RetrogeneDB ID: retro_cjac_1505

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 16:32639766..32640226(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OCIAD2
• Ensembl ID: ENSCJAG00000018637
• Aliases: None
• Description: OCIA domain containing 2 [Source:HGNC Symbol;Acc:28685]

Sequence

>retro_cjac_1505
ATGGCCTCAATGTCTATTCATGGAAACCAAGAAAAATGTCCCATTTACCACCACCAAGCAAGCAGAGCCTGCTGCTTTAT
CCAAAATCAAAACTGCACATCCACAGAGGAGAGATTTTAAACATTATAAGAGGATGTCAAGAAGAAAGTTTCTGCAAGAG
TGCTCTGCCTTTTCTCCTGTATGCACGCTTGTCACCCAGAGACTAGTCTGCCAAGGTTATTTAGCAGCTAATCCAAGATT
TGGATCACTGCCTAAAATTACACTTGTTAGTATCTTGGGATTTGGCCTTGGAAAGGTATCCTACATAAGAGTATGCCAGA
GTAAATTCCATTTCTTTGAAGATCAGCTCCTTGGGGCTGCTTTTGGTCCACAGCAGAACAAGCATTGATTGCTTACCTGT
GAAGAATGCAAAATAAAACATGGATTTGGTGAGAAGGGATGTTCACAGCCTTTGGCTTCC

Alignment

ORF - retro_cjac_1505 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.64 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASASTRGNQDKDP-HLPPPSKQSLLFCPKSKLHIHRAEISKIMRECQEESFWKRALPFSL-VSMLVTQG
          MAS.S..GNQ.K.P.HLPPPSKQSLL..PKSKLHIHR.EI..I.R.CQEESF.K.ALPF.L.V..LVTQ.
Retrocopy MASMSIHGNQEKCP<HLPPPSKQSLLLYPKSKLHIHRGEILNIIRGCQEESFCKSALPFLL<VCTLVTQR

Parental  LVYQGYLAANPRFGSLPKVAVAGLLGFGLGKVSYIGACQSKFHFFEDQLRGAGFGPQHNRHCLLTCEECK
          LV.QGYLAANPRFGSLPK......LGFGLGKVSYI..CQSKFHFFEDQL.GA.FGPQ.N.H.LLTCEECK
Retrocopy LVCQGYLAANPRFGSLPKITLVSILGFGLGKVSYIRVCQSKFHFFEDQLLGAAFGPQQNKH*LLTCEECK

Parental  IKHGLSEKGDSQPSAS
          IKHG..EKG.SQP.AS
Retrocopy IKHGFGEKGCSQPLAS

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	13.33 RPM
SRP051959_heart	0.00 RPM	16.10 RPM
SRP051959_kidney	0.02 RPM	26.18 RPM
SRP051959_liver	0.00 RPM	15.03 RPM
SRP051959_lung	0.00 RPM	1.95 RPM
SRP051959_lymph_node	0.00 RPM	1.07 RPM
SRP051959_skeletal_muscle	0.00 RPM	11.31 RPM
SRP051959_spleen	0.02 RPM	0.80 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1505 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1505 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1505 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2768
Pongo abelii	retro_pabe_3350

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018637	1 retrocopy	retro_cjac_1505 ,
Erinaceus europaeus	ENSEEUG00000006759	1 retrocopy	retro_eeur_504,
Homo sapiens	ENSG00000145247	1 retrocopy	retro_hsap_4082,
Gorilla gorilla	ENSGGOG00000013778	1 retrocopy	retro_ggor_2738,
Microcebus murinus	ENSMICG00000006147	1 retrocopy	retro_mmur_1402,
Macaca mulatta	ENSMMUG00000014869	1 retrocopy	retro_mmul_2353,
Monodelphis domestica	ENSMODG00000025531	1 retrocopy	retro_mdom_1006,
Nomascus leucogenys	ENSNLEG00000017430	1 retrocopy	retro_nleu_2048,
Oryctolagus cuniculus	ENSOCUG00000007907	2 retrocopies	retro_ocun_1734, retro_ocun_1780,
Otolemur garnettii	ENSOGAG00000011039	1 retrocopy	retro_ogar_561,
Pongo abelii	ENSPPYG00000014722	1 retrocopy	retro_pabe_3350,
Pan troglodytes	ENSPTRG00000016048	1 retrocopy	retro_ptro_2768,
Vicugna pacos	ENSVPAG00000011765	1 retrocopy	retro_vpac_331,