RetrogeneDB ID: retro_pabe_723

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 11:85614084..85615925(+)
• Located in intron of: ENSPPYG00000003758

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDON
• Ensembl ID: ENSPPYG00000004042
• Aliases: None
• Description: cell adhesion associated, oncogene regulated [Source:HGNC Symbol;Acc:17104]

Sequence

>retro_pabe_723
ATTCATCCTTCCCCATGACATCTAACTGCAGGAAATTGACTGAAAGTCAGTGGGGTTATCATGGAAGATACTGGGCTGTA
TCAGTGTTTAACAGATAATGGGACTGGATTTATGCAGTCTACTGGAAGACTTGAAATTGAAAAAAGACAATGGATTCAAG
CCAGTTATAATCATGGCACCAATAAGCACAAAGGTGGTATGTGGAGACTTTGTCACTGTGTCCTGCAATGCCACTGGGCT
GCCAGTTCCAGTCATTCCTTGGTTATGATAGCTATGGATTAATAGCCAGCCATCTGTCTTAAGTCCTTAGATCTAAGTCC
CCAAAGTCACACTTATCAAGACCTGGAATCTTGGACCTGAAGCCTGTCTACTTCATCATGTCCCAAGTTGGCTCAAGCTC
TCTCCTTATTCAGGATGTGACTCAGAAACATGTGGGGAAACACATATAGGAAGCTCCAGATGGACACAGTACCATGCTGG
GAGAAGCATCTCTCATAGTTGTTCCTTTTGAAACAAATACAAAAGTGGAAATAGTCACACTTTCTGCTGCTACTCAGAAT
GATGAAAGAAATAAAAGAGATGGTTCAGAAACTGGATTGAGCTCATGTCCAGTTAAGGTACATCCCAGTGCAGTGGAATC
AGCACCAGAGAAAAATGTTAATGGCATCGCTATTCCTGACGTCCCCATCATACTGATCTCCTGACAGAGCCACACACCAG
ATATATACAACCTGGTGTGGAGGGCAGGCAGGAATGGTGGGCTATCTATTAATGTGTATTTTATGAAATATCAAAAGATG
AACAATGGGGTTGATTTGGTAGGAAATGGGCATACAGTTCGAGTCCCAGGTAGTGAAAATGAGCTCCATTTAGCTGAAAT
AGGGCCATCTAGTCTTTACAAAGTCTTGATAGTAGCAAGAAGTGGAGCAGGTGAAGGACAAACTGCCATGCTTACCTTCT
GAAACAGCAAAGAAAAAAGAGCATTGACAAAAAACACCCAGGCATCCTGTCCACCCATGGGCATCCATAAGTATCCTGTT
GTTTCAGAAGCTGCAAACAATTTTAGAGTGGTACCTACAGATTCTTGAAGGCACAGCGAAGTTCCAGAGGCACCAAATGG
CCCTACTGTCTCCAATGCATCAGAGACATTAGTCTATGTCACTCAGATTCTTCTGGAAAATTGGGTTTCTCCAATCACTG
CTTTCAAAGTTGAATATGAAAGGATGAGGACCAGTGATTGGCTGGTGGCAGCTGAAGATATCCTTGCTTCCAGAATTTCC
ATGGAAGTTTATAGCTTAGAACCGGGTTCAACATACAAATTGAGAGTCATTGCTATCAATCATTAGGAAGGGAGTTTTAA
GAGTCCAGAATCTTGTCCTTATCAGGTGGCTGGGTTCCCCAGTCATTTCTTCAGCCATCCAATAATGGAACTCACATTGC
CTACACAGAGGCTGTCAGTGTTGCCCAGATAATGCTAAAGTGGACATACATTCCATGAAGTAACAATAACACTTCCATTC
TTTTATATCTATTACTGACCATCAGATAGTGACAATGACAGTGATTACAAGAGGGATGTAGTAGAAGGTTCAAAGGAGTG
GCACATGATTGGCCATCTGCTGTCAGAAACTTCCTATGGCATTAAAATGCAGTGCTTCAGTGAAGAAGAAAGTGAGTTTA
GCAGTGTGATGATCTGTGAGACTAAAGTAAAACGTGTTCCTGGAGCTTCTGAGTATCTGAAAGGCTTGAGTATCCCTCTG
AATTCTTCAGGAAGTGAAGGGAATGTGAGGCCAGCAACCAGCCCTGCCAGAAGCAGTGACGTGTTGTATCTGATCCTTGG
C

Alignment

ORF - retro_pabe_723 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.39 %
• Parental protein coverage: 55.58 %
• Number of stop codons detected: 10
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  IHPSARHLTAGNGLKISGVTVEDVGMYQCVADNGIGFMHSTGRLEIEN-DSGFKPVIITAPVSAKVADGD
          IHPS..HLTAGN.LK.SGV..ED.G.YQC..DNG.GFM.STGRLEIE..D.GFKPVII.AP.S.KV..GD
Retrocopy IHPSP*HLTAGN*LKVSGVIMEDTGLYQCLTDNGTGFMQSTGRLEIEK>DNGFKPVIIMAPISTKVVCGD

Parental  FVTLSCNASGLPVPVIRW-YDSHGLITSHPSQVLRSKSRKSQLSRPEGLNLEPVYFIMSQAGASSLHIQD
          FVT.SCNA.GLPVPVI.W.YDS.GLI.SH.S.VLRSKS.KS.LSRP..L.L.PVYFIMSQ.G.SSL.IQD
Retrocopy FVTVSCNATGLPVPVIPW>YDSYGLIASHLS*VLRSKSPKSHLSRPGILDLKPVYFIMSQVGSSSLLIQD

Parental  VTQEHAGKYICEATNEHGTTQAEASLMVVPFETNTKAEIATLPDAAQNDERNKRDGSETGLLSSFPVKVH
          VTQ.H.GK.I.EA...H.T...EASL.VVPFETNTK.EI.TL..A.QNDERNKRDGSETGL.SS.PVKVH
Retrocopy VTQKHVGKHI*EAPDGHSTMLGEASLIVVPFETNTKVEIVTLSAATQNDERNKRDGSETGL-SSCPVKVH

Parental  PSAVESAPEKNASGISVPDAPIILSPPQTHTPDTYNLVWRAGKDGGLPINAYFVKYRKLDDGVGMVGSWH
          PSAVESAPEKN..GI..PD.PIIL...Q.HTPD.YNLVWRAG..GGL.IN.YF.KY.K...GV..VG..H
Retrocopy PSAVESAPEKNVNGIAIPDVPIILIS*QSHTPDIYNLVWRAGRNGGLSINVYFMKYQKMNNGVDLVGNGH

Parental  TVRVPGSENELHLAELEPSSLYEVLMVARNAAGEGQPAMLTFRTSKEKTASSKNTQASSPPVGIPKYPVV
          TVRVPGSENELHLAE..PSSLY.VL.VAR..AGEGQ.AMLTF..SKEK.A..KNTQAS.PP.GI.KYPVV
Retrocopy TVRVPGSENELHLAEIGPSSLYKVLIVARSGAGEGQTAMLTF*NSKEKRALTKNTQASCPPMGIHKYPVV

Parental  SEAANNNFGVVLTDSSRHSGVPEAPDRPTVSTASETSVYVTWIPRANGGSPITAFKVEYKRMRTSNWLVA
          SEAA.NNF.VV.TDS.RHS.VPEAP..PTVS.ASET.VYVT.I...N..SPITAFKVEY.RMRTS.WLVA
Retrocopy SEAA-NNFRVVPTDS*RHSEVPEAPNGPTVSNASETLVYVTQILLENWVSPITAFKVEYERMRTSDWLVA

Parental  AEDIPPSKLSVEVRSLEPGSTYKFRVIAINHYGESFRSSASRPYQVAGFPNRFSNRPI-TGPHIAYTEAV
          AEDI..S..S.EV.SLEPGSTYK.RVIAINH...SF.S..S.PYQVAGFP..F...PI..G.HIAYTEAV
Retrocopy AEDILASRISMEVYSLEPGSTYKLRVIAINH*EGSFKSPESCPYQVAGFPSHFFSHPI<NGTHIAYTEAV

Parental  SDTQIMLKWTYIPSSNNNT-PIQGFYIYYRPTDSDNDSDYKRDVVEGSKQWHMIGHLQPETSYDIKMQCF
          S..QIMLKWTYIP.SNNNT.P....Y......D.D...DYKRDVVEGSK.WHMIGHL..ETSY.IKMQCF
Retrocopy SVAQIMLKWTYIP*SNNNT>PFFYIYY*PSDSDNDS--DYKRDVVEGSKEWHMIGHLLSETSYGIKMQCF

Parental  NEGGESEFSNVMICETKVKRVPGASEYPVKDLSTPPNSLGSGGNVGP-TTLARSSDMLYLIVG
          .E..ESEFS.VMICETKVKRVPGASEY..K.LS.P.NS.GS.GNV.P.T..ARSSD.LYLI.G
Retrocopy SE-EESEFSSVMICETKVKRVPGASEY-LKGLSIPLNSSGSEGNVRPATSPARSSDVLYLILG

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	3.65 RPM
SRP007412_cerebellum	0.00 RPM	27.48 RPM
SRP007412_heart	0.00 RPM	2.89 RPM
SRP007412_kidney	0.00 RPM	1.03 RPM
SRP007412_liver	0.00 RPM	0.49 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_723 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_723 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_723 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_872

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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,