RetrogeneDB ID: retro_hsap_675

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 10:52486893..52487592(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000213667
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PGGT1B
• Ensembl ID: ENSG00000164219
• Aliases: PGGT1B, BGGI, GGTI
• Description: protein geranylgeranyltransferase type I, beta subunit [Source:HGNC Symbol;Acc:8895]

Sequence

>retro_hsap_675
CAGGTCCTTCCCACAGAAGGCAGATGAAATCTAAATCGCTGTGGTTTCCGAGGCTCTTCATACCTGGGTATTCCTTTCAA
TCCATCAAAGGCTCCTGGAACAGCTCATCCTTATGATAGTGGCCACATTGCAATGACCTACACTGGCCTTTCATGCTTAG
TTATTCTTGGAGACGACTTAAGCCGAGTAAATAAAGAAGCTTGCTTAGCAGGCTTGAGAGCCCTTCAGCTGGAAGATGGG
AGTTTTTGTGCAGTACCTGAAGGCAGTGAAAATGATATGCGATTTTTGTACTGTGCTTCCTGTATTTGCTATATGCTCAA
TAACCAGTCAGGCATGGATATGAAAAAAGCCATCTCCTATATTAAAAGAAGTATGTCCTATGACAATGGACTGGCACAGG
GAGCTGGACTTGAATCTCATGGAGGATCTACTTTTTGTGGCATTGCCTCACTATGTCTGATGGGTAAACTAGAAGTTTTT
TCAGAAAAAGAATTGAACACGATAAAGAGGTGGTGTATAATGGGGCAACAAAATAGTTATCATGGAAGACCTAATAAGCC
TGTAGACACCCGTTATTCTTTTTGGGTGGGAGCAACTCTAAAGCTTCTAAAAATTTTCCAATACACTAACTTTGAGAAAA
ATAGAAATTCCATCTTATCAACTCAAGATCGCCTCGTAGGGGGATTTGCCAAGTGGCCA

Alignment

ORF - retro_hsap_675 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.87 %
• Parental protein coverage: 62.07 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QVLPTEDRSNLNRCGFRGSSYLGIPFNPSKAPGTAHPYDSGHIAMTYTGLSCLVILGDDLSRVNKEACLA
          QVLPTE.R.NLNRCGFRGSSYLGIPFNPSKAPGTAHPYDSGHIAMTYTGLSCLVILGDDLSRVNKEACLA
Retrocopy QVLPTEGR*NLNRCGFRGSSYLGIPFNPSKAPGTAHPYDSGHIAMTYTGLSCLVILGDDLSRVNKEACLA

Parental  GLRALQLEDGSFCAVPEGSENDMRFVYCASCICYMLNNWSGMDMKKAITYIRRSMSYDNGLAQGAGLESH
          GLRALQLEDGSFCAVPEGSENDMRF.YCASCICYMLNN.SGMDMKKAI.YI.RSMSYDNGLAQGAGLESH
Retrocopy GLRALQLEDGSFCAVPEGSENDMRFLYCASCICYMLNNQSGMDMKKAISYIKRSMSYDNGLAQGAGLESH

Parental  GGSTFCGIASLCLMGKLEEVFSEKELNRIKRWCIMRQQNGYHGRPNKPVDTCYSFWVGATLKLLKIFQYT
          GGSTFCGIASLCLMGKL.EVFSEKELN.IKRWCIM.QQN.YHGRPNKPVDT.YSFWVGATLKLLKIFQYT
Retrocopy GGSTFCGIASLCLMGKL-EVFSEKELNTIKRWCIMGQQNSYHGRPNKPVDTRYSFWVGATLKLLKIFQYT

Parental  NFEKNRNYILSTQDRLVGGFAKWP
          NFEKNRN.ILSTQDRLVGGFAKWP
Retrocopy NFEKNRNSILSTQDRLVGGFAKWP

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	16.94 RPM
bodymap2_adrenal	0.02 RPM	24.69 RPM
bodymap2_brain	0.02 RPM	15.05 RPM
bodymap2_breast	0.00 RPM	23.68 RPM
bodymap2_colon	0.02 RPM	16.57 RPM
bodymap2_heart	0.00 RPM	13.77 RPM
bodymap2_kidney	0.12 RPM	24.15 RPM
bodymap2_liver	0.04 RPM	15.02 RPM
bodymap2_lung	0.00 RPM	6.35 RPM
bodymap2_lymph_node	0.00 RPM	15.46 RPM
bodymap2_ovary	0.00 RPM	24.10 RPM
bodymap2_prostate	0.00 RPM	20.46 RPM
bodymap2_skeletal_muscle	0.00 RPM	11.08 RPM
bodymap2_testis	0.04 RPM	23.49 RPM
bodymap2_thyroid	0.00 RPM	26.34 RPM
bodymap2_white_blood_cells	0.00 RPM	32.84 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_675 was not detected

EST

No EST(s) were mapped for retro_hsap_675 retrocopy.

TSS

No TSS is located nearby retro_hsap_675 retrocopy 5' end.

Lab

retro_hsap_675 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_675 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_487
Homo sapiens	retro_hsap_698
Pan troglodytes	retro_ptro_444

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016700	1 retrocopy	retro_cjac_1058,
Cavia porcellus	ENSCPOG00000002443	1 retrocopy	retro_cpor_1344,
Homo sapiens	ENSG00000164219	2 retrocopies	retro_hsap_675 , retro_hsap_698,
Loxodonta africana	ENSLAFG00000003752	1 retrocopy	retro_lafr_668,
Pongo abelii	ENSPPYG00000015694	3 retrocopies	retro_pabe_527, retro_pabe_545, retro_pabe_640,
Pan troglodytes	ENSPTRG00000017146	2 retrocopies	retro_ptro_444, retro_ptro_487,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.03 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.03 RPM
CEU_NA12873	0.03 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.03 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.04 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.03 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 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	0.00 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.03 RPM
YRI_NA18907	0.03 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.03 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 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).