RetrogeneDB ID: retro_cjac_394

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:49237044..49237825(+)
• 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_394
GGACGCGAAGGCACCAAGCGCGCCCTGAAGGTGCAGCAGCGCGACGTGGACAGTACCATGCTGGCCTTCCTGGACATGGA
GCAGAAGGTGGAGTCGCTGTGGGACTAGCTGGCCTTAGTGCGCCAGGTTCACGAGTAGTAGGTAGCCAAGCTGCTGGCCA
CGCTGAAGGCGTAGTGACAGGCCGCGGCTGAGGTGGATGTGACTGTGGTTAAACCAGACCTAAGCTCAGCGCTGATGGAG
ATCCGCGCCCAGTATGAGTCCCTGGCCGCTAATAACCTGCAGTCCTCGGAGGAATGGTACAAGTCTAAGTTCGCTAACCT
GAATGAGCAGGGGCACGCGTAACCGAGGCTATCCCGGCCAGCTTCGAGGAGATCCACGAGTACCGACGCCAGCTGCAGGC
GCGCACCATCGAGATCGAGGGCCTGCGCGGGGCTAGCGAGTCCTTGGAGAGGCCGATCCTGGAGCTGGAGGAGCGGCACA
GCGAGGTGACTGGCTATCAGGATAGCCCTGGGCAGCTGGAGAATGATCCGAGGAACACCACGAGTGAGATGGCACGCAAC
CTTCGGGAACACCAGGACTTGCTCGGTGTCAAAGTGGCTCTTGACTTTGAGATAACAGCTTACAGGAAAATGCTGGAAGG
CGAAGAGACACGTTTTAGCACCAGTGAGGTAAGCATTTCGGGGCTGAATCCACTTCCCAATCCAAGTTCTCTGCTCCACT
TAGAATCCTCAGTTTTACAGTCTACAAAGTCTCATCCACTGGGCTATTACTTAAGAAAGAG

Alignment

ORF - retro_cjac_394 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.92 %
• Parental protein coverage: 52.3 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GREGAERALKAQQRDVDGATLARLDLEKKVESLLDELAFVRQVHDEEVAELLATLQASSQAAAEVDVAVA
          GREG..RALK.QQRDVD...LA.LD.E.KVESL.D.LA.VRQVH...VA.LLATL.A..QAAAEVDV.V.
Retrocopy GREGTKRALKVQQRDVDSTMLAFLDMEQKVESLWD*LALVRQVHE**VAKLLATLKA**QAAAEVDVTVV

Parental  KPDLSSALREIRAQYESLAAKNLQSAEEWYKSKFANLNEQ-AARSTEAIRASREEIHEYRRQLQARTIEI
          KPDLSSAL.EIRAQYESLAA.NLQS.EEWYKSKFANLNEQ..AR.TEAI.AS.EEIHEYRRQLQARTIEI
Retrocopy KPDLSSALMEIRAQYESLAANNLQSSEEWYKSKFANLNEQ<GARVTEAIPASFEEIHEYRRQLQARTIEI

Parental  EGLRGANESLERQILELEERHNAEVAGYQDSIGQLENDLRNTKSEMARHLREYQDLLNVKMALDIEIAAY
          EGLRGA.ESLER.ILELEERH..EV.GYQDS.GQLEND.RNT.SEMAR.LRE.QDLL.VK.ALD.EI.AY
Retrocopy EGLRGASESLERPILELEERH-SEVTGYQDSPGQLENDPRNTTSEMARNLREHQDLLGVKVALDFEITAY

Parental  RKLLEGEETRFSTSGLSISGLNPLPNPSYLL-PSRILSST-SKVSSTGLSLKKE
          RK.LEGEETRFSTS..SISGLNPLPNPS.LL.P.RILS.T..KVSSTGL.LKKE
Retrocopy RKMLEGEETRFSTSEVSISGLNPLPNPSSLL<PLRILSFTVYKVSSTGLLLKKE

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	0.00 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_394 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_394 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_394 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,