RetrogeneDB ID: retro_hsap_4696

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: X:70077013..70077594(+)
• Located in intron of: ENSG00000120498

Retrocopy information

• Ensembl ID: ENSG00000213747
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CCDC53
• Ensembl ID: ENSG00000120860
• Aliases: CCDC53, CGI-116
• Description: coiled-coil domain containing 53 [Source:HGNC Symbol;Acc:24256]

Sequence

>retro_hsap_4696
ATGGATAAAGATGGGCTTCCTCTCATGGGAGTCAGGCGTAGACTTGATCAAGGTGCCAGCTATTCAGCAGAAAAGAATGG
TGGCTTTTCTAAACCAAAATGTGGTACACACTGTATAGTGCCTCAATCGCTCTTCTACATTTAGTGAGGAGAAACTGGCA
AACCTTTATCTTGGTATCCAGCAAATTGAAACAATTCTCAATACTGTAGATGCAAAGTTGTCATCTATACCAGGCCTAGA
TGATGTCACATTTGAAGTATCTCCTTCAAGTGCCACTAGTGTCACAAATGGATCACATTCTGAAGTCACCTCAGAGTAAT
CACAGCAGGACAGTACATTAAGACTCTGGACCACAGGAAAGTTAAGTATCAGCAGGAAATATCTTAACTGTAGCTAAAGA
TTCAAGATATGTCATATATCTCAAAATGGTTCAAGTGAGTGTACCAGTGATGGCAATAAGAAAAATGATATCAGAAGGAC
TAGACCCAGATCTTCTTGAGAGGTCAGGTGCTCCAGTGCCTGATGGCAAAAGTGAAAATCCTGCAGAACAAAGTTCAGAT
AGCGAATCTTCTTTTAGTGAC

Alignment

ORF - retro_hsap_4696 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.55 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDEDGLPLMG-SGIDLTKVPAIQQKRTVAFLNQFVVHTVQFLNRFSTVCEEKLADLSLRIQQIETTLNIL
          MD.DGLPLMG.SG.DL.KVPAIQQKR.VAFLNQ.VVHTV..LNR.ST..EEKLA.L.L.IQQIET.LN..
Retrocopy MDKDGLPLMG>SGVDLIKVPAIQQKRMVAFLNQNVVHTV*CLNRSSTFSEEKLANLYLGIQQIETILNTV

Parental  DAKLSSIPGLDDVTVEVSPLNVTSVTNGAHPEATSEQPQQNSTQ-DSGLQESEVSAENILTVAKDPRYAR
          DAKLSSIPGLDDVT.EVSP...TSVTNG.H.E.TSE..QQ.ST..DSG.QES.VSA.NILTVAKD.RY..
Retrocopy DAKLSSIPGLDDVTFEVSPSSATSVTNGSHSEVTSE*SQQDSTL>DSGPQES*VSAGNILTVAKDSRYVI

Parental  YLKMVQVGVPVMAIRNKMISEGLDPDLLERPDAPVPDGESEKTVEESSDSESSFSD
          YLKMVQV.VPVMAIR.KMISEGLDPDLLER..APVPDG.SE...E.SSDSESSFSD
Retrocopy YLKMVQVSVPVMAIR-KMISEGLDPDLLERSGAPVPDGKSENPAEQSSDSESSFSD

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
bodymap2_adipose	0.00 RPM	12.32 RPM
bodymap2_adrenal	0.00 RPM	14.70 RPM
bodymap2_brain	0.00 RPM	21.38 RPM
bodymap2_breast	0.00 RPM	18.07 RPM
bodymap2_colon	0.00 RPM	21.66 RPM
bodymap2_heart	0.00 RPM	13.96 RPM
bodymap2_kidney	0.00 RPM	24.16 RPM
bodymap2_liver	0.00 RPM	10.18 RPM
bodymap2_lung	0.00 RPM	10.11 RPM
bodymap2_lymph_node	0.00 RPM	19.72 RPM
bodymap2_ovary	0.00 RPM	19.86 RPM
bodymap2_prostate	0.00 RPM	27.76 RPM
bodymap2_skeletal_muscle	0.00 RPM	8.91 RPM
bodymap2_testis	0.00 RPM	79.56 RPM
bodymap2_thyroid	0.00 RPM	17.25 RPM
bodymap2_white_blood_cells	0.00 RPM	15.69 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_4696 was not detected

EST

No EST(s) were mapped for retro_hsap_4696 retrocopy.

TSS

No TSS is located nearby retro_hsap_4696 retrocopy 5' end.

Lab

retro_hsap_4696 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4696 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_3121
Gorilla gorilla	retro_ggor_2922
Pongo abelii	retro_pabe_3649
Callithrix jacchus	retro_cjac_4073

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006329	1 retrocopy	retro_amel_791,
Canis familiaris	ENSCAFG00000007270	2 retrocopies	retro_cfam_53, retro_cfam_550,
Callithrix jacchus	ENSCJAG00000014225	1 retrocopy	retro_cjac_4073,
Echinops telfairi	ENSETEG00000002254	1 retrocopy	retro_etel_1917,
Felis catus	ENSFCAG00000019358	1 retrocopy	retro_fcat_498,
Homo sapiens	ENSG00000120860	1 retrocopy	retro_hsap_4696 ,
Gorilla gorilla	ENSGGOG00000014975	1 retrocopy	retro_ggor_2922,
Loxodonta africana	ENSLAFG00000007850	1 retrocopy	retro_lafr_761,
Macropus eugenii	ENSMEUG00000004888	3 retrocopies	retro_meug_1441, retro_meug_576, retro_meug_629,
Myotis lucifugus	ENSMLUG00000000401	4 retrocopies	retro_mluc_2014, retro_mluc_2015, retro_mluc_2633, retro_mluc_502,
Monodelphis domestica	ENSMODG00000002579	1 retrocopy	retro_mdom_959,
Mus musculus	ENSMUSG00000020056	1 retrocopy	retro_mmus_1773,
Nomascus leucogenys	ENSNLEG00000006365	1 retrocopy	retro_nleu_2366,
Otolemur garnettii	ENSOGAG00000003322	2 retrocopies	retro_ogar_3267, retro_ogar_738,
Pongo abelii	ENSPPYG00000004878	1 retrocopy	retro_pabe_3649,
Pan troglodytes	ENSPTRG00000005358	1 retrocopy	retro_ptro_3121,
Ictidomys tridecemlineatus	ENSSTOG00000001870	1 retrocopy	retro_itri_970,
Tupaia belangeri	ENSTBEG00000008498	3 retrocopies	retro_tbel_1036, retro_tbel_1165, retro_tbel_2967,
Tarsius syrichta	ENSTSYG00000000587	4 retrocopies	retro_tsyr_1100, retro_tsyr_265, retro_tsyr_443, retro_tsyr_955,
Tursiops truncatus	ENSTTRG00000017221	4 retrocopies	retro_ttru_1569, retro_ttru_1865, retro_ttru_1919, retro_ttru_935,
Vicugna pacos	ENSVPAG00000002010	1 retrocopy	retro_vpac_446,