RetrogeneDB ID: retro_cjac_2440

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:54402621..54403511(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RCC1
• Ensembl ID: ENSCJAG00000009686
• Aliases: None
• Description: regulator of chromosome condensation [Source:RefSeq peptide;Acc:NP_001192137]

Sequence

>retro_cjac_2440
AAGAGAAAGTAGCCAGCCCTGGTGCTGGTTTCAGAGGATGCTGTGTAGGCTGAGGGTGGGGACATGCACACCATCATGTG
TCTGAGCAAAATGACCGGGTCTAGTGCTTCAGCTGCCATGATGAGGGTGTTGTGGGAAGGGGCACATCAGTGGAGGGCTC
AGGGATGGTCCCCGGGGAAGTGGAACTGCAAAAGAAGACAATACAGGTATCAGCAGGAGACAGTCACACAGCGGTCCTCA
CCGAAGATGGCTGTGTCTTCCTCCGGGGCTGTTTCCAGAACAATTACAGGGTCATCAGGCTGTTGGAACCCACATAGAAG
AGAGTGATGCTTGTGCAAGTGCAGCTGGACGTGCTCACTGTGAGGGTGGCCCCAGGAAATGGCCACTTGGTGATGCTGAC
AGCTGACAGCGACCTCTGTACCCTGCGCTGTGGGCGCAGGGCCATCTGGGCCCTGTGCCTGAATTATGCGCCAACCATGA
TGGCCAACAGGGCATGATTCCTGGTCCCTTGGATAGGATGCTGAAATTCCGGGGAAGCTGGGACCGTATGAGATTCCAGG
TTGCCTTCTGTGGCCCCGGCTTCACCATTCCATCCCCTGTGAGGGGTACATACACAGTATATGGCTTTGGCCTTTTCAAC
AACCGTCAGCTTGGAACCCCAGGCAGAGATTCTTGCTTCATACCCCAGAACCTGGGATGCTTCTAGAACTCTACCCAGGC
CAGGTGGGAGTCGCTGGTGGCAGCACCATACAGTCTTCACAGATTCAGAAGGGAAAGCACGAAGCCTGGGTCAGGCTGAA
TATAGACAGTGGGCCTTTCATGGGTGCTAAGGAGAAGAACATGCCCACCCTCATCTCCAGGCTGGTGCTGTCTCCTCAGT
GGCTTTGGGC

Alignment

ORF - retro_cjac_2440 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.71 %
• Parental protein coverage: 65.35 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  ERKKPALVSIPEDVVQAEAGGMHTV-CLSK-SGQVYSFGCNDEGALGRDTSVEGSEMVPGKVELQEKVVQ
          .RK.PALV...ED.V.AE.G.MHT..CLSK....V..F.C.DEG..GR.TSVEGS.MVPG.VELQ.K..Q
Retrocopy KRK*PALVLVSEDAV*AEGGDMHTIMCLSK<NDRV*CFSCHDEGVVGRGTSVEGSGMVPGEVELQKKTIQ

Parental  VSAGDSHTAALTEDGRVFLWGSFRDNNGVIGLLEPMKKSMVPVQVQLDVTVVKVASGNDHLVMLTADGDL
          VSAGDSHTA.LTEDG.VFL.G.F..N..VI.LLEP..K....VQVQLDV..V.VA.GN.HLVMLTAD.DL
Retrocopy VSAGDSHTAVLTEDGCVFLRGCFQNNYRVIRLLEPT*KRVMLVQVQLDVLTVRVAPGNGHLVMLTADSDL

Parental  YTLGCGE-QGQLGRVPELFANRGGRQGLERLLVPKCVMLKSRGSRGHVRFQDAFCGAYFTFAISREG--H
          .TL.CG..QG.LG.VPEL.AN..G.QG......P...MLK.RGS....RFQ.AFCG..FT......G...
Retrocopy CTLRCGR<QGHLGPVPELCANHDGQQGM--IPGPLDRMLKFRGSWDRMRFQVAFCGPGFTIPSPVRGTYT

Parental  VYGFGLSNYHQLGTPGTESCFIPQNLTSFKNSTKS-WVRFSGG-QHHTVCMDSEGKAYSLGRAEYGR-LG
          VYGFGL.N..QLGTPG..SCFIPQNL..F.NST....V...GG.QHHTV..DSEGKA.SLG.AEY....G
Retrocopy VYGFGLFNNRQLGTPGRDSCFIPQNLGCF*NSTQA<QVGVAGG<QHHTVFTDSEGKARSLGQAEYRQ<VG

Parental  LGEGAEEKSIP-TLISRL-PAVSSVACG
          L.........P.TLISRL..AVSSVA.G
Retrocopy LSWVLRRRTCP<TLISRL<GAVSSVALG

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	7.97 RPM
SRP051959_heart	0.00 RPM	2.26 RPM
SRP051959_kidney	0.00 RPM	4.64 RPM
SRP051959_liver	0.00 RPM	6.39 RPM
SRP051959_lung	0.00 RPM	5.27 RPM
SRP051959_lymph_node	0.02 RPM	9.00 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.25 RPM
SRP051959_spleen	0.00 RPM	5.92 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2440 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2440 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2440 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009686	3 retrocopies	retro_cjac_2440 , retro_cjac_3424, retro_cjac_3856,
Erinaceus europaeus	ENSEEUG00000004565	1 retrocopy	retro_eeur_418,
Myotis lucifugus	ENSMLUG00000017075	1 retrocopy	retro_mluc_2278,
Rattus norvegicus	ENSRNOG00000050106	1 retrocopy	retro_rnor_2886,