RetrogeneDB ID: retro_ptro_805

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:20833959..20835573(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: GRK4
• Ensembl ID: ENSPTRG00000015853
• Aliases: None
• Description: G protein-coupled receptor kinase 4 [Source:HGNC Symbol;Acc:4543]

Sequence

>retro_ptro_805
ATGGAGCTCGAGAACATCGTAGCGGACACGGTGCTCCTCAAGGCCCGGGAAGGTGGCGGTGGAAATCGCAAAGGCAAAAG
CAAGAAATGGCGGCAGATGCTCCAGTTCCCCCACATCAGCCAGTGCGAAGAGCTGCGGCTCAGTCTCGAACGTGACTATC
ACAGCCTGTGCGAGCGGCAGCCCATCGGGCGCCTGCTGTTCTGAGAGTTCTGTGCCGCCAGGCCGGAGCTGAGCCGTTGC
ATCGCCTTCCAGGATGGGATGGCCGAGTATGAAGCGACCCCGGGTGAGAAGCGGAAGGCATGTGGGCGGCGGCTAATGCA
GAATTTTCTGAGCCACAGGTTCCTGACCTCATCCCTGAAGTCCCCCCGGCAGCTGGTGACGAACTGCACCCAGCGGCTGG
AGCAGGGGCCCTGCAAAGAACTCTCCCAGGAACTCACCCGGGTGACCCACGGGTACCTGAGCATGGCCCCTTTTGCCGAC
TACCTCAACAGCATCTACTTCAACCGTTTCCTGCAGTGGAAGTGGCTGGAAAGGCAGCCAGTGACCAAAAATACCTTCAG
GCAGTACCGAGTCCTGGGCAAAGGTGGCTTTGGGGAGGTGTGCGCCTGCCAGGTGCGGGCCACAGGCAAGATGTACGCCT
TCAAGAAGCTAGAGAAAAAGCGGATCAAGAAGCAGAAAGGGGAGGCCATGGCGCTGAACGAGAAGCAGATCCTGGAGAAA
GTGAACAGTAGATTTATAGTGAGCTTGGCCTACACCTGTGAGACCAAGGAGGCGCTGTGCCTGGTGCTGACGCTGATGAA
CGGGGGCGACCTCAATTTCCACATCTGCCACATGGGCCGGGCTGGCTTCCCCGAAGCGCAGGCCGTCTTCTACGTCCCGA
GATCTGCTTGCGGTCTGGAGGACCTGCACCGGGAGCGCAGAGTGTACAGGGACCTGAAGCCAGGAACATCTTGCTGGATG
ACCACGGCCACATCCTCGTCTCCGACCTGGGACTGGCTGTGCACGTGCCCGAGGGCCAGACCATCAAAGGCCGTGTGGGC
ACCATGAGCTACATGGCTCCACAGGTGGTGAAGAATGAACCGTACACTTTCAGCTCTGACTGTTGGGCGCTAGGCTGCCT
CCCGTAGGAGATGATTGCAGGCCAGTTGCCCTTCCAGCAGAGGAAGAAGAAGATCAAGCGGGAGGAGGTGGAGCGGCTGG
TGAAGGAGGACCCCGAGGAGTATTCCGAGCGCTTTTCCCCGCAGGCATGCTCACTCCGCTCACAGCTCCTCTGCAAGGAC
CCCGCTGAACGCCTGGGGTGTCGTGGGGGCAGTGCCCGCGAAGTGAAGGAGCACCCCCTCTTGAAGAAGCTGAACTTCAG
GCGGGTGGGAGCCGGCATGCTGGAGCCGCCCTTCAAGCCTGACCCTCGGGCCATTTGCTGCAAGGATGTTCTGGACATTG
AACAGTTCTCTAGGGTCAAGGGTGTGGAGCTGGAGCCTACCGACCAAGACTTCTACCAGAAGTTTGCCCTGTGGCAGCGT
GCCCATCCCCTGGCAGAACGGGATGGTGGAGACTGAGTGCTTCCAGGAGCTGAATGTCTTTGGGCTGGATGGCTCAGTTC
CCCCAGACCTGGAC

Alignment

ORF - retro_ptro_805 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.06 %
• Parental protein coverage: 93.25 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MELENIVANSLLLKARQGGYGKKSGRSKKWREILTLPPVSQCSELRHSIEKDYSSLCDKQPIGRLLFRQF
          MELENIVA...LLKAR.GG.G...G.SKKWR..L..P..SQC.ELR.S.E.DY.SLC..QPIGRLLF..F
Retrocopy MELENIVADTVLLKAREGGGGNRKGKSKKWRQMLQFPHISQCEELRLSLERDYHSLCERQPIGRLLF*EF

Parental  CDTKPTLKRHIEFLDAVAEYEVADDEDRSDCGLSILDRFFNNKLAAP-LPEIPP-DVVTECRLGLKEDNP
          C...P.L.R.I.F.D..AEYE....E.R..CG......F..........PE.PP...VT.C...L.E..P
Retrocopy CAARPELSRCIAFQDGMAEYEATPGEKRKACGRRLMQNFLSHRFLTS<IPEVPP>QLVTNCTQRL-EQGP

Parental  SKKVFEECTRVAHNYLRGEPFEEYQESSYFSQFLQWKWLERQPVTKNTFRHYRVLGKGGFGEVCACQVRA
          .K....E.TRV.H.YL...PF..Y..S.YF..FLQWKWLERQPVTKNTFR.YRVLGKGGFGEVCACQVRA
Retrocopy CKELSQELTRVTHGYLSMAPFADYLNSIYFNRFLQWKWLERQPVTKNTFRQYRVLGKGGFGEVCACQVRA

Parental  TGKMYACKKLQKKRIKKRKGEAMALNEKRILEKVQSRFVVSLAYAYETKDALCLVLTIMNGGDLKFHIYN
          TGKMYA.KKL.KKRIKK.KGEAMALNEK.ILEKV.SRF.VSLAY..ETK.ALCLVLT.MNGGDL.FHI..
Retrocopy TGKMYAFKKLEKKRIKKQKGEAMALNEKQILEKVNSRFIVSLAYTCETKEALCLVLTLMNGGDLNFHICH

Parental  LGNPGFDEQRAVFYAAELCCGLEDLQRERIVYRDLKP-ENILLDDRGHIRISDLGLATEIPEGQRVRGRV
          .G..GF.E..AVFY.....CGLEDL.RER.VYRDLKP..NILLDD.GHI..SDLGLA...PEGQ...GRV
Retrocopy MGRAGFPEAQAVFYVPRSACGLEDLHRERRVYRDLKP<RNILLDDHGHILVSDLGLAVHVPEGQTIKGRV

Parental  GTVGYMAPEVVNNEKYTFSPDWWGLGCLIYEMIQGHSPFKKYKEKVKWEEVDQRIKNDTEEYSEKFSEDA
          GT..YMAP.VV.NE.YTFS.D.W.LGCL..EMI.G..PF...K.K.K.EEV....K.D.EEYSE.FS..A
Retrocopy GTMSYMAPQVVKNEPYTFSSDCWALGCLP*EMIAGQLPFQQRKKKIKREEVERLVKEDPEEYSERFSPQA

Parental  KSICRMLLTKNPSKRLGCRGEGAAGVKQHPVFKDINFRRLEANMLEPPFCPDPHAVYCKDVLDIEQFSVV
          .S....LL.K.P..RLGCRG..A..VK.HP..K..NFRR..A.MLEPPF.PDP.A..CKDVLDIEQFS.V
Retrocopy CSLRSQLLCKDPAERLGCRGGSAREVKEHPLLKKLNFRRVGAGMLEPPFKPDPRAICCKDVLDIEQFSRV

Parental  KGIYLDTADEDFYARFA-TGCVSIPWQNEMIESGCFKDINKSESEEALPLDLD
          KG..L...D.DFY..FA..G.V.IPWQN.M.E..CF...N........P.DLD
Retrocopy KGVELEPTDQDFYQKFA>CGSVPIPWQNGMVETECFQELNVFGLDGSVPPDLD

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
SRP007412_brain_prefrontal_cortex	1.64 RPM	19.52 RPM
SRP007412_cerebellum	1.22 RPM	17.82 RPM
SRP007412_heart	0.20 RPM	9.06 RPM
SRP007412_kidney	0.71 RPM	6.38 RPM
SRP007412_liver	0.46 RPM	2.59 RPM
SRP007412_testis	20.55 RPM	348.50 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_805 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_805 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_805 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1172
Gorilla gorilla	retro_ggor_912

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000015019	1 retrocopy	retro_lafr_967,
Pan troglodytes	ENSPTRG00000015853	1 retrocopy	retro_ptro_805 ,