RetrogeneDB ID: retro_cjac_4126

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:124587019..124587461(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB28
• Ensembl ID: ENSCJAG00000012136
• Aliases: None
• Description: RAB28, member RAS oncogene family [Source:HGNC Symbol;Acc:9768]

Sequence

>retro_cjac_4126
CAAACTATAGGACTGGATTTCTTTTGAGAAGGGTAACAATGCCAGGACACTTGAATGCTGCTCTCTAGTTTGGGATATAG
GAGGGCAGATAATAGGAAGCAAAATGCTGGACAAATGCATCTATGGAGCACAGAAATCCTCTTGGTATATGATATCACAA
ATTATCAAAGCTTTGAGAATTTTTATAAGATTAGTGGAGAAAGCGAGTGAAGAGTCAGAAACTCAGCCTCTGGTTGCCTT
GGTGGACAATAAAACTGATTTGGAGCATATTCAAACAGTAAAACCTAAAAAACACTTATGGTTTTCCCAGGAAAATGGTT
TTAATAGCTGCTTTGTTTCAACCAAAGCAAGATGCTTTGTCTTCCTGTGTTTTCAGAAAGTTGCTGCTGAAATCCTTGGA
ATCAAATTAAACAAACTAGAAATAAGTTTTAAACAAAGTCAC

Alignment

ORF - retro_cjac_4126 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.61 %
• Parental protein coverage: 73.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QTIGLDFF-LRRITLPGNLNVTL-QIWDIGGQTIGGKMLDKYIYGAQG-ILLVYDITNYQSFENLEDWYT
          QTIGLDFF.LRR.T.PG.LN..L...WDIGGQ.IG.KMLDK.IYGAQ..ILLVYDITNYQSF...E..Y.
Retrocopy QTIGLDFF<LRRVTMPGHLNAAL<LVWDIGGQIIGSKMLDKCIYGAQK<ILLVYDITNYQSF---ENFYK

Parental  V-VKKVSEESETQPLVALVGNKIDLEHMRTIKPEKHLRFCQENGFSSHFVSAKTGDSVFLCFQKVAAEIL
          ..V.K.SEESETQPLVALV.NK.DLEH..T.KP.KHL.F.QENGF.S.FVS.K....VFLCFQKVAAEIL
Retrocopy I>VEKASEESETQPLVALVDNKTDLEHIQTVKPKKHLWFSQENGFNSCFVSTKARCFVFLCFQKVAAEIL

Parental  GIKLNKAEIEQSQGH
          GIKLNK.EI...Q.H
Retrocopy GIKLNKLEISFKQSH

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	0.09 RPM	15.44 RPM
SRP051959_heart	0.33 RPM	13.79 RPM
SRP051959_kidney	0.18 RPM	28.11 RPM
SRP051959_liver	0.04 RPM	17.78 RPM
SRP051959_lung	0.21 RPM	19.02 RPM
SRP051959_lymph_node	0.16 RPM	13.31 RPM
SRP051959_skeletal_muscle	0.17 RPM	11.27 RPM
SRP051959_spleen	0.19 RPM	21.18 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4126 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4126 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4126 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001523	1 retrocopy	retro_chof_1365,
Callithrix jacchus	ENSCJAG00000012136	2 retrocopies	retro_cjac_2713, retro_cjac_4126 ,
Dasypus novemcinctus	ENSDNOG00000007750	4 retrocopies	retro_dnov_1426, retro_dnov_1771, retro_dnov_2419, retro_dnov_381,
Dipodomys ordii	ENSDORG00000012378	1 retrocopy	retro_dord_682,
Homo sapiens	ENSG00000157869	7 retrocopies	retro_hsap_4166, retro_hsap_4259, retro_hsap_4261, retro_hsap_4263, retro_hsap_4265, retro_hsap_4317, retro_hsap_4762,
Gorilla gorilla	ENSGGOG00000024190	1 retrocopy	retro_ggor_2966,
Macropus eugenii	ENSMEUG00000006792	4 retrocopies	retro_meug_1079, retro_meug_1182, retro_meug_1510, retro_meug_913,
Macaca mulatta	ENSMMUG00000022025	1 retrocopy	retro_mmul_1172,
Nomascus leucogenys	ENSNLEG00000016243	1 retrocopy	retro_nleu_2292,
Pongo abelii	ENSPPYG00000014610	1 retrocopy	retro_pabe_3707,
Pan troglodytes	ENSPTRG00000015920	2 retrocopies	retro_ptro_2893, retro_ptro_3171,
Rattus norvegicus	ENSRNOG00000017074	1 retrocopy	retro_rnor_1075,
Sarcophilus harrisii	ENSSHAG00000009274	1 retrocopy	retro_shar_602,
Sus scrofa	ENSSSCG00000022358	2 retrocopies	retro_sscr_482, retro_sscr_514,
Ictidomys tridecemlineatus	ENSSTOG00000004135	1 retrocopy	retro_itri_27,
Tarsius syrichta	ENSTSYG00000010939	2 retrocopies	retro_tsyr_1450, retro_tsyr_1750,