RetrogeneDB ID: retro_cjac_2672

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:137743546..137743950(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000008211
• Aliases: None
• Description: None

Sequence

>retro_cjac_2672
GATGTCTATGGCAACAATATTCTCTAATATGCTGTGTATACTAAGAGTACTTTCCTGGTAGAAAAACTGCTTTCACGTCA
TGCAAATATTGAAGTGCTAAACAAGAAAACACACAGACAACTTTTGCTTCCTACAGTTTGCAAAAGACAGCAAATGCTGA
AATTTTTAGTGAAGAAACAAGCAAGTATACATCCTCTTGATAGGTTGCAAAGAATAGCCCTCATTCTTGCTGTACATTAT
GGCTTGTAAGGCATAGACAGCATTCTTCAACAAAATACAGGCATTACTGCCTTTACTCAAGATATGTATGGGAAGACTGC
AGAAGACTATGCTATTTCTGGTGTTCTGACAACATTCAGCAACAAATTTTGCAACATAAAAAGAAGATACTTGAAAATAG
TCTT

Alignment

ORF - retro_cjac_2672 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.47 %
• Parental protein coverage: 50.57 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DVFGNTALHYAVYNSVTSLAEKLLSYHANTEAINKEGNTPLLLAVICKRQKMVKFLVKNQANVHAVDNFN
          DV.GN..L.YAVY...T.L.EKLLS.HAN.E..NK.....LLL...CKRQ.M.KFLVK.QA..H..D...
Retrocopy DVYGNNIL*YAVYTKSTFLVEKLLSRHANIEVLNKKTHRQLLLPTVCKRQQMLKFLVKKQASIHPLDRLQ

Parental  RTALMLASYHDFPSIVSLLLKE-NVSIFSQDMFGQTAEDYAVYCGLL-RIQQQILEHKNKIFKHHL
          R.AL.LA.......I.S.L........F.QDM.G.TAEDYA....L...IQQQIL.HK.KI....L
Retrocopy RIALILAVHYGL*GIDSILQQNTGITAFTQDMYGKTAEDYAISGVLT<NIQQQILQHKKKILENSL

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	0.42 RPM	0.16 RPM
SRP051959_heart	0.70 RPM	1.28 RPM
SRP051959_kidney	0.80 RPM	0.38 RPM
SRP051959_liver	0.13 RPM	0.26 RPM
SRP051959_lung	0.94 RPM	0.21 RPM
SRP051959_lymph_node	0.78 RPM	0.07 RPM
SRP051959_skeletal_muscle	0.07 RPM	0.17 RPM
SRP051959_spleen	0.29 RPM	0.82 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2672 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2672 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2672 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008211	2 retrocopies	retro_cjac_2331, retro_cjac_2672 ,
Microcebus murinus	ENSMICG00000017899	2 retrocopies	retro_mmur_1151, retro_mmur_246,
Macaca mulatta	ENSMMUG00000008983	1 retrocopy	retro_mmul_1761,
Nomascus leucogenys	ENSNLEG00000016858	1 retrocopy	retro_nleu_2713,
Pongo abelii	ENSPPYG00000019046	1 retrocopy	retro_pabe_1037,
Tupaia belangeri	ENSTBEG00000017150	1 retrocopy	retro_tbel_490,