RetrogeneDB ID: retro_hsap_3541

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 6:160514579..160514963(+)
• Located in intron of: ENSG00000197081

Retrocopy information

• Ensembl ID: ENSG00000213073
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CHP1
• Ensembl ID: ENSG00000187446
• Aliases: CHP1, CHP, SLC9A1BP, Sid470p, p22, p24
• Description: calcineurin-like EF-hand protein 1 [Source:HGNC Symbol;Acc:17433]

Sequence

>retro_hsap_3541
CAGGACGATTTCCAGGGGATTCCAGAACTTGCCATCAACCCAGTGGGGGACTGGATCATCAATGCCTTCCTTCCAGAGGG
AGAGGACCAGGTAAACTTCCGTGGATTCCTGCAAACTCTGGCTCATTTCCAAACCATTGAGGATAATGAAAAGAGCAAAG
TTGTGAATGGACCTGAACCACTCAACAGCCGAAGCAACAAACTGCAGTTTGCTTTTCGACTATATGATTTGGATAAAGAT
AACAAGATCTCTCGTGATGAGCTGTTAAGGGTGCTGTGCATGATGGTCCAAATAAATATCTCAGATAAGCAGCTGGGCAG
TATCGCAGACAGGACCATTCAGGAGGCTGATCAGCATGGGGACAGTGCCATATCTTTATCACAG

Alignment

ORF - retro_hsap_3541 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.81 %
• Parental protein coverage: 65.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  REDFQRIPELAINPLGDRIINAFFPEGEDQVNFRGFMRTLAHFRPIEDNEKSKDVNGPEPLNSRSNKLHF
          ..DFQ.IPELAINP.GD.IINAF.PEGEDQVNFRGF..TLAHF..IEDNEKSK.VNGPEPLNSRSNKL.F
Retrocopy QDDFQGIPELAINPVGDWIINAFLPEGEDQVNFRGFLQTLAHFQTIEDNEKSKVVNGPEPLNSRSNKLQF

Parental  AFRLYDLDKDEKISRDELLQVLRMMVGVNISDEQLGSIADRTIQEADQDGDSAISFTE
          AFRLYDLDKD.KISRDELL.VL.MMV..NISD.QLGSIADRTIQEADQ.GDSAIS...
Retrocopy AFRLYDLDKDNKISRDELLRVLCMMVQINISDKQLGSIADRTIQEADQHGDSAISLSQ

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	0.10 RPM	245.75 RPM
bodymap2_adrenal	0.49 RPM	63.78 RPM
bodymap2_brain	0.09 RPM	127.14 RPM
bodymap2_breast	0.16 RPM	241.40 RPM
bodymap2_colon	0.27 RPM	136.98 RPM
bodymap2_heart	0.30 RPM	100.74 RPM
bodymap2_kidney	0.39 RPM	197.37 RPM
bodymap2_liver	0.28 RPM	308.93 RPM
bodymap2_lung	0.18 RPM	189.28 RPM
bodymap2_lymph_node	0.26 RPM	90.84 RPM
bodymap2_ovary	0.42 RPM	94.30 RPM
bodymap2_prostate	0.14 RPM	116.17 RPM
bodymap2_skeletal_muscle	0.05 RPM	237.62 RPM
bodymap2_testis	0.06 RPM	89.36 RPM
bodymap2_thyroid	0.21 RPM	124.31 RPM
bodymap2_white_blood_cells	0.45 RPM	196.15 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3541 was not detected

EST

No EST(s) were mapped for retro_hsap_3541 retrocopy.

TSS

No TSS is located nearby retro_hsap_3541 retrocopy 5' end.

Lab

retro_hsap_3541 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3541 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2392

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009525	1 retrocopy	retro_cfam_2136,
Cavia porcellus	ENSCPOG00000010577	2 retrocopies	retro_cpor_1224, retro_cpor_726,
Homo sapiens	ENSG00000187446	2 retrocopies	retro_hsap_3334, retro_hsap_3541 ,
Homo sapiens	ENSG00000221823	1 retrocopy	retro_hsap_3,
Gorilla gorilla	ENSGGOG00000007312	2 retrocopies	retro_ggor_1293, retro_ggor_2392,
Macaca mulatta	ENSMMUG00000017092	2 retrocopies	retro_mmul_1809, retro_mmul_2088,
Mus musculus	ENSMUSG00000014077	4 retrocopies	retro_mmus_1458, retro_mmus_2094, retro_mmus_3133, retro_mmus_3469,
Nomascus leucogenys	ENSNLEG00000003465	4 retrocopies	retro_nleu_1678, retro_nleu_2269, retro_nleu_2608, retro_nleu_2609,
Procavia capensis	ENSPCAG00000005419	1 retrocopy	retro_pcap_240,
Pongo abelii	ENSPPYG00000006370	2 retrocopies	retro_pabe_2749, retro_pabe_2925,
Pan troglodytes	ENSPTRG00000006942	2 retrocopies	retro_ptro_2144, retro_ptro_2407,
Rattus norvegicus	ENSRNOG00000004742	2 retrocopies	retro_rnor_2034, retro_rnor_2223,
Ictidomys tridecemlineatus	ENSSTOG00000014503	1 retrocopy	retro_itri_227,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.26 RPM
CEU_NA11843	0.20 RPM
CEU_NA11930	0.42 RPM
CEU_NA12004	0.08 RPM
CEU_NA12400	0.67 RPM
CEU_NA12751	0.73 RPM
CEU_NA12760	0.54 RPM
CEU_NA12827	0.61 RPM
CEU_NA12872	0.38 RPM
CEU_NA12873	0.38 RPM
FIN_HG00183	0.52 RPM
FIN_HG00277	1.11 RPM
FIN_HG00315	0.22 RPM
FIN_HG00321	0.79 RPM
FIN_HG00328	0.07 RPM
FIN_HG00338	0.23 RPM
FIN_HG00349	0.31 RPM
FIN_HG00375	0.20 RPM
FIN_HG00377	0.33 RPM
FIN_HG00378	0.47 RPM
GBR_HG00099	0.29 RPM
GBR_HG00111	0.43 RPM
GBR_HG00114	0.34 RPM
GBR_HG00119	0.38 RPM
GBR_HG00131	0.55 RPM
GBR_HG00133	0.65 RPM
GBR_HG00134	0.31 RPM
GBR_HG00137	0.58 RPM
GBR_HG00142	0.89 RPM
GBR_HG00143	0.26 RPM
TSI_NA20512	0.08 RPM
TSI_NA20513	0.56 RPM
TSI_NA20518	0.50 RPM
TSI_NA20532	0.44 RPM
TSI_NA20538	0.83 RPM
TSI_NA20756	0.38 RPM
TSI_NA20765	0.39 RPM
TSI_NA20771	0.17 RPM
TSI_NA20786	0.29 RPM
TSI_NA20798	0.28 RPM
YRI_NA18870	0.34 RPM
YRI_NA18907	0.28 RPM
YRI_NA18916	0.48 RPM
YRI_NA19093	0.42 RPM
YRI_NA19099	0.37 RPM
YRI_NA19114	0.18 RPM
YRI_NA19118	0.35 RPM
YRI_NA19213	0.69 RPM
YRI_NA19214	0.69 RPM
YRI_NA19223	0.34 RPM

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Indel association:

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