RetrogeneDB ID: retro_hsap_1172

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 13:21893294..21895042(+)
• Located in intron of: ENSG00000224429

Retrocopy information

• Ensembl ID: ENSG00000215571
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GRK6
• Ensembl ID: ENSG00000198055
• Aliases: GRK6, GPRK6
• Description: G protein-coupled receptor kinase 6 [Source:HGNC Symbol;Acc:4545]

Sequence

>retro_hsap_1172
ATGGAGCTCGAGAACATCGTAGCGGACACGGTGCTCCTCAAGGCCCGGGAAGGTAGCGGTGGAAATCGCAAAGGCAAAAG
CAAGAAATGGCGGCAGATGCTCCAGTTCCCCCACATCAGCCAGTGCGAAGAGCTGCGGCTCAGTCTCGAACGTGACTATC
ACAGCCTGTGCGAGCGGCAGCCCATCGGGCGCCTGCTGTTCTGAGAGTTCTGTGCCACCAGGCCGGAGCTGAGCCGTTGC
ATCGCCTTCCAGGATGGGATGGCCGAGTATGAAGCGACCCCGGATGAGAAGCGGAAGGCATGTGGGCGGCGGCTAATGCA
GAATTTTCTTGAGCCACAGGTTCCTGACCTCATCCCTGAGGTCCCCCCGGCAGCTGGTGACGAACTGCACCCAGCGGCTG
GAGCAGGGGCCCTGCAAAGAACTCTCCCAGGAACTCACCCGGGTGACCCACGGGTACCTGAGCATGGCCCCTTTTGCCGA
CTACCTCAACAGCATCTACTTCAACCGTTTCCTGCAGTGGAAGTGGCTGGAAAGGCAGCCAGTGACCAAAAATACCTTCA
GGCAGTACCGAGTCCTGGGCAAAGGTGGCTTTGGGGAGGTGTGCGCCTGCCAGGTGCGGGCCACAGGCAAGATGTACGCC
TTCAAGAAGCTAGAAAAAAAGCGGATCAAGAAGCAGAAAGGGGAGGCCATGGCGCTGAACGAGAAGCAGATCCTGGAGAG
AGTGAACAGTAGGTTTATAGTGAGCTTGGCCTACACCTGTGAGACCAAGGAGGCGCTGTGCCTGGTGCTGACGCTGATGA
ACGGGGGCGACCTCAATTTCCACATCTGCCACATGGGCCGGGCTGGCTTCCCCGAAGCGCAGGCCGTCTTCTACGTCCCG
AGATCTGCTTGCGGTCTGGAGGACCTGCACCGGGAGCGCATAGTGTACAGGGACCTGAAGCCAGGAACATCTTGCTGGAT
GACCACGGCCACATCCTCGTCTCCGACCTGGGACTGGCTGTGCACGTGCCCGAGGGCCAGACCATCAAAGGCCGTGTGGG
CACCGTGAGCTACATGGCTCCAGAGGTGGTGAAGAATGAACCGTACACTTTCAGCTCTGACTGTTGGGCGCTAGGCTGCC
TCCCGCAGGAGATGATTGCAGGCCAGTCGCTCTTCCAGCAGAGGAAGAAGATGATCAAGCGGGAGGAGGTGGAGCGGCTG
GTGAAGGAGGACCCCGAGGAGTATTCCGAGCGCTTTTCCCCGCAGGCCTGCTCACAGCTCCTCTGCAAGGACCCCGCTGA
ACGCCTGGGGTGTCGTGGGGGCAGTGCCCGCGAAGTGAAGGAGCACCCCCTGTTGAAGAAGCTGAACTTCAAGCGGGTGG
GAGCCGGCATGCTGGAGCCGCCCTTCAAGCCTGACCCTCGGGCCATTTACTGCAAGGATATTCTGGACATTAAACAGTTC
TCTAGGGTCAAGGGTGTGGAGCTGGAGGCTACCGACCAAGACTTCTACCAGAAGTTTGCCACAGGCAGTGTGCCCATCCC
CTGGCAGAAGGGGATGGTGGAGACTGAGTGCTTCCAGGAGCTGAATGTCTTTGGGCTGGATGGCTCAGTTCCCCCAGACC
TGGACTGGAAGGGCCAGCCACCTGCAAGGGACTGCTGCAGAGACTCTTCAGTCGCCAAAGGATTGCTGTGGAAACTGCGG
GGACAGCGAGGAAGAGCTCCCTACCCGCCTCTAGCCCCCAGCCAGAGGCCCCCACGGGCAGTGGGCGG

Alignment

ORF - retro_hsap_1172 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.01 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MELENIVANTVLLKAREGGGGNRKGKSKKWRQMLQFPHISQCEELRLSLERDYHSLCERQPIGRLLFREF
          MELENIVA.TVLLKAREG.GGNRKGKSKKWRQMLQFPHISQCEELRLSLERDYHSLCERQPIGRLLF.EF
Retrocopy MELENIVADTVLLKAREGSGGNRKGKSKKWRQMLQFPHISQCEELRLSLERDYHSLCERQPIGRLLF*EF

Parental  CATRPELSRCVAFLDGVAEYEVTPDDKRKACGRQLTQNFLSHTGPDLIPEVP-RQLVTNCTQRLEQGPCK
          CATRPELSRC.AF.DG.AEYE.TPD.KRKACGR.L.QNFL....PDLIPEVP.RQLVTNCTQRLEQGPCK
Retrocopy CATRPELSRCIAFQDGMAEYEATPDEKRKACGRRLMQNFLEPQVPDLIPEVP>RQLVTNCTQRLEQGPCK

Parental  DLFQELTRLTHEYLSVAPFADYLDSIYFNRFLQWKWLERQPVTKNTFRQYRVLGKGGFGEVCACQVRATG
          .L.QELTR.TH.YLS.APFADYL.SIYFNRFLQWKWLERQPVTKNTFRQYRVLGKGGFGEVCACQVRATG
Retrocopy ELSQELTRVTHGYLSMAPFADYLNSIYFNRFLQWKWLERQPVTKNTFRQYRVLGKGGFGEVCACQVRATG

Parental  KMYACKKLEKKRIKKRKGEAMALNEKQILEKVNSRFVVSLAYAYETKDALCLVLTLMNGGDLKFHIYHMG
          KMYA.KKLEKKRIKK.KGEAMALNEKQILE.VNSRF.VSLAY..ETK.ALCLVLTLMNGGDL.FHI.HMG
Retrocopy KMYAFKKLEKKRIKKQKGEAMALNEKQILERVNSRFIVSLAYTCETKEALCLVLTLMNGGDLNFHICHMG

Parental  QAGFPEARAVFYAAEICCGLEDLHRERIVYRDLKP-ENILLDDHGHIRISDLGLAVHVPEGQTIKGRVGT
          .AGFPEA.AVFY.....CGLEDLHRERIVYRDLKP..NILLDDHGHI..SDLGLAVHVPEGQTIKGRVGT
Retrocopy RAGFPEAQAVFYVPRSACGLEDLHRERIVYRDLKP<RNILLDDHGHILVSDLGLAVHVPEGQTIKGRVGT

Parental  VGYMAPEVVKNERYTFSPDWWALGCLLYEMIAGQSPFQQRKKKIKREEVERLVKEVPEEYSERFSPQARS
          V.YMAPEVVKNE.YTFS.D.WALGCL..EMIAGQS.FQQRKK.IKREEVERLVKE.PEEYSERFSPQA..
Retrocopy VSYMAPEVVKNEPYTFSSDCWALGCLPQEMIAGQSLFQQRKKMIKREEVERLVKEDPEEYSERFSPQA--

Parental  LCSQLLCKDPAERLGCRGGSAREVKEHPLFKKLNFKRLGAGMLEPPFKPDPQAIYCKDVLDIEQFSTVKG
          .CSQLLCKDPAERLGCRGGSAREVKEHPL.KKLNFKR.GAGMLEPPFKPDP.AIYCKD.LDI.QFS.VKG
Retrocopy -CSQLLCKDPAERLGCRGGSAREVKEHPLLKKLNFKRVGAGMLEPPFKPDPRAIYCKDILDIKQFSRVKG

Parental  VELEPTDQDFYQKFATGSVPIPWQNEMVETECFQELNVFGLDGSVPPDLDWKGQPPAPPK-KGLLQRLFS
          VELE.TDQDFYQKFATGSVPIPWQ..MVETECFQELNVFGLDGSVPPDLDWKGQ...PP..KGLLQRLFS
Retrocopy VELEATDQDFYQKFATGSVPIPWQKGMVETECFQELNVFGLDGSVPPDLDWKGQ---PPA<KGLLQRLFS

Parental  RQRIAVETAATARKSSPPASSPQPEAPTSSWR
          RQRIAVETA.TARKSS.PASSPQPEAPT.S.R
Retrocopy RQRIAVETAGTARKSSLPASSPQPEAPTGSGR

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	13.91 RPM
bodymap2_adrenal	0.18 RPM	58.38 RPM
bodymap2_brain	0.09 RPM	10.06 RPM
bodymap2_breast	0.04 RPM	11.63 RPM
bodymap2_colon	0.10 RPM	12.18 RPM
bodymap2_heart	0.00 RPM	6.31 RPM
bodymap2_kidney	0.00 RPM	7.63 RPM
bodymap2_liver	0.00 RPM	6.17 RPM
bodymap2_lung	0.00 RPM	16.79 RPM
bodymap2_lymph_node	0.15 RPM	34.92 RPM
bodymap2_ovary	0.04 RPM	15.38 RPM
bodymap2_prostate	0.00 RPM	12.33 RPM
bodymap2_skeletal_muscle	0.00 RPM	11.55 RPM
bodymap2_testis	0.55 RPM	22.96 RPM
bodymap2_thyroid	0.02 RPM	14.50 RPM
bodymap2_white_blood_cells	0.06 RPM	119.19 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1172 was not detected

EST

2 EST(s) were mapped to retro_hsap_1172 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AA583854	21893326	21893745	99.3	416	2	412
DC330003	21893230	21893812	99.9	581	1	580

TSS

No TSS is located nearby retro_hsap_1172 retrocopy 5' end.

Lab

retro_hsap_1172 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1172 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_805
Gorilla gorilla	retro_ggor_912

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006775	1 retrocopy	retro_cjac_3926,
Homo sapiens	ENSG00000198055	1 retrocopy	retro_hsap_1172 ,
Gorilla gorilla	ENSGGOG00000009669	1 retrocopy	retro_ggor_912,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.39 RPM
CEU_NA11843	0.37 RPM
CEU_NA11930	0.39 RPM
CEU_NA12004	0.57 RPM
CEU_NA12400	0.67 RPM
CEU_NA12751	0.41 RPM
CEU_NA12760	0.54 RPM
CEU_NA12827	0.19 RPM
CEU_NA12872	0.30 RPM
CEU_NA12873	0.54 RPM
FIN_HG00183	0.38 RPM
FIN_HG00277	0.37 RPM
FIN_HG00315	0.47 RPM
FIN_HG00321	0.21 RPM
FIN_HG00328	0.28 RPM
FIN_HG00338	0.30 RPM
FIN_HG00349	0.34 RPM
FIN_HG00375	0.22 RPM
FIN_HG00377	0.43 RPM
FIN_HG00378	0.51 RPM
GBR_HG00099	0.41 RPM
GBR_HG00111	0.49 RPM
GBR_HG00114	0.53 RPM
GBR_HG00119	0.29 RPM
GBR_HG00131	0.34 RPM
GBR_HG00133	0.46 RPM
GBR_HG00134	0.74 RPM
GBR_HG00137	0.41 RPM
GBR_HG00142	0.44 RPM
GBR_HG00143	0.57 RPM
TSI_NA20512	0.65 RPM
TSI_NA20513	0.70 RPM
TSI_NA20518	0.42 RPM
TSI_NA20532	0.48 RPM
TSI_NA20538	0.23 RPM
TSI_NA20756	0.55 RPM
TSI_NA20765	0.48 RPM
TSI_NA20771	0.23 RPM
TSI_NA20786	0.42 RPM
TSI_NA20798	0.37 RPM
YRI_NA18870	0.74 RPM
YRI_NA18907	0.69 RPM
YRI_NA18916	0.55 RPM
YRI_NA19093	0.47 RPM
YRI_NA19099	0.61 RPM
YRI_NA19114	0.52 RPM
YRI_NA19118	0.81 RPM
YRI_NA19213	0.33 RPM
YRI_NA19214	0.42 RPM
YRI_NA19223	0.56 RPM

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Indel association:

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