RetrogeneDB ID: retro_hsap_4143

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 9:22747699..22748136(+)
• Located in intron of: ENSG00000234840

Retrocopy information

• Ensembl ID: ENSG00000236739
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CLIC4
• Ensembl ID: ENSG00000169504
• Aliases: CLIC4, CLIC4L, H1, MTCLIC, huH1, p64H1
• Description: chloride intracellular channel 4 [Source:HGNC Symbol;Acc:13518]

Sequence

>retro_hsap_4143
ATAACTTTCAACAGTGAAGTCAAAACAGATGTAAATAAGATTGAGGAATTTCTTGAAGAAGTCTTAAGCCCTCCCACGTA
CTTAAAGCCTTCACCAAAACACCCAGAATCAAATACTGCTGGAATGGACATCTTTGCCAAATTCTCTGCATATATCAAGA
ATTCAAGGCCAGAGGCTAATGAAGCACTGGAGAGGGGTCTCCTGAAAACCCTGCAGAAACTGGATGAATATCTGAATTCT
CCTCTCCCTGATGAAATTGATGAAAATAGTATGGAGGACGTTAAGTTTTCTAAACGTAAATTTCTGGACAGCAATGAAAT
GACATTAGCTGATTGCAATCTGCTGTCAAAGCTGCATATTGTCAAGGTTGTGGCCAAAAAAATCGCAACTTTGATATTCC
AAAAGAAATGACTGTCATCTGGAGATACCTAACTAAC

Alignment

ORF - retro_hsap_4143 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.2 %
• Parental protein coverage: 57.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ITFNSEVKTDVNKIEEFLEEVLCPPKYLKLSPKHPESNTAGMDIFAKFSAYIKNSRPEANEALERGLLKT
          ITFNSEVKTDVNKIEEFLEEVL.PP.YLK.SPKHPESNTAGMDIFAKFSAYIKNSRPEANEALERGLLKT
Retrocopy ITFNSEVKTDVNKIEEFLEEVLSPPTYLKPSPKHPESNTAGMDIFAKFSAYIKNSRPEANEALERGLLKT

Parental  LQKLDEYLNSPLPDEIDENSMEDIKFSTRKFLDGNEMTLADCNLLPKLHIVKVVAKKY-RNFDIPKEMTG
          LQKLDEYLNSPLPDEIDENSMED.KFS.RKFLD.NEMTLADCNLL.KLHIVKVVAKK..RNFDIPKEMT.
Retrocopy LQKLDEYLNSPLPDEIDENSMEDVKFSKRKFLDSNEMTLADCNLLSKLHIVKVVAKKI<RNFDIPKEMTV

Parental  IWRYLTN
          IWRYLTN
Retrocopy IWRYLTN

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	631.42 RPM
bodymap2_adrenal	0.00 RPM	353.04 RPM
bodymap2_brain	0.05 RPM	407.20 RPM
bodymap2_breast	0.56 RPM	542.89 RPM
bodymap2_colon	0.00 RPM	1057.01 RPM
bodymap2_heart	0.00 RPM	655.00 RPM
bodymap2_kidney	0.02 RPM	494.14 RPM
bodymap2_liver	0.04 RPM	66.64 RPM
bodymap2_lung	0.00 RPM	1407.65 RPM
bodymap2_lymph_node	0.02 RPM	405.33 RPM
bodymap2_ovary	0.00 RPM	427.62 RPM
bodymap2_prostate	0.00 RPM	1326.15 RPM
bodymap2_skeletal_muscle	0.02 RPM	115.60 RPM
bodymap2_testis	0.00 RPM	473.27 RPM
bodymap2_thyroid	0.06 RPM	234.71 RPM
bodymap2_white_blood_cells	0.00 RPM	99.80 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4143 was not detected

EST

No EST(s) were mapped for retro_hsap_4143 retrocopy.

TSS

No TSS is located nearby retro_hsap_4143 retrocopy 5' end.

Lab

retro_hsap_4143 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4143 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2816
Gorilla gorilla	retro_ggor_2783
Pongo abelii	retro_pabe_3466

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007591	10 retrocopies	retro_chof_1284, retro_chof_1401, retro_chof_1446, retro_chof_1654, retro_chof_2177, retro_chof_2673, retro_chof_784, retro_chof_789, retro_chof_808, retro_chof_947,
Callithrix jacchus	ENSCJAG00000020833	2 retrocopies	retro_cjac_1713, retro_cjac_461,
Cavia porcellus	ENSCPOG00000004010	1 retrocopy	retro_cpor_1490,
Homo sapiens	ENSG00000169504	2 retrocopies	retro_hsap_4143 , retro_hsap_4678,
Gorilla gorilla	ENSGGOG00000005586	2 retrocopies	retro_ggor_1579, retro_ggor_2783,
Macropus eugenii	ENSMEUG00000008789	1 retrocopy	retro_meug_780,
Macaca mulatta	ENSMMUG00000002416	2 retrocopies	retro_mmul_1183, retro_mmul_2488,
Mus musculus	ENSMUSG00000037242	2 retrocopies	retro_mmus_2259, retro_mmus_945,
Nomascus leucogenys	ENSNLEG00000008997	3 retrocopies	retro_nleu_1457, retro_nleu_1785, retro_nleu_2168,
Otolemur garnettii	ENSOGAG00000014620	1 retrocopy	retro_ogar_2672,
Pongo abelii	ENSPPYG00000001715	3 retrocopies	retro_pabe_219, retro_pabe_3466, retro_pabe_3632,
Pan troglodytes	ENSPTRG00000000350	3 retrocopies	retro_ptro_2816, retro_ptro_3107, retro_ptro_396,
Pteropus vampyrus	ENSPVAG00000005838	1 retrocopy	retro_pvam_812,
Ictidomys tridecemlineatus	ENSSTOG00000002184	1 retrocopy	retro_itri_52,
Tarsius syrichta	ENSTSYG00000008978	1 retrocopy	retro_tsyr_252,
Vicugna pacos	ENSVPAG00000007699	1 retrocopy	retro_vpac_475,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.02 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.04 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.04 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.03 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.07 RPM
FIN_HG00315	0.03 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.02 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.04 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	0.06 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.03 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.02 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.03 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	0.04 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.02 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).