RetrogeneDB ID: retro_cjac_987

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:71794934..71795741(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RMDN3
• Ensembl ID: ENSCJAG00000020807
• Aliases: None
• Description: regulator of microtubule dynamics 3 [Source:HGNC Symbol;Acc:25550]

Sequence

>retro_cjac_987
GTGATGCTGCTGTGGGCTGTCCCTGGTGGGGCTGGAGATGCCGCAGTGCTGCCCAGCCTTCCACGGGAAGGTCAGGAGAA
GGTGCTGGACCGCCGGGACTTTGTGCTGACCAGCCTTGTGGCGCTGCGACAGGAGGTGGAGGAGTTAAGGAGCAGCCTGC
TAGGGCTTGCAGGGGAGATAGTTGGGGAGTTCCAATCCCACATGGAAGAGAACCAGAGAGTGGCTAGGCGGGGAAGGTCT
CCTTTTGTCCGGGAGAGGGGTGACTCCACTGGCTCCAGCTCTGTCTATTTCACGGCTTCCTCCGGAGCTACCTTTACAGA
TGCCGAGAGCGAAGGGGATTATATAACAGCCAATGCAGAGTCTCACAATGAATGGGACTCTGACAAAGAGAGTGAGGATG
GGGAAGATGAAGCAAGTTGTGAGACTGTGAAGATGGGGAGAAAGGATTCTCTGGATCTGGAGGTGGAGGAAGCTTCAGGT
ATGGTGCCCAGTGCCCTGGAGACTGGAACTTCCTCAGGCTTGGAGGACATGCTGCCCCTCCTGCAGCAGGCAGATGAGAT
GCACCAGGGTGATGAGCAGGGCAAGCGGGAGGGCTTCCAGCTGCTGCTCAACAACAAGCTGGCGTATGGAAGCTGGCAGG
ACTTTCTCTGGCGCCTGGCCCGGGCCTACAGTGACATGTGTGAGCTCACTGAGGAGGTGAGCAAGAAGAAGTCATAGGCC
TTAGCTGGAAAAGAAGAAGCAGAGGCTGCTCTAGAGAAGGGGGAGGAGAGTACTGACTGTCACCTGTGGTATGCAGTGCT
TTGTGGT

Alignment

ORF - retro_cjac_987 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.19 %
• Parental protein coverage: 57.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VMLLRAVPGGAGDAAVLPSLPREGQEKVLDRLDFVLTSLVALRQEVEELRSSLRGLAGEIVGEVRSHMEE
          VMLL.AVPGGAGDAAVLPSLPREGQEKVLDR.DFVLTSLVALRQEVEELRSSL.GLAGEIVGE..SHMEE
Retrocopy VMLLWAVPGGAGDAAVLPSLPREGQEKVLDRRDFVLTSLVALRQEVEELRSSLLGLAGEIVGEFQSHMEE

Parental  NQRVARRRRFPFVRERSDSTGSSSVYFTASSGATFTDAESEGGLQTANAESDNERDSDKESEDGEDEASC
          NQRVARR.R.PFVRER.DSTGSSSVYFTASSGATFTDAESEG...TANAES.NE.DSDKESEDGEDEASC
Retrocopy NQRVARRGRSPFVRERGDSTGSSSVYFTASSGATFTDAESEGDYITANAESHNEWDSDKESEDGEDEASC

Parental  ETVKMGRKDSLDLEVEAASGLVPSALETGASSGLEDMLPLLQQADEMHQGDEQGKREGFQLLLNNKLAYG
          ETVKMGRKDSLDLEVE.ASG.VPSALETG.SSGLEDMLPLLQQADEMHQGDEQGKREGFQLLLNNKLAYG
Retrocopy ETVKMGRKDSLDLEVEEASGMVPSALETGTSSGLEDMLPLLQQADEMHQGDEQGKREGFQLLLNNKLAYG

Parental  SQQDFLWRLARAYSDMCELTEEVSEKKSYALAGKEEAEAALEKGEESADCHMWYAVLCG
          S.QDFLWRLARAYSDMCELTEEVS.KKS.ALAGKEEAEAALEKGEES.DCH.WYAVLCG
Retrocopy SWQDFLWRLARAYSDMCELTEEVSKKKS*ALAGKEEAEAALEKGEESTDCHLWYAVLCG

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	0.04 RPM	27.25 RPM
SRP051959_heart	0.02 RPM	17.86 RPM
SRP051959_kidney	0.07 RPM	47.43 RPM
SRP051959_liver	0.06 RPM	25.80 RPM
SRP051959_lung	0.05 RPM	26.78 RPM
SRP051959_lymph_node	0.00 RPM	13.08 RPM
SRP051959_skeletal_muscle	0.02 RPM	22.10 RPM
SRP051959_spleen	0.06 RPM	15.53 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_987 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_987 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_987 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	ENSCJAG00000020807	1 retrocopy	retro_cjac_987 ,
Oryctolagus cuniculus	ENSOCUG00000016912	1 retrocopy	retro_ocun_1250,