RetrogeneDB ID: retro_cjac_3469

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01180985.1:11028..11763(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RANBP10
• Ensembl ID: ENSCJAG00000016055
• Aliases: None
• Description: None

Sequence

>retro_cjac_3469
GAGAAGGAGCTGCAGCCGCGGCTGAAGCGCCTCGACCCGGCTGTGAACGAGCAGGAGACGCCGCTGCCCCGCTCCTGGAG
CAGGAAGGACAAGGTCGGCTACATCGGCCTCTCTCAGAACAACCTGCGGGTGCACTACAAAGGTCATGGCAAAACCCCAA
AAGATGCAGCATCAGTTCGAGCCACGCATCCAATACCAGCAGCCTGTGGGATTTATTATTTTGAAGTAAAAATTGTCAGT
AAGGGAAGAGATGGTTACATGGGAATTGGTCTTTCTGCTCAAGGTGTGAACATGAATAGACTACCAGGTTGGGATAAGCA
TTCATATGGTTACCATGGGGATGGTGGACATTCGTTTTGTTCTTCTGGAACTGGACAACCTGATGGACCAGCTTTCACAA
CTGGTGATGTCATTGGCTGTTGTGTTAATCTTATCAACAATACCCGCTTTTACATCAAGAATGGACATAGTTTAGGTATT
GCTTTCACTGACCTACCGCCAAATTTGTATCCTACCATGGGGCTTCGGACACCAGGAGAAGTGGTTGATGCCAATTTTGG
TCAACATCCTTTCGTGTTTGATATAGAAGACTATATGCGAGAGTGGTGAACCAAAATCCAGGCACAGATAGACCGGTTTC
CTATCGGAGACCGAGAAGGAGAATGGCAGACCATGATACAAAAAATGGTTTCATCTTATTTAGTCCACCATGGGTACTGT
GCCACAGCAGAGGCC

Alignment

ORF - retro_cjac_3469 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.27 %
• Parental protein coverage: 78.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EQELSRRLQHLYPAVNQQETPLPRSWSPKDKYNYIGLSQGNLRVHYKGHGKNHKDAASVRATHPIPAACG
          E.EL..RL..L.PAVN.QETPLPRSWS.KDK..YIGLSQ.NLRVHYKGHGK..KDAASVRATHPIPAACG
Retrocopy EKELQPRLKRLDPAVNEQETPLPRSWSRKDKVGYIGLSQNNLRVHYKGHGKTPKDAASVRATHPIPAACG

Parental  IYYFEVKIVSKGRDGYMGIGLSAQGVNMNRLPGWDKHSYGYHGDDGHSFCSSGTGQPYGPTFTTGDVIGC
          IYYFEVKIVSKGRDGYMGIGLSAQGVNMNRLPGWDKHSYGYHGD.GHSFCSSGTGQP.GP.FTTGDVIGC
Retrocopy IYYFEVKIVSKGRDGYMGIGLSAQGVNMNRLPGWDKHSYGYHGDGGHSFCSSGTGQPDGPAFTTGDVIGC

Parental  CVNLINGTCFYTKNGHSLGIAFTDLPANLYPTVGLQTPGEIVDANFGQQPFLFDIEDYMREWRAKVQGTV
          CVNLIN.T.FY.KNGHSLGIAFTDLP.NLYPT.GL.TPGE.VDANFGQ.PF.FDIEDYMREW..K.Q...
Retrocopy CVNLINNTRFYIKNGHSLGIAFTDLPPNLYPTMGLRTPGEVVDANFGQHPFVFDIEDYMREW*TKIQAQI

Parental  HCFPISARLGEWQAVLQNMVSSYLVHHGYCATATA
          ..FPI..R.GEWQ...Q.MVSSYLVHHGYCATA.A
Retrocopy DRFPIGDREGEWQTMIQKMVSSYLVHHGYCATAEA

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	6.72 RPM
SRP051959_heart	0.86 RPM	11.40 RPM
SRP051959_kidney	0.40 RPM	8.54 RPM
SRP051959_liver	0.45 RPM	12.04 RPM
SRP051959_lung	0.76 RPM	9.96 RPM
SRP051959_lymph_node	0.78 RPM	6.99 RPM
SRP051959_skeletal_muscle	1.44 RPM	15.68 RPM
SRP051959_spleen	0.53 RPM	11.26 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3469 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3469 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3469 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016055	1 retrocopy	retro_cjac_3469 ,
Callithrix jacchus	ENSCJAG00000019797	1 retrocopy	retro_cjac_3848,