RetrogeneDB ID: retro_cjac_1611

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 17:66737567..66738257(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RFC3
• Ensembl ID: ENSCJAG00000018380
• Aliases: None
• Description: None

Sequence

>retro_cjac_1611
ATGAGCCTCTGGATAGACACGTACCAGCCCTAGTCCTGGGGTGGATGGAGTATCACAGGGAGAAGGTGGCCCAGCTGCAC
AACCTGGTACAGGGTGGTGACTTTCCTCACTTTTAAGTGCAAGGACCATCAGGTGCTGGAAAAAAGACAAGTGCTATGTG
TGTTCTACATGAACTTTATGGTGTTGGAGTGGAAAAATTGAGAATTGAACATCAGACCATCAAAACTCCATCTAAAAAAA
TTGAAATTAGCATTACTGCATGTAATTACCACCTTGAAGTTAATCCCAGTGATGCGGGAAATATTGACGAGGTAGTAATT
CAGAAGATGTTGAAAACAGTGGCTCAATCACAGGAACTTGAAACAAACTCTCAGATATTTAAAAATGGTATTATTGATAG
AAGTTGACAAATTCACCAAAGATGCTCATCATTTCTTGCAAAGAACCATGGAAAAGTGTATGTCCACCTGCACATTGATC
TTGTGCTGTAATTACACATCTGATATGATACCACCTATTTGTAGCAGGTGCTGGGCAATTTGCGTGCTTGTTCCCAGCAT
TGGGGATATTTACCTTGTGTTATGTACTGTGTGCAAGAAGGAAGGTCTGAATCTTCCTTCACAACTGACCCATAGACTTG
CAGAGAAGTCCTGCAGAAATCTCGGAAAAGCCCAGCTAATGTGTGAAGCA

Alignment

ORF - retro_cjac_1611 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.64 %
• Parental protein coverage: 65.17 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSLWVDKYRPCS-LGRLDYHKEQAAQLRNLVQCGDFPHLLVYGPSGAGKKTRIMCILRELYGVGVEKLRI
          MSLW.D.Y.P.S.LG...YH.E..AQL.NLVQ.GDFPH..V.GPSGAGKKT..MC.L.ELYGVGVEKLRI
Retrocopy MSLWIDTYQP*S<LGWMEYHREKVAQLHNLVQGGDFPHF*VQGPSGAGKKTSAMCVLHELYGVGVEKLRI

Parental  EHQTITTPSKKKIEISTIASNYHLEVNPSDAGNSDRVVIQEMLKTVAQSQQLETNSQRDFK-VVLLTEVD
          EHQTI.TPS.KKIEIS..A.NYHLEVNPSDAGN.D.VVIQ.MLKTVAQSQ.LETNSQ..FK..VLL.EVD
Retrocopy EHQTIKTPS-KKIEISITACNYHLEVNPSDAGNIDEVVIQKMLKTVAQSQELETNSQ-IFK>MVLLIEVD

Parental  KLTKDAQHALRRTMEKYMSTCRLILCCNSTSKVIPPIRSRCLAVRVPAPSIEDICHVLSTVCKKEGLNLP
          K.TKDA.H.L.RTMEK.MSTC.LILCCN.TS..IPPI.SRC.A..V..PSI.DI..VL.TVCKKEGLNLP
Retrocopy KFTKDAHHFLQRTMEKCMSTCTLILCCNYTSDMIPPICSRCWAICVLVPSIGDIYLVLCTVCKKEGLNLP

Parental  PQLAHRLAEKSCRNLRKALLMCEA
          .QL.HRLAEKSCRNL.KA.LMCEA
Retrocopy SQLTHRLAEKSCRNLGKAQLMCEA

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	6.39 RPM
SRP051959_heart	0.00 RPM	5.54 RPM
SRP051959_kidney	0.02 RPM	3.64 RPM
SRP051959_liver	0.00 RPM	1.52 RPM
SRP051959_lung	0.00 RPM	5.84 RPM
SRP051959_lymph_node	0.00 RPM	6.60 RPM
SRP051959_skeletal_muscle	0.00 RPM	3.91 RPM
SRP051959_spleen	0.00 RPM	6.26 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1611 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1611 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1611 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018380	1 retrocopy	retro_cjac_1611 ,
Cavia porcellus	ENSCPOG00000008739	1 retrocopy	retro_cpor_405,
Myotis lucifugus	ENSMLUG00000014088	1 retrocopy	retro_mluc_1754,
Mustela putorius furo	ENSMPUG00000001885	1 retrocopy	retro_mputfur_1073,
Nomascus leucogenys	ENSNLEG00000001169	1 retrocopy	retro_nleu_674,
Pongo abelii	ENSPPYG00000005272	1 retrocopy	retro_pabe_2420,
Tupaia belangeri	ENSTBEG00000004725	1 retrocopy	retro_tbel_4191,
Tarsius syrichta	ENSTSYG00000009501	2 retrocopies	retro_tsyr_1772, retro_tsyr_331,