RetrogeneDB ID: retro_cjac_1688

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 18:38717117..38717787(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AKR1D1
• Ensembl ID: ENSCJAG00000012872
• Aliases: None
• Description: None

Sequence

>retro_cjac_1688
GAAGTAACAGAAGGAAAAATGCAGAGGAAGGATATCTTCTTCCATGGAAAGCTGTGGGCTACAAATATGACCCAGAGCTG
GTCTGCCCAAGCCTAGGGAGAATGCTGAAGGTCCTCCAGCTAGATTGCATGGATCTTTACATCATTGAAATACCCAATAC
TCCCTTAAGCCAGGAGATGAAATCTATCCTATAGTGAGAATGGCAAATGTTTACATCACAAGTCAAATCTGTGTGCCACT
TGGGAGACTTTGCACACTTTGGAAGCGTGCAAAGACGCTGGCTTCGTGAAATCCCTCCAAGTATCCAGTTTTAACAGCAG
GCCAGCTGGAGCTCATCTTGAGCAATCCAGGACTCAAACCCAGGCCAGTCAGCAACCAGGGTGAGTGCCACCCATATTTC
ACCCAGCCAAAACTCTTGAAATTTTGCCAACAACATGACATTGTCATGATTGCCTATAGCCCTTTGGGGACCGCTAGGAA
TCCAACCTGGGTGAATATGTCTTCTCTACCTTCGTTAAAGGATGCACTTCTAAAAAGGTGCAATAAGACAATAGCTGAAG
TTGTTTTGCATTTCAACATCCAGCAAGGGATAGTTGCCATTCCTAAAAGCTTCAATCCTGAAGGGATCAAGGAAAACCTT
CAGGTGTTTGACTTTTCTGCACTAAATGAA

Alignment

ORF - retro_cjac_1688 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.24 %
• Parental protein coverage: 68.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  KIAEGKVQREDIFYCGKLWATN-HVPEMVRPTLERTLRVLQLDYVDLYI-IELPM-AFKPGDEVYP-RDE
          ...EGK.QR.DIF..GKLWATN...PE.V.P.L.R.L.VLQLD..DLYI....P....KPGDE.YP...E
Retrocopy EVTEGKMQRKDIFFHGKLWATN<YDPELVCPSLGRMLKVLQLDCMDLYI>LKYPI>SLKPGDEIYP<YSE

Parental  NGKWLYHKSNLCATWEAM---EACKDAGLVKSLGVSNFNRR-QLELILNKPGLKHKPVSNQVECHPYFTQ
          NGK.L.HKSNLCATWE.....EACKDAG.VKSL.VS.FN.R.QLELIL..PGLK..PVSNQ.ECHPYFTQ
Retrocopy NGKCLHHKSNLCATWETLHTLEACKDAGFVKSLQVSSFNSR>QLELILSNPGLKPRPVSNQGECHPYFTQ

Parental  PKLLKFCQQHDIVIIAYSPLGTSRNPFWVDVSIPPLLKDTLLNSLGKKYNKTAAQIVLRFNIQRGVVVIP
          PKLLKFCQQHDIV.IAYSPLGT.RNP.WV..S..P.LKD.LL....K..NKT.A..VL.FNIQ.G.V.IP
Retrocopy PKLLKFCQQHDIVMIAYSPLGTARNPTWVNMSSLPSLKDALL----KRCNKTIAEVVLHFNIQQGIVAIP

Parental  KSFNPKRIKENFQIFDFSLTEE
          KSFNP..IKEN.Q.FDFS...E
Retrocopy KSFNPEGIKENLQVFDFSALNE

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	0.02 RPM
SRP051959_heart	0.09 RPM	0.04 RPM
SRP051959_kidney	0.00 RPM	0.18 RPM
SRP051959_liver	0.04 RPM	84.54 RPM
SRP051959_lung	0.00 RPM	0.05 RPM
SRP051959_lymph_node	0.02 RPM	0.00 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.00 RPM
SRP051959_spleen	0.04 RPM	0.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1688 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1688 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1688 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012231	14 retrocopies	retro_cjac_1140, retro_cjac_1167, retro_cjac_1718, retro_cjac_1973, retro_cjac_2550, retro_cjac_3102, retro_cjac_3143, retro_cjac_3297, retro_cjac_3692, retro_cjac_3840, retro_cjac_3872, retro_cjac_3910, retro_cjac_476, retro_cjac_621,
Callithrix jacchus	ENSCJAG00000012250	1 retrocopy	retro_cjac_3038,
Callithrix jacchus	ENSCJAG00000012872	1 retrocopy	retro_cjac_1688 ,
Callithrix jacchus	ENSCJAG00000013633	2 retrocopies	retro_cjac_3093, retro_cjac_3334,
Homo sapiens	ENSG00000122787	1 retrocopy	retro_hsap_257,
Gorilla gorilla	ENSGGOG00000014684	1 retrocopy	retro_ggor_307,
Nomascus leucogenys	ENSNLEG00000013710	1 retrocopy	retro_nleu_860,
Pongo abelii	ENSPPYG00000018037	1 retrocopy	retro_pabe_406,
Pan troglodytes	ENSPTRG00000019740	1 retrocopy	retro_ptro_217,
Rattus norvegicus	ENSRNOG00000013004	1 retrocopy	retro_rnor_2559,