RetrogeneDB ID: retro_hsap_67

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 4:37962055..37962631(+)
• Located in intron of: ENSG00000065882

Retrocopy information

• Ensembl ID: ENSG00000250254
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PTTG1
• Ensembl ID: ENSG00000164611
• Aliases: PTTG1, EAP1, HPTTG, PTTG, TUTR1
• Description: pituitary tumor-transforming 1 [Source:HGNC Symbol;Acc:9690]

Sequence

>retro_hsap_67
ATGGCTACTCTGATCTACGTTGATAAGGAAATTGGAGAACCAGGCACCCGTGTGGCTGCCAAGGATGTGCTGAAGCTGGA
GTCTAGACCTTCAATCAAAGCATTAGATGGGATATCTCAAGTTTTAACACGACGTTTTGGCAAAACATACGATGCTCCAT
CAGCCTTACCTAAAGCTACCAGAAAGGCTTTGGGCACTGTCAACAGAGCTACAGAAAAGTCAGTAAAGACCAATGGACCC
AGAAAACAAAAACAGCCAAGCTTTTCTGCCAAAAAGATGACCGAGAAGACTGTTAAAACAAAAAGTTCTGTTCCTGCCTC
AGATGACGCCTATCCAGAAATAGAAAAATTCTTTCCCTTCAATCTTCTAGACTTTGAGAGTTTTGACCTGCCTGAAGAGC
GCCAGATTGCACACCTCCCCTTGAGTGGAGTGCCTCTCATGATCCTTGATGAGGAGGGAGAGCTTGAAAAGCTGTTTCAG
CTGGGCCCCCCTTCACCTGTGAAAATGCCCTCTCCACCATGGGAATGCAATCTGTTTGCAGTCTCCTTCAAGCATTCTGT
CGACCCTGGATGTTGA

Alignment

ORF - retro_hsap_67 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.45 %
• Parental protein coverage: 88.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATLIYVDKENGEPGTRVVAKDGLKLGSGPSIKALDGRSQVSTPRFGKTFDAPPALPKATRKALGTVNRA
          MATLIYVDKE.GEPGTRV.AKD.LKL.S.PSIKALDG.SQV.T.RFGKT.DAP.ALPKATRKALGTVNRA
Retrocopy MATLIYVDKEIGEPGTRVAAKDVLKLESRPSIKALDGISQVLTRRFGKTYDAPSALPKATRKALGTVNRA

Parental  TEKSVKTKGPLKQKQPSFSAKKMTEKTVKAKSSVPASDDAYPEIEKFFPFNPLDFESFDLPEEHQIAHLP
          TEKSVKT.GP.KQKQPSFSAKKMTEKTVK.KSSVPASDDAYPEIEKFFPFN.LDFESFDLPEE.QIAHLP
Retrocopy TEKSVKTNGPRKQKQPSFSAKKMTEKTVKTKSSVPASDDAYPEIEKFFPFNLLDFESFDLPEERQIAHLP

Parental  LSGVPLMILDEERELEKLFQLGPPSPVKMPSPPWESNL
          LSGVPLMILDEE.ELEKLFQLGPPSPVKMPSPPWE.NL
Retrocopy LSGVPLMILDEEGELEKLFQLGPPSPVKMPSPPWECNL

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	0.04 RPM	1.21 RPM
bodymap2_adrenal	0.14 RPM	3.99 RPM
bodymap2_brain	0.00 RPM	2.70 RPM
bodymap2_breast	0.00 RPM	1.32 RPM
bodymap2_colon	0.97 RPM	2.82 RPM
bodymap2_heart	0.13 RPM	0.33 RPM
bodymap2_kidney	0.00 RPM	0.45 RPM
bodymap2_liver	0.00 RPM	0.46 RPM
bodymap2_lung	0.00 RPM	6.91 RPM
bodymap2_lymph_node	0.40 RPM	6.49 RPM
bodymap2_ovary	0.06 RPM	1.14 RPM
bodymap2_prostate	0.17 RPM	2.08 RPM
bodymap2_skeletal_muscle	0.07 RPM	0.24 RPM
bodymap2_testis	0.00 RPM	52.73 RPM
bodymap2_thyroid	0.00 RPM	5.50 RPM
bodymap2_white_blood_cells	0.10 RPM	4.47 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_67 was not detected

EST

No EST(s) were mapped for retro_hsap_67 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_143575	485 libraries	306 libraries	656 libraries	267 libraries	115 libraries

The graphical summary, for retro_hsap_67 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_67 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_67 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1974
Gorilla gorilla	retro_ggor_2022
Pongo abelii	retro_pabe_2428
Callithrix jacchus	retro_cjac_2293

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 72 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012184	2 retrocopies	retro_btau_122, retro_btau_53,
Canis familiaris	ENSCAFG00000017264	1 retrocopy	retro_cfam_1586,
Choloepus hoffmanni	ENSCHOG00000009464	11 retrocopies	retro_chof_1246, retro_chof_1518, retro_chof_1679, retro_chof_2027, retro_chof_2161, retro_chof_2304, retro_chof_2459, retro_chof_2463, retro_chof_2690, retro_chof_426, retro_chof_526,
Callithrix jacchus	ENSCJAG00000019165	4 retrocopies	retro_cjac_2184, retro_cjac_2293, retro_cjac_2530, retro_cjac_3062,
Cavia porcellus	ENSCPOG00000011971	2 retrocopies	retro_cpor_1151, retro_cpor_820,
Dasypus novemcinctus	ENSDNOG00000024080	4 retrocopies	retro_dnov_1400, retro_dnov_2553, retro_dnov_918, retro_dnov_949,
Dipodomys ordii	ENSDORG00000007968	1 retrocopy	retro_dord_779,
Felis catus	ENSFCAG00000024074	3 retrocopies	retro_fcat_1153, retro_fcat_846, retro_fcat_878,
Homo sapiens	ENSG00000164611	4 retrocopies	retro_hsap_3823, retro_hsap_4068, retro_hsap_67 , retro_hsap_881,
Gorilla gorilla	ENSGGOG00000016937	5 retrocopies	retro_ggor_2022, retro_ggor_2572, retro_ggor_2573, retro_ggor_2731, retro_ggor_714,
Loxodonta africana	ENSLAFG00000011135	1 retrocopy	retro_lafr_258,
Macropus eugenii	ENSMEUG00000005993	1 retrocopy	retro_meug_577,
Microcebus murinus	ENSMICG00000006363	1 retrocopy	retro_mmur_181,
Myotis lucifugus	ENSMLUG00000002317	1 retrocopy	retro_mluc_1080,
Macaca mulatta	ENSMMUG00000023077	3 retrocopies	retro_mmul_1052, retro_mmul_1629, retro_mmul_2347,
Mustela putorius furo	ENSMPUG00000013241	3 retrocopies	retro_mputfur_1358, retro_mputfur_429, retro_mputfur_813,
Nomascus leucogenys	ENSNLEG00000004396	5 retrocopies	retro_nleu_218, retro_nleu_2487, retro_nleu_2527, retro_nleu_2528, retro_nleu_830,
Oryctolagus cuniculus	ENSOCUG00000014877	2 retrocopies	retro_ocun_150, retro_ocun_1565,
Otolemur garnettii	ENSOGAG00000012307	2 retrocopies	retro_ogar_2802, retro_ogar_990,
Pongo abelii	ENSPPYG00000016009	4 retrocopies	retro_pabe_2428, retro_pabe_3071, retro_pabe_3341, retro_pabe_674,
Pan troglodytes	ENSPTRG00000017492	4 retrocopies	retro_ptro_1974, retro_ptro_2601, retro_ptro_2757, retro_ptro_610,
Pteropus vampyrus	ENSPVAG00000015938	2 retrocopies	retro_pvam_431, retro_pvam_704,
Sarcophilus harrisii	ENSSHAG00000010267	1 retrocopy	retro_shar_104,
Tupaia belangeri	ENSTBEG00000015966	2 retrocopies	retro_tbel_2399, retro_tbel_771,
Tursiops truncatus	ENSTTRG00000011570	1 retrocopy	retro_ttru_259,
Vicugna pacos	ENSVPAG00000009594	2 retrocopies	retro_vpac_178, retro_vpac_33,

Population studies

Expression level across human populations :

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