RetrogeneDB ID: retro_ptro_607

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:49209281..49211724(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDON
• Ensembl ID: ENSPTRG00000004452
• Aliases: None
• Description: None

Sequence

>retro_ptro_607
AATATTGCTCCAGGAAGCAACTGGAAGAAGGTTATATTCTCATGTTGCGACAGATAGCATTGACCCAGTAGACTCTGGAA
ACTATTCCCGCATGGTGGGAAACAAGACTGGAGATGTAAAATATGTGACATACATGGTTAATGTGCTTGAATATGCTTCC
ATTTATAAAGGACTACAGGATCAGTCTCTGGGTGCCACAGCACATTTTACCTGTCATATTCATGGAAACCCAGCCGCCAA
CCATACTTGGTTTTATATTGCACAGCCTATTCATCCTTCCCCATGACATCTAACTGCAGGAAATTGACTGAAAGTCAGTG
GGGTTATCATGGAAGATACTGGGCTGTATCAGTGTTTAACAGATAATGGGACTGGATTTATGCAGTCTACTGGAAGACTT
GAAATTGGAAAAAGACAATGGATTCAAGCCAGTTATAATCATGGCACCAATAAGTGCAAAGGTGGTATGTGGAGTCTTTG
TCACTGTGTCCTGCAATGCCACTGGGCTGCCAGTTCCAGTCATTCCTTGGTTATGACAGCTATGGATTAATAGCCAGCCA
TCTGTCTTAAGTCCTTAGATCTAAGTCCCCAAAGTCACACTTATCAAGACCTGGAATCTTGGACCTGAAGCCTATCTACT
TTATCATGTCCCAAGTTGGCTCTAGCTGTCTCCATATTCAGGATGTGACTCAGAAACATGTGGGGAAACACATATAGGAA
GCTGCAGATGGACACAGTACCATGCAGGGAGAAGCATCTCTCATGGTTGTTCCTTTTGAAACAAATACAAAAGTGGAAAC
AGTCACACTTTCTGCTGCTACTCAGAATGATGAAAGAAATAAAAGAGATGGTTCAGAAACTGGATTGAGCTCATGTCCAG
TTAAGGTACATCCCAGTGCAGTGGAATCAGCATCAGAGAAAAATGTTAATGGCATCACTGTTCCTGACGCCCCCATCATA
CTGATCTCTTGACAGACCCACACACCAGATACGTACAACCTGGTGTGGAGGGCAGGCAGGAATGGTAGGCTATCCATTAA
CGTGTATTTTATGAAATATCAAAAGATGAACAATGGGATTGGTTTGGTAGGAATTGGGCATACGGTTCGAGTCCCAGATA
GTGAAAATAAGCTCCATTTAGCTGAACTAGGGCCGTCTAGTCTTTACAAAGTCTTGATAGTAGCAAGAAGTGGAGCAGGT
GAAGGACAAACTGCCATGCTTACCTTCTGAAACAGCAAAGAAAAAAGAGCATTGACAAAAAACACCCAGGCATCCTGTCC
ACCCATGGGCATCCATAAGTATCCTGTTGTTTCAGAAGCTGCAAATAATTTTGGAGTGGTACTTACAGATTCTTGAAGGC
ACAGCGAAGTTCCAGAGGTACCAAATGGCCCTACTATCTCCAATGCATCAGAGACATTGGTCTATGTCACTCAGATTCTT
CTGGAAAATTGGGTTTCTCCAATCGCTGCTTTCAAAGTTGAATATGAAAGGATGAGGACCAGTGATTGGCTGGTGGCAGC
TGAAGATATCCTTGCTTCCAAAATTTCCATTGAAGTTCGTAGCTTAGAACTGAGTTCAACATACAAATTGAAAGTCATTG
CTATCAATCATTAGGAAGGGAGTTTTAAGAGTGCAGAATCTTGTCCTTATCAGGTGGCTGGCTTCCCCAGTCATTTTTTC
AGCCATCCAATAATGGAACTCACATTGCCTACACAGAGGCTGTCAGTGTTGCCCAGATAGTGCTAAAGTGGACGTACATT
CCATGAAGTAGCAATAACACTTCCATTCTTTTATATCTATTACTGACCATCAGATAGTGACAATGACAGTGATTACAAGA
GGGATGTAGTGGAAGGTTCAAAGGAGCGGCACATGATTGGCCATCTGCTGTCAGAAACTTCCTATGGCATTAAAATGCAG
TGCTTCAGTGAAGGAGAAGAAAGTGAGTTTATCAATGTGGTGATCTGCGAGAGTAAAGTAAAACGTGTTCCTGGAGCTTC
TGAGTATCCTAAAGGCTTGAGTATCCCTCTGAATTATTCAGGAAGTGAAGGAAATGTGAGGCCAGCAACCAGCCCTGCCA
GAAGCAGTGACATGTTATATCTGATCCTTGGCTGTATGCTGGGTGTCATGGTCCTTATTTTTGTGGCTTTTTATTGCAAT
GTGCCTGTGGAAGAATCACCCACAGAATATCATAGAGAAATATGACCCACTGGGTTATCTCTACCAGGGATCAGATATTA
ATGGGCAGATGGTGGAATACACCACTCTCTCAGGAGCAAATGAGATAAATGGAAATGTTCATGGAGGCTTCCTGAGCCAT
GGCAGTCTCAGCAGTGGCTCTTCCCACCTTCACCATAAGGTCTCCAATGGAGTCAATGCAACTGTGAATGGGAGCTTAAA
TGGAGGACTTTACTCTGAGCACACTAACTCTCTAACCAGGACA

Alignment

ORF - retro_ptro_607 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.09 %
• Parental protein coverage: 64.92 %
• Number of stop codons detected: 10
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  DIAPGSNW-RRLYSHLATDSVDPADSGNYSCMAGNKSGDVKYVTYMVNVLEHASISKGLQDQIVSLGATV
          .IAPGSNW.RRLYSH.ATDS.DP.DSGNYS.M.GNK.GDVKYVTYMVNVLE.ASI.KGLQDQ..SLGAT.
Retrocopy NIAPGSNW>RRLYSHVATDSIDPVDSGNYSRMVGNKTGDVKYVTYMVNVLEYASIYKGLQDQ--SLGATA

Parental  HFTCDVHGNPAPNCTWFHNAQPIHPSARHLTAGNGLKISGVTVEDVGMYQCVADNGIGFMHSTGRLEI-E
          HFTC..HGNPA.N.TWF..AQPIHPS..HLTAGN.LK.SGV..ED.G.YQC..DNG.GFM.STGRLEI.E
Retrocopy HFTCHIHGNPAANHTWFYIAQPIHPSP*HLTAGN*LKVSGVIMEDTGLYQCLTDNGTGFMQSTGRLEI>E

Parental  NDGGFKPVIIMAPVSAKVADGDFVTLSCNASGLPVPVIRW-YDSHGLITSHPSQVLRSKSRKSQLSRPEG
          .D.GFKPVIIMAP.SAKV..G.FVT.SCNA.GLPVPVI.W.YDS.GLI.SH.S.VLRSKS.KS.LSRP..
Retrocopy KDNGFKPVIIMAPISAKVVCGVFVTVSCNATGLPVPVIPW>YDSYGLIASHLS*VLRSKSPKSHLSRPGI

Parental  LNLEPVYFVMSQAGASSLHIQAVTQEHAGKYICEATNEHGTTQAEASLMVVPFETNTKAETVTLPDAAQN
          L.L.P.YF.MSQ.G.S.LHIQ.VTQ.H.GK.I.EA...H.T.Q.EASLMVVPFETNTK.ETVTL..A.QN
Retrocopy LDLKPIYFIMSQVGSSCLHIQDVTQKHVGKHI*EAADGHSTMQGEASLMVVPFETNTKVETVTLSAATQN

Parental  DDRSKRDGSETGLLSSFPVKVHPSAVESAPEKNASGISVPDAPIILSPPQTHTPDTYNLVWRAGKDGGLP
          D.R.KRDGSETGL.SS.PVKVHPSAVESA.EKN..GI.VPDAPIIL...QTHTPDTYNLVWRAG..G.L.
Retrocopy DERNKRDGSETGL-SSCPVKVHPSAVESASEKNVNGITVPDAPIILIS*QTHTPDTYNLVWRAGRNGRLS

Parental  INAYFVKYRKLDDGVGMLGSWHTVRVPGSENELHLAELEPSSLYEVLMVARSAAGEGQPAMLTFRTSKEK
          IN.YF.KY.K...G.G..G..HTVRVP.SEN.LHLAEL.PSSLY.VL.VARS.AGEGQ.AMLTF..SKEK
Retrocopy INVYFMKYQKMNNGIGLVGIGHTVRVPDSENKLHLAELGPSSLYKVLIVARSGAGEGQTAMLTF*NSKEK

Parental  TASSKNTQASSPPVGIPKYPAVSEAANNNFGVVLTDSSRHSGVPEAPDRPTISTASETSVYVTWIPRANG
          .A..KNTQAS.PP.GI.KYP.VSEAA.NNFGVVLTDS.RHS.VPE.P..PTIS.ASET.VYVT.I...N.
Retrocopy RALTKNTQASCPPMGIHKYPVVSEAA-NNFGVVLTDS*RHSEVPEVPNGPTISNASETLVYVTQILLENW

Parental  GSPITAFKVEYKRMRTSNWLVAAEDIPPSKLSVEVRSLEPGSTYKFRVIAINHYGESFRSSASRPYQVAG
          .SPI.AFKVEY.RMRTS.WLVAAEDI..SK.S.EVRSLE..STYK..VIAINH...SF.S..S.PYQVAG
Retrocopy VSPIAAFKVEYERMRTSDWLVAAEDILASKISIEVRSLELSSTYKLKVIAINH*EGSFKSAESCPYQVAG

Parental  FPNRFSNRPI-TGPHIAYTEAVSDTQIMLKWTYIPSSNNNT-PIQGFYIYYRPTDSDNDSDYKRDVVEGS
          FP..F...PI..G.HIAYTEAVS..QI.LKWTYIP.S.NNT.P....Y......D.D...DYKRDVVEGS
Retrocopy FPSHFFSHPI<NGTHIAYTEAVSVAQIVLKWTYIP*SSNNT>PFFYIYY*PSDSDNDS--DYKRDVVEGS

Parental  KQWHMIGHLQPETSYDIKMQCFNEGGESEFSNVMICETKVKRVPGASEYPVKDLSTPPNSLGSGGNVGPA
          K..HMIGHL..ETSY.IKMQCF.EG.ESEF.NV.ICE.KVKRVPGASEYP.K.LS.P.N..GS.GNV.PA
Retrocopy KERHMIGHLLSETSYGIKMQCFSEGEESEFINVVICESKVKRVPGASEYP-KGLSIPLNYSGSEGNVRPA

Parental  TSPARSSDMLYLIVGCVLGVMVLI-LMVFIAMCLWKNRQQNTIQKYDPPGYLYQGSDVNGQMVDYTTLSG
          TSPARSSDMLYLI.GC.LGVMVLI.L..FIAMCLWKN..QN.I.KYDP.GYLYQGSD.NGQMV.YTTLSG
Retrocopy TSPARSSDMLYLILGCMLGVMVLI>LWLFIAMCLWKNHPQNIIEKYDPLGYLYQGSDINGQMVEYTTLSG

Parental  ASQINGNVHGGFLTNGGLSSGYSHLHHKVPNGVNGIVNGSLNGGLYSGHTNSLTRT
          A..INGNVHGGFL..G.LSSG.SHLHHKV.NGVN..VNGSLNGGLYS.HTNSLTRT
Retrocopy ANEINGNVHGGFLSHGSLSSGSSHLHHKVSNGVNATVNGSLNGGLYSEHTNSLTRT

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	0.00 RPM	8.51 RPM
SRP007412_cerebellum	0.00 RPM	95.64 RPM
SRP007412_heart	0.00 RPM	15.07 RPM
SRP007412_kidney	0.00 RPM	11.06 RPM
SRP007412_liver	0.00 RPM	5.70 RPM
SRP007412_testis	0.00 RPM	23.50 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_607 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_607 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_607 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000064309	1 retrocopy	retro_hsap_872,
Macaca mulatta	ENSMMUG00000007628	1 retrocopy	retro_mmul_1079,
Pongo abelii	ENSPPYG00000004042	1 retrocopy	retro_pabe_723,
Pan troglodytes	ENSPTRG00000004452	1 retrocopy	retro_ptro_607 ,