RetrogeneDB ID: retro_cjac_1713

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 19:42322346..42322729(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CLIC4
• Ensembl ID: ENSCJAG00000020833
• Aliases: None
• Description: chloride intracellular channel 4 [Source:HGNC Symbol;Acc:13518]

Sequence

>retro_cjac_1713
AAATTCTCTGTATATATCAAGAATTCAAGGCCAGAGGCTGATGAAGTACTGGTGAAGGGTCTCTTGAAAACCCTGCAGAA
ACTGAATGAGTATCTGAGTTCTCTCCTCCCTGATAAAATTGATAAAAATAGGATGGAGAGCATTAACTTTTTTACACATA
AATTTCTAGCTGGCAATGAAGTGACATTAGCTGATCGGCTGCCAAAACTGCATATTGTCAATGTGGTGGCGAAAAAAATC
ACAACTTTGATATTCCAAAAAGAATGACTGACACATGGAGCTACCTAACTAATGCATGAAGACAGGGATGAGTTTACCAA
TACCTGTCCCATGATTAGAAGCTTGAAATAGCCCATAGTGATATATCCGAAAAACTCACCAAG

Alignment

ORF - retro_cjac_1713 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.17 %
• Parental protein coverage: 51.38 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KFSAYIKNSRPEANEALERGLLKTLQKLDEYLNSPLPDEIDENSMEDIKFSTRKFLDGNEMTLADCNLLP
          KFS.YIKNSRPEA.E.L..GLLKTLQKL.EYL.S.LPD.ID.N.ME.I.F.T.KFL.GNE.TLAD...LP
Retrocopy KFSVYIKNSRPEADEVLVKGLLKTLQKLNEYLSSLLPDKIDKNRMESINFFTHKFLAGNEVTLAD--RLP

Parental  KLHIVKVVAKKY-RNFDIPKEMTGIWRYLTNA-YSRDEFTNTCP-SDKEVEIAYSDVAKRLTK
          KLHIV.VVAKK...NFDIPK.MT..W.YLTNA...RDEFTNTCP..D...EIA.SD....LTK
Retrocopy KLHIVNVVAKKI<HNFDIPKRMTDTWSYLTNA>EDRDEFTNTCP<HD*KLEIAHSDISEKLTK

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	51.90 RPM
SRP051959_heart	0.00 RPM	315.13 RPM
SRP051959_kidney	0.02 RPM	210.66 RPM
SRP051959_liver	0.04 RPM	77.78 RPM
SRP051959_lung	0.11 RPM	170.73 RPM
SRP051959_lymph_node	1.23 RPM	25.39 RPM
SRP051959_skeletal_muscle	0.00 RPM	53.63 RPM
SRP051959_spleen	0.25 RPM	49.85 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1713 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1713 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1713 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_396
Pongo abelii	retro_pabe_219

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007591	10 retrocopies	retro_chof_1284, retro_chof_1401, retro_chof_1446, retro_chof_1654, retro_chof_2177, retro_chof_2673, retro_chof_784, retro_chof_789, retro_chof_808, retro_chof_947,
Callithrix jacchus	ENSCJAG00000002788	1 retrocopy	retro_cjac_2972,
Callithrix jacchus	ENSCJAG00000020833	2 retrocopies	retro_cjac_1713 , retro_cjac_461,
Cavia porcellus	ENSCPOG00000004010	1 retrocopy	retro_cpor_1490,
Homo sapiens	ENSG00000169504	2 retrocopies	retro_hsap_4143, retro_hsap_4678,
Gorilla gorilla	ENSGGOG00000005586	2 retrocopies	retro_ggor_1579, retro_ggor_2783,
Macropus eugenii	ENSMEUG00000008789	1 retrocopy	retro_meug_780,
Macaca mulatta	ENSMMUG00000002416	2 retrocopies	retro_mmul_1183, retro_mmul_2488,
Mus musculus	ENSMUSG00000037242	2 retrocopies	retro_mmus_2259, retro_mmus_945,
Nomascus leucogenys	ENSNLEG00000008997	3 retrocopies	retro_nleu_1457, retro_nleu_1785, retro_nleu_2168,
Otolemur garnettii	ENSOGAG00000014620	1 retrocopy	retro_ogar_2672,
Pongo abelii	ENSPPYG00000001715	3 retrocopies	retro_pabe_219, retro_pabe_3466, retro_pabe_3632,
Pan troglodytes	ENSPTRG00000000350	3 retrocopies	retro_ptro_2816, retro_ptro_3107, retro_ptro_396,
Pteropus vampyrus	ENSPVAG00000005838	1 retrocopy	retro_pvam_812,
Ictidomys tridecemlineatus	ENSSTOG00000002184	1 retrocopy	retro_itri_52,
Tarsius syrichta	ENSTSYG00000008978	1 retrocopy	retro_tsyr_252,
Vicugna pacos	ENSVPAG00000007699	1 retrocopy	retro_vpac_475,