RetrogeneDB ID: retro_hsap_2481

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 20:42151889..42152060(-)
• Located in intron of: ENSG00000185513

Retrocopy information

• Ensembl ID: ENSG00000234271
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TMEM14C
• Ensembl ID: ENSG00000111843
• Aliases: TMEM14C, C6orf53, MSTP073, NET26, bA421M1.6
• Description: transmembrane protein 14C [Source:HGNC Symbol;Acc:20952]

Sequence

>retro_hsap_2481
TCTCAGGATCCAAGGGATGCTTGGGTTTTCCTTGCTACGTCTGAGACCTTGGCTGGCATTATGGGAATGAGATTCTACCA
CTCTGGAAAATTTATGTCTCCAGGTTTAATTGCAGGTACCAGTTTGCTGATGGTCGCCAAGCTTGGAATCAGTACGTTGA
ACAAACCCCAT

Alignment

ORF - retro_hsap_2481 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.7 %
• Parental protein coverage: 50.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SQDPRNVWVFLATSGTLAGIMGMRFYHSGKFMPAGLIAGASLLMVAKVGVSMFNRPH
          SQDPR..WVFLATS.TLAGIMGMRFYHSGKFM..GLIAG.SLLMVAK.G.S..N.PH
Retrocopy SQDPRDAWVFLATSETLAGIMGMRFYHSGKFMSPGLIAGTSLLMVAKLGISTLNKPH

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	43.49 RPM
bodymap2_adrenal	0.08 RPM	49.47 RPM
bodymap2_brain	0.23 RPM	46.34 RPM
bodymap2_breast	0.06 RPM	75.41 RPM
bodymap2_colon	0.02 RPM	62.67 RPM
bodymap2_heart	0.02 RPM	54.15 RPM
bodymap2_kidney	0.00 RPM	67.38 RPM
bodymap2_liver	0.02 RPM	44.11 RPM
bodymap2_lung	0.04 RPM	62.08 RPM
bodymap2_lymph_node	0.00 RPM	57.58 RPM
bodymap2_ovary	0.02 RPM	62.32 RPM
bodymap2_prostate	0.00 RPM	102.64 RPM
bodymap2_skeletal_muscle	0.00 RPM	28.99 RPM
bodymap2_testis	0.02 RPM	66.12 RPM
bodymap2_thyroid	0.08 RPM	66.98 RPM
bodymap2_white_blood_cells	0.00 RPM	36.05 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2481 was not detected

EST

No EST(s) were mapped for retro_hsap_2481 retrocopy.

TSS

No TSS is located nearby retro_hsap_2481 retrocopy 5' end.

Lab

retro_hsap_2481 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2481 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1435

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 55 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002614	3 retrocopies	retro_amel_1256, retro_amel_939, retro_amel_957,
Bos taurus	ENSBTAG00000005808	1 retrocopy	retro_btau_970,
Canis familiaris	ENSCAFG00000009692	2 retrocopies	retro_cfam_115, retro_cfam_1716,
Dasypus novemcinctus	ENSDNOG00000007732	6 retrocopies	retro_dnov_1220, retro_dnov_1547, retro_dnov_1968, retro_dnov_289, retro_dnov_316, retro_dnov_367,
Equus caballus	ENSECAG00000026994	1 retrocopy	retro_ecab_659,
Erinaceus europaeus	ENSEEUG00000009000	1 retrocopy	retro_eeur_26,
Felis catus	ENSFCAG00000014178	5 retrocopies	retro_fcat_301, retro_fcat_314, retro_fcat_367, retro_fcat_93, retro_fcat_983,
Homo sapiens	ENSG00000111843	2 retrocopies	retro_hsap_1793, retro_hsap_2481 ,
Homo sapiens	ENSG00000137210	1 retrocopy	retro_hsap_684,
Loxodonta africana	ENSLAFG00000009795	2 retrocopies	retro_lafr_1233, retro_lafr_1246,
Macropus eugenii	ENSMEUG00000000210	1 retrocopy	retro_meug_1704,
Macaca mulatta	ENSMMUG00000018788	2 retrocopies	retro_mmul_1244, retro_mmul_1597,
Mustela putorius furo	ENSMPUG00000000613	2 retrocopies	retro_mputfur_1322, retro_mputfur_226,
Mus musculus	ENSMUSG00000021361	2 retrocopies	retro_mmus_1634, retro_mmus_2355,
Nomascus leucogenys	ENSNLEG00000000564	3 retrocopies	retro_nleu_269, retro_nleu_2933, retro_nleu_607,
Oryctolagus cuniculus	ENSOCUG00000016368	3 retrocopies	retro_ocun_1129, retro_ocun_1348, retro_ocun_284,
Otolemur garnettii	ENSOGAG00000012165	3 retrocopies	retro_ogar_1155, retro_ogar_2425, retro_ogar_3462,
Ochotona princeps	ENSOPRG00000014366	4 retrocopies	retro_opri_192, retro_opri_29, retro_opri_409, retro_opri_898,
Pan troglodytes	ENSPTRG00000017720	2 retrocopies	retro_ptro_1199, retro_ptro_1435,
Rattus norvegicus	ENSRNOG00000015437	2 retrocopies	retro_rnor_1595, retro_rnor_33,
Sarcophilus harrisii	ENSSHAG00000011456	1 retrocopy	retro_shar_177,
Sus scrofa	ENSSSCG00000001038	3 retrocopies	retro_sscr_438, retro_sscr_449, retro_sscr_614,
Ictidomys tridecemlineatus	ENSSTOG00000022833	1 retrocopy	retro_itri_47,
Tursiops truncatus	ENSTTRG00000003666	2 retrocopies	retro_ttru_1504, retro_ttru_258,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.04 RPM
CEU_NA11843	0.06 RPM
CEU_NA11930	0.10 RPM
CEU_NA12004	0.04 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.02 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.05 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.08 RPM
FIN_HG00277	0.04 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.06 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.06 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.03 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.06 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.03 RPM
GBR_HG00133	0.05 RPM
GBR_HG00134	0.04 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.06 RPM
GBR_HG00143	0.03 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.02 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.14 RPM
TSI_NA20538	0.05 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.08 RPM
TSI_NA20771	0.06 RPM
TSI_NA20786	0.03 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.03 RPM
YRI_NA19099	0.03 RPM
YRI_NA19114	0.03 RPM
YRI_NA19118	0.06 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.02 RPM
YRI_NA19223	0.06 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).