RetrogeneDB ID: retro_cjac_1884

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:12065703..12066643(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDC16
• Ensembl ID: ENSCJAG00000019010
• Aliases: None
• Description: None

Sequence

>retro_cjac_1884
CTGGTGGATTTATAGCCTAGTAATCCTGTGTCTTGGTCTGCAGTGGGATGTTGCCACCTCATGGTTGGTCATTAAAATGA
ACGTGCCACAAGATATCTCGGCAAAGCCACACACTTGAGATGATCTACGGACCTGCATGGGTAGCCTGCGGACATTCACT
TGTGGTGGAGAGTGAGCATGACCAAGCGATGGCCGCTTACTTCACAGCAGCACAGCTGATGAAAGGGTGTTGTTTGCCTA
TGTGGTATATTGGATTGGAATATGGTTTGACCAATAACTCAAAATGAGCTGAAAGGTTCTTCAGCCAAGCTCCAAGCATT
GCACCAAAAGACCTTTTTGTTATGCATGAGGTCGGAGTGGTTGCATTTCAGAATGGAGAACGGCAAACAGCTGAAAAATG
GTTTCTTGCTGCTTTGGAAAAAAGTAAAGCAATTGGGAATGAGGTAACAGTTGACAAACGGGAACCTTTGTTGAACAACT
TGGGGCATGTCTGCAGAAAACTTAAAAAGTTCGCCGAGATCTTGGACTACCACCGTCAGGCTCCGGTGGTGATTCCTCAG
AATGCATCCGCCTACTCTGCTATCGGATACATCCACAGTCTGATGGGCAGCTTTGAAAATGCTGTGGACCACTTCCACAC
AGCCCTAGTCTTAGGCGAGTTGATACGTTTTCTGTTACAACGCTTGCTCATTGCATCGAAATGAACATTGGTGATTCTGA
AGCTCATATCAGAGCAGACATTAAAGACAAATTAAAATGTTACGACTTTGATGTGCAGACAATGAAGACACTAAAAAACA
TGATCTCACCTCCCTGGGGTTTCAGGGAAGTGGAAGTAGAAAAACAGACTGCAGAAGAAACAGGGCTTACTCCATTGGAA
ACCTCGAGGAAAACTCCTGATTCCAGACCTCCCTTGGAAGAAACCATTGAAATTGAAATG

Alignment

ORF - retro_cjac_1884 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.13 %
• Parental protein coverage: 50.65 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LVDLYPSNPVSWFAVGCYYLMVGHKNEHARRYLSKAT-TLEKTYGPAWIAYGHSFAVESEHDQAMAAYFT
          LVDL.PSNPVSW.AVGC..LMVGH.NE.A.RYL.KAT.TLE..YGPAW.A.GHS..VESEHDQAMAAYFT
Retrocopy LVDL*PSNPVSWSAVGCCHLMVGH*NERATRYLGKAT<TLEMIYGPAWVACGHSLVVESEHDQAMAAYFT

Parental  AAQLMKGCHLPMLYIGLEYGLTNNSKLAERFFSQALSIAPEDPFVMHEVGVVAFQNGEWKTAEKWFLDAL
          AAQLMKGC.LPM.YIGLEYGLTNNSK.AERFFSQA.SIAP.D.FVMHEVGVVAFQNGE..TAEKWFL.AL
Retrocopy AAQLMKGCCLPMWYIGLEYGLTNNSK*AERFFSQAPSIAPKDLFVMHEVGVVAFQNGERQTAEKWFLAAL

Parental  EKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKYAEALDYHRQALVLIPQNASTYSAIGYIHSLMGNFENAV
          EK.KAIGNEVTVDK.EPLLNNLGHVCRKLKK.AE.LDYHRQA.V.IPQNAS.YSAIGYIHSLMG.FENAV
Retrocopy EKSKAIGNEVTVDKREPLLNNLGHVCRKLKKFAEILDYHRQAPVVIPQNASAYSAIGYIHSLMGSFENAV

Parental  DYFHTAL-GLRRDDTFSVTMLGHCIEMYIGDSEAYIGADIKDKLKCYDFDVHTMKTLKNIISPPWDFREF
          D.FHTAL..LRR.DTFSVT.L.HCIEM.IGDSEA.I.ADIKDKLKCYDFDV.TMKTLKN.ISPPW.FRE.
Retrocopy DHFHTAL<SLRRVDTFSVTTLAHCIEMNIGDSEAHIRADIKDKLKCYDFDVQTMKTLKNMISPPWGFREV

Parental  EVEKQTAEETGLTPLETSRKTPDSRPSLEETFEIEM
          EVEKQTAEETGLTPLETSRKTPDSRP.LEET.EIEM
Retrocopy EVEKQTAEETGLTPLETSRKTPDSRPPLEETIEIEM

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	0.20 RPM	25.76 RPM
SRP051959_heart	0.16 RPM	30.85 RPM
SRP051959_kidney	0.16 RPM	33.94 RPM
SRP051959_liver	0.04 RPM	51.18 RPM
SRP051959_lung	0.13 RPM	39.27 RPM
SRP051959_lymph_node	0.21 RPM	50.25 RPM
SRP051959_skeletal_muscle	0.07 RPM	26.45 RPM
SRP051959_spleen	0.17 RPM	52.92 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1884 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1884 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1884 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019010	1 retrocopy	retro_cjac_1884 ,
Microcebus murinus	ENSMICG00000012596	1 retrocopy	retro_mmur_301,
Myotis lucifugus	ENSMLUG00000015888	1 retrocopy	retro_mluc_772,