RetrogeneDB ID: retro_hsap_3381

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 5:125221973..125222429(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000249904
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: C1orf146
• Ensembl ID: ENSG00000203910
• Aliases: None
• Description: chromosome 1 open reading frame 146 [Source:HGNC Symbol;Acc:24032]

Sequence

>retro_hsap_3381
GTTAGTATTAGCTCATTTCTTTAGTGTTATGAAGTTGTAGCTGCCCTAGAAAATTAAAGCCGTAAGTTTTGGTAGTCAAA
TAAATGGAAAATGGATCAATTATTTTCCTTTTTCTGTAGTTACATTTTAATTGGTGGATGCTAAGGAATGCCTATGTTAG
CTGAAGCACTATTTCTAGCAAAATATGAGAAGTTCATAAATATTCACTGAAATAACTTTTTGAATTTATCTGCTGCCCTT
TATGGACTTGAGAAATGGGAACTGTTGAGTATTCAGCAGAGATTTCTGAGTAGTAATTTACAAATAGTTTCAGTATAAAA
CATAGTCAGTGTTATTAATCTTGTACACACTATAGCTAAGACCACCCTATATAGAAATATGGATAGCTTATGCTATGGAG
TAGCAGCTAAAGCTTATATCATCGAGTAAAATCCTGGTTGAAAAACACAAGATAAA

Alignment

ORF - retro_hsap_3381 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.96 %
• Parental protein coverage: 86.11 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IIISSSLKSYEVATALENRSHKVRYSDS-VENGSIIF-SLSGVAFLLMDTKECL-LSTEEIFLAKIEKFI
          ..ISS.L..YEV..ALEN.S.K...S....ENGSIIF...S.V.F.L.D.KECL....E..FLAK.EKFI
Retrocopy VSISSFL*CYEVVAALEN*SRKFW*SNK<MENGSIIF<PFSVVTF*LVDAKECL<MLAEALFLAKYEKFI

Parental  NIHQNSFLVLSAALHGPEEWKLMFRIQQRFLGCNLRILPVHNTVNAINLMCTIAKTTSKPYIDSICYRMI
          NIH.N.FL.LSAAL.G.E.W.L...IQQRFL..NL.I..V.N.V..INL..TIAKTT.....DS.CY...
Retrocopy NIH*NNFLNLSAALYGLEKWELL-SIQQRFLSSNLQIVSV*NIVSVINLVHTIAKTTLYRNMDSLCYG-V

Parental  TAKAYIIEQSPVWKTLQK
          .AKAYIIE..P..KT..K
Retrocopy AAKAYIIE*NPG*KTQDK

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	0.00 RPM
bodymap2_adrenal	0.00 RPM	0.18 RPM
bodymap2_brain	0.00 RPM	0.61 RPM
bodymap2_breast	0.00 RPM	0.08 RPM
bodymap2_colon	0.00 RPM	0.00 RPM
bodymap2_heart	0.00 RPM	0.00 RPM
bodymap2_kidney	0.00 RPM	0.10 RPM
bodymap2_liver	0.00 RPM	0.00 RPM
bodymap2_lung	0.00 RPM	0.00 RPM
bodymap2_lymph_node	0.00 RPM	0.15 RPM
bodymap2_ovary	0.00 RPM	0.31 RPM
bodymap2_prostate	0.00 RPM	0.00 RPM
bodymap2_skeletal_muscle	0.00 RPM	0.00 RPM
bodymap2_testis	0.00 RPM	5.69 RPM
bodymap2_thyroid	0.00 RPM	0.02 RPM
bodymap2_white_blood_cells	0.00 RPM	0.18 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3381 was not detected

EST

No EST(s) were mapped for retro_hsap_3381 retrocopy.

TSS

No TSS is located nearby retro_hsap_3381 retrocopy 5' end.

Lab

retro_hsap_3381 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3381 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2298
Gorilla gorilla	retro_ggor_2289
Pongo abelii	retro_pabe_2780
Macaca mulatta	retro_mmul_2107
Callithrix jacchus	retro_cjac_1817

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000027936	1 retrocopy	retro_btau_490,
Choloepus hoffmanni	ENSCHOG00000004012	1 retrocopy	retro_chof_2167,
Callithrix jacchus	ENSCJAG00000017547	1 retrocopy	retro_cjac_1817,
Erinaceus europaeus	ENSEEUG00000003083	1 retrocopy	retro_eeur_601,
Homo sapiens	ENSG00000203910	1 retrocopy	retro_hsap_3381 ,
Gorilla gorilla	ENSGGOG00000006653	1 retrocopy	retro_ggor_2289,
Macropus eugenii	ENSMEUG00000013311	1 retrocopy	retro_meug_143,
Myotis lucifugus	ENSMLUG00000016984	1 retrocopy	retro_mluc_1260,
Macaca mulatta	ENSMMUG00000010094	1 retrocopy	retro_mmul_2107,
Nomascus leucogenys	ENSNLEG00000010426	1 retrocopy	retro_nleu_970,
Pongo abelii	ENSPPYG00000001156	1 retrocopy	retro_pabe_2780,
Pan troglodytes	ENSPTRG00000030530	1 retrocopy	retro_ptro_2298,
Ictidomys tridecemlineatus	ENSSTOG00000012506	1 retrocopy	retro_itri_404,
Tursiops truncatus	ENSTTRG00000014426	1 retrocopy	retro_ttru_1727,

Population studies

Expression level across human populations :

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

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Indel association:

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