RetrogeneDB ID: retro_hsap_304

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:212109527..212109832(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000233626
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PIN4
• Ensembl ID: ENSG00000102309
• Aliases: PIN4, EPVH, PAR14, PAR17
• Description: protein (peptidylprolyl cis/trans isomerase) NIMA-interacting, 4 (parvulin) [Source:HGNC Symbol;Acc:8992]

Sequence

>retro_hsap_304
TTACTTAAAAAATTATCTGGAAACAACAACAAAATATTTTTAGAACAGCAAATTTCAAAAATGATGCCCAAAGGAAAAAA
CGGTTCTGGAAAAGGGGGAAATGGGGACATGTCTCTGGGAGCAACAGTGCTGATGAGAAGGCTCAGGGCCCCAAAGTGGG
TGGCGACACAGCAAACAGACACATTCTACGCGAAAAACATGGCAAAACGACGGAAGCCATGGAAAAGTTAAAATCTAGTA
TGAGACTCAATGAAGTGTCTCCACAATATAGTGAAGATAAAAGCCAGGCCAGGGGACAACTTGGG

Alignment

ORF - retro_hsap_304 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.5 %
• Parental protein coverage: 66.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LLKGLVRQLERFSVQQQASKMPPKGKSGSGKAGKG-GAASGSDSADKKAQGPKGGGNAVKVRHILCEKHG
          LLK.L..........QQ.SKM.PKGK.GSGK.G.G.G..SGS.SAD.KAQGPK.GG.....RHIL.EKHG
Retrocopy LLKKLSGNNNKIFLEQQISKMMPKGKNGSGKGGNG<GHVSGSNSADEKAQGPKVGGDTAN-RHILREKHG

Parental  KIMEAMEKLKSGMRFNEVAAQYSEDKARQGGDLG
          K..EAMEKLKS.MR.NEV..QYSEDK....G.LG
Retrocopy KTTEAMEKLKSSMRLNEVSPQYSEDKSQARGQLG

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	8.75 RPM
bodymap2_adrenal	0.06 RPM	15.78 RPM
bodymap2_brain	0.00 RPM	14.74 RPM
bodymap2_breast	0.02 RPM	12.88 RPM
bodymap2_colon	0.15 RPM	21.35 RPM
bodymap2_heart	0.00 RPM	6.48 RPM
bodymap2_kidney	0.00 RPM	18.41 RPM
bodymap2_liver	0.02 RPM	15.06 RPM
bodymap2_lung	0.04 RPM	7.95 RPM
bodymap2_lymph_node	0.15 RPM	15.44 RPM
bodymap2_ovary	0.00 RPM	14.61 RPM
bodymap2_prostate	0.00 RPM	18.76 RPM
bodymap2_skeletal_muscle	0.15 RPM	8.00 RPM
bodymap2_testis	0.26 RPM	14.50 RPM
bodymap2_thyroid	0.00 RPM	18.61 RPM
bodymap2_white_blood_cells	0.08 RPM	8.80 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_hsap_304 in 1 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF002CQA	POLR2A	1:212108492..212109062

EST

No EST(s) were mapped for retro_hsap_304 retrocopy.

TSS

No TSS is located nearby retro_hsap_304 retrocopy 5' end.

Lab

retro_hsap_304 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_304 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_338
Callithrix jacchus	retro_cjac_1729

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 58 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005801	1 retrocopy	retro_amel_1553,
Canis familiaris	ENSCAFG00000032230	1 retrocopy	retro_cfam_212,
Callithrix jacchus	ENSCJAG00000004992	10 retrocopies	retro_cjac_1218, retro_cjac_1587, retro_cjac_1631, retro_cjac_1720, retro_cjac_1729, retro_cjac_1746, retro_cjac_1863, retro_cjac_2670, retro_cjac_2704, retro_cjac_2829,
Cavia porcellus	ENSCPOG00000011401	1 retrocopy	retro_cpor_631,
Dipodomys ordii	ENSDORG00000006985	2 retrocopies	retro_dord_109, retro_dord_352,
Felis catus	ENSFCAG00000012036	5 retrocopies	retro_fcat_1325, retro_fcat_1411, retro_fcat_581, retro_fcat_723, retro_fcat_769,
Homo sapiens	ENSG00000102309	3 retrocopies	retro_hsap_1562, retro_hsap_1604, retro_hsap_304 ,
Gorilla gorilla	ENSGGOG00000016008	4 retrocopies	retro_ggor_1187, retro_ggor_1210, retro_ggor_328, retro_ggor_338,
Loxodonta africana	ENSLAFG00000018261	1 retrocopy	retro_lafr_212,
Macropus eugenii	ENSMEUG00000003611	1 retrocopy	retro_meug_368,
Microcebus murinus	ENSMICG00000001640	4 retrocopies	retro_mmur_138, retro_mmur_294, retro_mmur_483, retro_mmur_674,
Myotis lucifugus	ENSMLUG00000012073	2 retrocopies	retro_mluc_2189, retro_mluc_923,
Mustela putorius furo	ENSMPUG00000005287	3 retrocopies	retro_mputfur_1285, retro_mputfur_417, retro_mputfur_858,
Mus musculus	ENSMUSG00000079480	8 retrocopies	retro_mmus_1656, retro_mmus_1703, retro_mmus_2205, retro_mmus_2741, retro_mmus_2921, retro_mmus_3673, retro_mmus_399, retro_mmus_821,
Oryctolagus cuniculus	ENSOCUG00000008715	2 retrocopies	retro_ocun_137, retro_ocun_835,
Pongo abelii	ENSPPYG00000020460	2 retrocopies	retro_pabe_146, retro_pabe_384,
Rattus norvegicus	ENSRNOG00000050051	6 retrocopies	retro_rnor_1755, retro_rnor_2368, retro_rnor_2575, retro_rnor_2576, retro_rnor_480, retro_rnor_553,
Sorex araneus	ENSSARG00000003732	2 retrocopies	retro_sara_201, retro_sara_248,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.04 RPM
CEU_NA11843	0.14 RPM
CEU_NA11930	0.03 RPM
CEU_NA12004	0.15 RPM
CEU_NA12400	0.07 RPM
CEU_NA12751	0.02 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.05 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.14 RPM
FIN_HG00277	0.15 RPM
FIN_HG00315	0.17 RPM
FIN_HG00321	0.06 RPM
FIN_HG00328	0.09 RPM
FIN_HG00338	0.11 RPM
FIN_HG00349	0.06 RPM
FIN_HG00375	0.12 RPM
FIN_HG00377	0.03 RPM
FIN_HG00378	0.08 RPM
GBR_HG00099	0.20 RPM
GBR_HG00111	0.26 RPM
GBR_HG00114	0.05 RPM
GBR_HG00119	0.05 RPM
GBR_HG00131	0.06 RPM
GBR_HG00133	0.07 RPM
GBR_HG00134	0.09 RPM
GBR_HG00137	0.11 RPM
GBR_HG00142	0.06 RPM
GBR_HG00143	0.10 RPM
TSI_NA20512	0.06 RPM
TSI_NA20513	0.02 RPM
TSI_NA20518	0.14 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.09 RPM
TSI_NA20756	0.12 RPM
TSI_NA20765	0.04 RPM
TSI_NA20771	0.06 RPM
TSI_NA20786	0.08 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.03 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.04 RPM
YRI_NA19093	0.05 RPM
YRI_NA19099	0.08 RPM
YRI_NA19114	0.03 RPM
YRI_NA19118	0.19 RPM
YRI_NA19213	0.17 RPM
YRI_NA19214	0.02 RPM
YRI_NA19223	0.12 RPM

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Indel association:

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