RetrogeneDB ID: retro_cjac_1012

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:16694335..16694912(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GMNN
• Ensembl ID: ENSCJAG00000006161
• Aliases: GMNN, geminin
• Description: geminin, DNA replication inhibitor [Source:HGNC Symbol;Acc:17493]

Sequence

>retro_cjac_1012
ATGAACCCTGGTATAAAGTACAATCAAGAAAGAATCAAAGAGAATGTAAACAACAGTCCTTTCCCAAGAAGAGCTCTGAT
GATTCATTCTTCCACAGCCAGATCTCTTGTTGGAAGGAAAAAAGATTGGCCAAAGGCATACCCAAGAGGAAGCATCAGAA
TGACCAGTTGACAGCTAGGACTTCCCACTCTAGAGCTGTCATTGTCCCAGAATATAGAGACAGTTAAAATCTTGAAGGAG
TCACCCAAGAAGCATTTGATTTTAGGATTAAAGGAAATTCATCCCTTCAATATTGGAGAGTAGCAGCAGAAGAACAAAGG
AAGACCCTCTGTGAAACACTTAAGGAAAATGAGAAGCTTCACAGAGAAATTGAACAAAGAACAATGAAGCTGCCTGCCTG
GAACAGGAGACTAATGAATTGGCAGAAGCAGGGGAACATGTACAGTCTATGACAGAGGCAACCCAAAGATTGAATGATGA
ACCTCTGGATAACTCTGAAGCACCAGATAGTCAGGAATTTGATTCTGAAGAGGAAACTGGTGGGGATTCTTAAGTGGAAT
ACCCAAAAATTGCCACA

Alignment

ORF - retro_cjac_1012 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.71 %
• Parental protein coverage: 92.34 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MNPNMKQKQEEIKENIKNCSVPRRTLKMIQPSASGSLVGR-ENELSTGLSKRKHRNDQVTSATS-SPGVI
          MNP..K..QE.IKEN..N...PRR.L.MI..S...SLVGR.E..L..G..KRKH.NDQ.T..TS.S..VI
Retrocopy MNPGIKYNQERIKENVNNSPFPRRAL-MIHSSTARSLVGR<EKRLAKGIPKRKHQNDQLTARTSHSRAVI

Parental  VPESSENKNLGGVTQEAYDLMIKENPSSQYWKEAAEKRRKALYEALKENEKLHKEIEQ-KDKEIARLKKE
          VPE.....NL.GVTQEA.D..IK.N.S.QYW..AAE..RK.L.E.LKENEKLH.EIEQ.K..E.A.L..E
Retrocopy VPEYRDS*NLEGVTQEAFDFRIKGNSSLQYWRVAAEEQRKTLCETLKENEKLHREIEQ<KNNEAACLEQE

Parental  NKELAEVAEHVQYMAELIERLNGEPLDNLESLDSQEFDSEEETGEDSEVEESEIGT
          ..ELAE..EHVQ.M.E...RLN.EPLDN.E..DSQEFDSEEETG.DS.VE...I.T
Retrocopy TNELAEAGEHVQSMTEATQRLNDEPLDNSEAPDSQEFDSEEETGGDS*VEYPKIAT

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	0.02 RPM	4.35 RPM
SRP051959_heart	0.00 RPM	3.49 RPM
SRP051959_kidney	0.00 RPM	2.93 RPM
SRP051959_liver	0.02 RPM	3.47 RPM
SRP051959_lung	0.00 RPM	3.74 RPM
SRP051959_lymph_node	0.05 RPM	5.48 RPM
SRP051959_skeletal_muscle	0.00 RPM	1.53 RPM
SRP051959_spleen	0.06 RPM	4.75 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1012 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1012 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1012 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006161	1 retrocopy	retro_cjac_1012 ,
Microcebus murinus	ENSMICG00000014010	1 retrocopy	retro_mmur_594,
Myotis lucifugus	ENSMLUG00000014849	2 retrocopies	retro_mluc_1589, retro_mluc_743,
Monodelphis domestica	ENSMODG00000011682	1 retrocopy	retro_mdom_1800,
Mus musculus	ENSMUSG00000006715	2 retrocopies	retro_mmus_1525, retro_mmus_2213,
Oryctolagus cuniculus	ENSOCUG00000000728	1 retrocopy	retro_ocun_613,
Otolemur garnettii	ENSOGAG00000004982	1 retrocopy	retro_ogar_1726,
Ochotona princeps	ENSOPRG00000007969	1 retrocopy	retro_opri_439,
Rattus norvegicus	ENSRNOG00000018782	1 retrocopy	retro_rnor_820,
Sarcophilus harrisii	ENSSHAG00000004058	2 retrocopies	retro_shar_581, retro_shar_769,
Tupaia belangeri	ENSTBEG00000010502	2 retrocopies	retro_tbel_1028, retro_tbel_353,