RetrogeneDB ID: retro_hsap_1372

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 14:91885801..91886092(+)
• Located in intron of: ENSG00000258798

Retrocopy information

• Ensembl ID: ENSG00000258446
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CMC1
• Ensembl ID: ENSG00000187118
• Aliases: None
• Description: COX assembly mitochondrial protein 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:28783]

Sequence

>retro_hsap_1372
CTCAGACGTGTCGAAAAAGATGTTTTGATCCCTAAAATAATGAGAGAAAAGGCCAGAGAGAGGTCTTCTGACAAGTTCAA
GATTTTACCAAATGTTGCAAGAACTCTGGAATCCTTATGGTAGTAAAATGCTGGAAAGAAAATTCTGCATTGAAAGAATG
TCTTAACAGCTCACTATAATGACCCAGCCTTTTATGAATAATGCAAAGTGGAAAACCTGAAGGAAAAGGAAGAATTCAGA
AAAACTGGAATTTCTACAAAGAAAAGTCTACAGAAGCTGCCCACAAGTGTG

Alignment

ORF - retro_hsap_1372 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.84 %
• Parental protein coverage: 85.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LRHVEKDVLIPKIMREKAKERCSE-QVQDFTKCCKNSGVLMVVKCRKENSALKEC-LTAYYNDPAFYEEC
          LR.VEKDVLIPKIMREKA.ER.S..QVQDFTKCCKNSG.LMVVKC.KENSALKEC.LTA.YNDPAFYE.C
Retrocopy LRRVEKDVLIPKIMREKARERSSD<QVQDFTKCCKNSGILMVVKCWKENSALKEC>LTAHYNDPAFYE*C

Parental  KMEYLKEREEFRKTGIPTKKRLQKLPTSM
          K.E.LKE.EEFRKTGI.TKK.LQKLPTS.
Retrocopy KVENLKEKEEFRKTGISTKKSLQKLPTSV

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	6.04 RPM
bodymap2_adrenal	0.00 RPM	19.73 RPM
bodymap2_brain	0.00 RPM	7.76 RPM
bodymap2_breast	0.08 RPM	11.48 RPM
bodymap2_colon	0.00 RPM	11.08 RPM
bodymap2_heart	0.00 RPM	11.72 RPM
bodymap2_kidney	0.00 RPM	18.94 RPM
bodymap2_liver	0.00 RPM	10.98 RPM
bodymap2_lung	0.00 RPM	17.14 RPM
bodymap2_lymph_node	0.00 RPM	26.09 RPM
bodymap2_ovary	0.00 RPM	9.54 RPM
bodymap2_prostate	0.00 RPM	9.47 RPM
bodymap2_skeletal_muscle	0.00 RPM	3.06 RPM
bodymap2_testis	0.02 RPM	20.15 RPM
bodymap2_thyroid	0.00 RPM	7.12 RPM
bodymap2_white_blood_cells	0.00 RPM	33.71 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_hsap_1372 in 3 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF002CSY	POLR2A	14:91884009..91885064
ENCFF002CZD	POLR2A	14:91884311..91884821
ENCFF002CZQ	POLR2A	14:91884360..91884810

EST

No EST(s) were mapped for retro_hsap_1372 retrocopy.

TSS

No TSS is located nearby retro_hsap_1372 retrocopy 5' end.

Lab

retro_hsap_1372 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1372 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_942
Gorilla gorilla	retro_ggor_1067
Pongo abelii	retro_pabe_1139

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004272	2 retrocopies	retro_cjac_2600, retro_cjac_2653,
Dasypus novemcinctus	ENSDNOG00000018923	2 retrocopies	retro_dnov_111, retro_dnov_651,
Homo sapiens	ENSG00000187118	4 retrocopies	retro_hsap_1372 , retro_hsap_1764, retro_hsap_3229, retro_hsap_984,
Gorilla gorilla	ENSGGOG00000012406	4 retrocopies	retro_ggor_1067, retro_ggor_2196, retro_ggor_2245, retro_ggor_786,
Microcebus murinus	ENSMICG00000011702	2 retrocopies	retro_mmur_366, retro_mmur_759,
Myotis lucifugus	ENSMLUG00000000044	2 retrocopies	retro_mluc_1063, retro_mluc_759,
Nomascus leucogenys	ENSNLEG00000004066	4 retrocopies	retro_nleu_1075, retro_nleu_2763, retro_nleu_2830, retro_nleu_949,
Oryctolagus cuniculus	ENSOCUG00000012793	2 retrocopies	retro_ocun_1592, retro_ocun_1637,
Ochotona princeps	ENSOPRG00000009474	1 retrocopy	retro_opri_463,
Pongo abelii	ENSPPYG00000014054	4 retrocopies	retro_pabe_1139, retro_pabe_1533, retro_pabe_2677, retro_pabe_833,
Pan troglodytes	ENSPTRG00000014706	4 retrocopies	retro_ptro_1207, retro_ptro_2181, retro_ptro_763, retro_ptro_942,
Rattus norvegicus	ENSRNOG00000010149	1 retrocopy	retro_rnor_914,
Sorex araneus	ENSSARG00000001629	1 retrocopy	retro_sara_186,
Tupaia belangeri	ENSTBEG00000002573	4 retrocopies	retro_tbel_3026, retro_tbel_3858, retro_tbel_4018, retro_tbel_4214,
Tarsius syrichta	ENSTSYG00000011371	2 retrocopies	retro_tsyr_1764, retro_tsyr_178,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.04 RPM
CEU_NA11843	0.03 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.08 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.05 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.09 RPM
CEU_NA12872	0.03 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.11 RPM
FIN_HG00277	0.04 RPM
FIN_HG00315	0.06 RPM
FIN_HG00321	0.06 RPM
FIN_HG00328	0.05 RPM
FIN_HG00338	0.09 RPM
FIN_HG00349	0.11 RPM
FIN_HG00375	0.10 RPM
FIN_HG00377	0.10 RPM
FIN_HG00378	0.04 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.04 RPM
GBR_HG00114	0.05 RPM
GBR_HG00119	0.02 RPM
GBR_HG00131	0.09 RPM
GBR_HG00133	0.05 RPM
GBR_HG00134	0.04 RPM
GBR_HG00137	0.05 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.06 RPM
TSI_NA20513	0.05 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.10 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.02 RPM
TSI_NA20771	0.09 RPM
TSI_NA20786	0.08 RPM
TSI_NA20798	0.03 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.11 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.04 RPM
YRI_NA19213	0.02 RPM
YRI_NA19214	0.05 RPM
YRI_NA19223	0.02 RPM

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Indel association:

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