLQ..TIEIEGLR.ANE.LER.ILELEER.NAEVA
Retrocopy AEEWYKSKFANLNEQAACSTEAMRASREEIHEYQGQLQTCTIEIEGLRRANEPLERPILELEERRNAEVA

Parental  GYQDSIGQLENDLRNTKSEMARHLREYQDLLNVKMALDIEIAAYRKLLEGEETRFSTSGLSISGLNPLPN
          GYQD.IGQLENDLRNTKSEMA.HL.EYQDLLNVKMALDIEIAAYRKLLEGEETRFSTSGLSISGLNPLPN
Retrocopy GYQDNIGQLENDLRNTKSEMACHLWEYQDLLNVKMALDIEIAAYRKLLEGEETRFSTSGLSISGLNPLPN

Parental  PSY-LLPSRILSS-TSKVSSTGLSLKKEEEEEEASKVASKKTSQIGESFEEILEETVISTKKTEKSNIEE
          PSY.L.P....S..TSK.SSTGLSLKK.EEEEEASKVASKKTSQIGESFE.ILEETVISTKKTEKSN.EE
Retrocopy PSYPLPPRILSSN>TSKISSTGLSLKK-EEEEEASKVASKKTSQIGESFEDILEETVISTKKTEKSNTEE

Parental  TTISSQKI
          TTISSQKI
Retrocopy TTISSQKI

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	0.00 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	0.04 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_1685 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1685 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1685 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,