RetrogeneDB ID: retro_ptro_833

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:76917405..76920526(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DHX9
• Ensembl ID: ENSPTRG00000001759
• Aliases: None
• Description: None

Sequence

>retro_ptro_833
TCCTGGGACCAAGGAGCCAACTTGAAGGATTACTACTCAAGAAAGGAAGAACAAGAAGTGCAAGCGACTCTAGAGTCAGA
AGAGGTGGATTTAAATGCTGGGCTTCATGGAAACTGGACCTTGGAAAATGCTAAAACTCATCTAAACCAATATTTTCAGA
AAGAAAAAAGCCAAGGAGAATATAAGTACACCCAAGTGGGTCCTGATCACAACAGGAGCTTTACTGCAGAAATAACCATT
TACATCAAGCAGCTGGGCAGAAGGATTTCTGCACATGAACATGGATCAAATAAGAAATTGGCAGCACAGTCCTGTGCCCT
GTCACTAGTCAGACAACTCTACCATCTTGGAGTGGTTGAAGCTTACTTCGGACTTACAAAGAAGGAAGGAGAGAGAGTGG
AACCTTACAAGGTAAACCTCTCTCATGATTTACAGCATCAGCCACAAAACATCATTTGAGAGCTAAATCTTGAGATTATG
CCCCCGCCTGAAGATCCTTCTATGCCAGTTGCACTCAACATTGGCAAATTGGCTCACTTTGAACCATCTCGGTGACAAAA
CCAAGTGTGTATAGTTCCTCGGTCACCTCCACAATCCAGATGGAATCCTTGGACTACTAGCAACATTGCTGAGGGACCTC
TGGGCTTTTGCTTCTCCAGAGCAAATAAGCTTGGACCTCAAGAATGAATTGGTGTACCAGTTGGAACAGGATCATGATTT
GCCAGCAATCTTGCAGGAGCGAGAGTTACTGCCTGTGAAGAAATTTGAAAGTGAGATTCTGGAAGCAATCAGTCAAAATT
CAGTTGTCATTATTAGAGGGGCTGCTGGATGTGGTAAAACCACACAGGTTCCCCAGTTCATTCTAGATGACTTTATCCAG
AATGACTGACAGCAGAGTGTAACATTGTAGTAACTCAGCCCAGAAGAATCAGTGTAGTTTCCGTGGCAGAGCGAGTTGCA
TTTGAGAGAGGAGAAGAGTCTGTAAAAAGCTGTGGTTACAGTGTTCAGTTTGAGTCTGTACTTCCTTGTCCTCATGCCAG
TATAATGCTTTGTACTGTAGGTGTGCTCCTAAGAAAATTAGAAGCAGGCATTTGAGGAATCAGTCATGTAATTGTAGATG
AAATACATGGAAGAGACATTAATACTGACTTCCTTTTGGTAGTACTGCGTGAAGTTGTTTCAGCTTACCCTGAAGTTCTC
ATTGTTCTTATGTCCACTTCTATTGATACCAGCATGTTGTGTGAATATTTCTTCAATTGCCCCATCATTTAAGTGTATGG
GAGGACTTACCCAGTTCAAGAATATTTTCTGGAAGACTGCATTCAGATGACCCACTTTGTTCCTTCACCGAAAACCAAGA
AGAAGGACAAGGATGATGATGGTGGTGAGGATGATAATGCAAATTGCAACTTGATCCGTGGTGATGAATATGGTCCAGAA
ACAAGGATGAGCATGTCTCAATTGAATGAAAAAGAAACTCCTTTTGAACTCGTCGAAGCTCTCTTTAAGTACATTGAAAC
CCTTAATATTCCCAGAGCTGTGTTGGTATTTTTGCCTGGCTGGAATTTGATTTATACTATGCAGAAGCATTTGGAAATGA
ATCCACATTTTGGAAGCCATCAGTATCAGATTCTACCTCTGCATTCTCAGATTCCTCGACAGGAACAGCGCAAAGTGTTT
GATCCAGTACCAGTTGGAGTAACCAAGGTTATTTTGTCAACAAATATTGCTGAAACAAGCATTATCATAAATGATGTTGT
TTATGTCGTTGACTCCCGCAAGCAGAAAGTGAAACTCTTCGCTACTCACAACAATATGACCAACTATGCTACAGTGTGGG
GATCAAAAACAAACCTTGAACAGCGGAAAGGGCGAGCTGGCCGAATACGGCCTGGATTCTGCTTTCACCTCTGCAGCCGA
GCTCGTTTTGAGAGACTTGAAACCCACATGACACCAGAGATGTTCCAAACACCATTGCATGAAGTTGCTCTTAGCATAAA
ACTTCTGTGTCTAGTTGGAATTGGCCAGTTTCTGGCCAAAGCAATTGAAACTCTCCCTTTGGATGCTGTGATTGAAGCAG
AACACACTCTTAGAGAGCTTGATGCATTAGATGCCAATGATGATTTGACTCCATTGGGGCGAATCCTGGCTAACCTCCCC
ATTGAGCCTCGTTTTGGCAAAATGATGATAATGGTGTGTATTTTCTATGTGGGAGATGCTATCTGTACCATTCCTGCTTC
TACCTGCTTTCCAGAGCCTTTTATCAATGAAGGAAAGTGGCTGGGCTACAACCATTGAAATTTTGCTGGAAACGGATTTT
CTCATCATGTAGCCCTTTTATCAGTATTCCAAGCCGGAGATGATACTAGAATGGGTGGAGAAGAAGCAGAAATACGTTTT
TGTGCGCACAAAAGACTTAATATGGCTACACTAAGAATGACTTGGGAAGTCAAAGTTCAGCTCAAAGAGATTCTGATTAA
TTCTGGGTTTCCAGAAGATTGTTTGGTGACACAAGTGTTTACTAACACTGGACCAGATAATAATTTGGATGTTGTTATCT
CTCTTCCTGGCCTTTGGTGTGTACCCCAATGTATGCTATCATAAGGAAAAGACAAAGATTCTCACCACTGAAGGGTGTAA
TGCACTTATCCACAAATCATCTGTTAATTGTCCTTTTAGTAGCCAAGACATGAAGTACCCATCTCCCTTCTTTGCATTTG
GTGAAAAGATTCGAACTCGAGCCATCTCTGCTAAAGGCATCACTTTAGTCACCCCACTACAGTTGCTTCTCTTTGCCTCC
AAGAAAGTCCAATCTGATGGGCAGATTGTGCTTGCAGATGACTGGATTAAACTGCAAATATCTCATGAAGCTGCTGCCTG
CATCACCGCTCTCCAGGCAGCCACTGAGGCTCTGGTTGTTGAAGTAACCAAACAACCTGCTATCATCAGCCAGTTGGACC
CCGTAAATGAAAGTATACTGAACATGATCCGTCAAATCTCTAGACCCTCAGCTGCTGATATCAACCTTATGATTGGCAGT
ACATGGTATGGAGATGGTCCAGGTCCTCCTAAGATGGCCCGATATGACAATGGAAGCGGATATAGAAGGGGAGGTTCTAG
T

Alignment

ORF - retro_ptro_833 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.86 %
• Parental protein coverage: 82.05 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TWDRGANLKDYYSRKEEQEVQATLESEEVDLNAGLHGNWTLENAKARLNQYFQKEKIQGEYKYTQVGPDH
          .WD.GANLKDYYSRKEEQEVQATLESEEVDLNAGLHGNWTLENAK..LNQYFQKEK.QGEYKYTQVGPDH
Retrocopy SWDQGANLKDYYSRKEEQEVQATLESEEVDLNAGLHGNWTLENAKTHLNQYFQKEKSQGEYKYTQVGPDH

Parental  NRSFIAEMTIYIKQLGRRIFAREHGSNKKLAAQSCALSLVRQLYHLGVVEAYSGLTKKKEGETVEPYKVN
          NRSF.AE.TIYIKQLGRRI.A.EHGSNKKLAAQSCALSLVRQLYHLGVVEAY.GLTKK.EGE.VEPYKVN
Retrocopy NRSFTAEITIYIKQLGRRISAHEHGSNKKLAAQSCALSLVRQLYHLGVVEAYFGLTKK-EGERVEPYKVN

Parental  LSQDLEHQLQNIIQELNLEILPPPEDPSVPVALNIGKLAQFEPSQRQNQVGVVPWSPPQSNWNPWTSSNI
          LS.DL.HQ.QNII.ELNLEI.PPPEDPS.PVALNIGKLA.FEPS..QNQV..VP.SPPQS.WNPWT.SNI
Retrocopy LSHDLQHQPQNII*ELNLEIMPPPEDPSMPVALNIGKLAHFEPSR*QNQVCIVPRSPPQSRWNPWTTSNI

Parental  DEGPL-AFATPEQISMDLKNELMYQLEQDHDLQAILQERELLPVKKFESEILEAISQNSVVIIRGATGCG
          .EGPL.AFA.PEQIS.DLKNEL.YQLEQDHDL.AILQERELLPVKKFESEILEAISQNSVVIIRGA.GCG
Retrocopy AEGPL>AFASPEQISLDLKNELVYQLEQDHDLPAILQERELLPVKKFESEILEAISQNSVVIIRGAAGCG

Parental  KTTQVPQFILDDFIQND-RAAECNIVVTQPRRISAVSVAERVAFERGEEPGKSCGYSVRFESILPRPHAS
          KTTQVPQFILDDFIQND...AECNIVVTQPRRIS.VSVAERVAFERGEE..KSCGYSV.FES.LP.PHAS
Retrocopy KTTQVPQFILDDFIQND<LTAECNIVVTQPRRISVVSVAERVAFERGEESVKSCGYSVQFESVLPCPHAS

Parental  IMFCTVGVLLRKLEAGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPEVRIVLMSATIDTSMFCEYF
          IM.CTVGVLLRKLEAGI.GISHVIVDEIH.RDINTDFLLVVLR.VV.AYPEV.IVLMS..IDTSM.CEYF
Retrocopy IMLCTVGVLLRKLEAGI*GISHVIVDEIHGRDINTDFLLVVLREVVSAYPEVLIVLMSTSIDTSMLCEYF

Parental  FNCPIIEVYGRTYPVQEYFLEDCIQMTHFVPPPKDKKKKDKDDDGGEDDDANCNLICGDEYGPETRLSMS
          FNCPII.VYGRTYPVQEYFLEDCIQMTHFVP.PK.KKK.DKDDDGGEDD.ANCNLI.GDEYGPETR.SMS
Retrocopy FNCPII*VYGRTYPVQEYFLEDCIQMTHFVPSPKTKKK-DKDDDGGEDDNANCNLIRGDEYGPETRMSMS

Parental  QLNEKETPFELIEALLKYIETLNVPGAVLVFLPGWNLIYTMQKHLEMNPHFGSHRYQILPLHSQIPREEQ
          QLNEKETPFEL.EAL.KYIETLN.P.AVLVFLPGWNLIYTMQKHLEMNPHFGSH.YQILPLHSQIPR.EQ
Retrocopy QLNEKETPFELVEALFKYIETLNIPRAVLVFLPGWNLIYTMQKHLEMNPHFGSHQYQILPLHSQIPRQEQ

Parental  RKVFDPVPVGVTKVILSTNIAETSITINDVVYVIDSCKQKVKLFTAHNNMTNYATVWASKTNLEQRKGRA
          RKVFDPVPVGVTKVILSTNIAETSI.INDVVYV.DS.KQKVKLF..HNNMTNYATVW.SKTNLEQRKGRA
Retrocopy RKVFDPVPVGVTKVILSTNIAETSIIINDVVYVVDSRKQKVKLFATHNNMTNYATVWGSKTNLEQRKGRA

Parental  GRVRPGFCFHLCSRARFERLETHMTPEMFRTPLHEIALSIKLLRLGGIGQFLAKAIEPPPLDAVIEAEHT
          GR.RPGFCFHLCSRARFERLETHMTPEMF.TPLHE.ALSIKLL.L.GIGQFLAKAIE..PLDAVIEAEHT
Retrocopy GRIRPGFCFHLCSRARFERLETHMTPEMFQTPLHEVALSIKLLCLVGIGQFLAKAIETLPLDAVIEAEHT

Parental  LRELDALDANDELTPLGRILAKLPIEPRFGKMMIMGCIFYVGDAICTIAAATCFPEPFINEGKRLGYIHR
          LRELDALDAND.LTPLGRILA.LPIEPRFGKMMIM.CIFYVGDAICTI.A.TCFPEPFINEGK.LGY.H.
Retrocopy LRELDALDANDDLTPLGRILANLPIEPRFGKMMIMVCIFYVGDAICTIPASTCFPEPFINEGKWLGYNH*

Parental  NFAGNRFSDHVALLSVFQAWDDARMGGEEAEIRFCEHKRLNMATLRMTWEAKVQLKEILINSGFPEDCLL
          NFAGN.FS.HVALLSVFQA.DD.RMGGEEAEIRFC.HKRLNMATLRMTWE.KVQLKEILINSGFPEDCL.
Retrocopy NFAGNGFSHHVALLSVFQAGDDTRMGGEEAEIRFCAHKRLNMATLRMTWEVKVQLKEILINSGFPEDCLV

Parental  TQVFTNTGPDNNLDVVISL-LAFGVYPNVCYHKEKRKILTTEGRNALIHKSSVNCPFSSQDMKYPSPFFV
          TQVFTNTGPDNNLDVVISL.LAFGVYPNVCYHKEK.KILTTEG.NALIHKSSVNCPFSSQDMKYPSPFF.
Retrocopy TQVFTNTGPDNNLDVVISL>LAFGVYPNVCYHKEKTKILTTEGCNALIHKSSVNCPFSSQDMKYPSPFFA

Parental  FGEKIRTRAISAKGMTLVTPLQLLLFASKKVQSDGQIVLVDDWIKLQISHEAAACITGLRAAMEALVVEV
          FGEKIRTRAISAKG.TLVTPLQLLLFASKKVQSDGQIVL.DDWIKLQISHEAAACIT.L.AA.EALVVEV
Retrocopy FGEKIRTRAISAKGITLVTPLQLLLFASKKVQSDGQIVLADDWIKLQISHEAAACITALQAATEALVVEV

Parental  TKQPAIISQLDPVNERMLNMIRQISRPSAAGINLMIGSTRYGDGPRPPKMARYDNGSGYRRGGSS
          TKQPAIISQLDPVNE..LNMIRQISRPSAA.INLMIGST.YGDGP.PPKMARYDNGSGYRRGGSS
Retrocopy TKQPAIISQLDPVNESILNMIRQISRPSAADINLMIGSTWYGDGPGPPKMARYDNGSGYRRGGSS

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	0.07 RPM	81.26 RPM
SRP007412_cerebellum	0.14 RPM	137.84 RPM
SRP007412_heart	0.06 RPM	61.38 RPM
SRP007412_kidney	0.00 RPM	116.19 RPM
SRP007412_liver	0.03 RPM	73.46 RPM
SRP007412_testis	0.42 RPM	206.66 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_833 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_833 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_833 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1216
Gorilla gorilla	retro_ggor_947

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000135829	1 retrocopy	retro_hsap_1216,
Gorilla gorilla	ENSGGOG00000013533	1 retrocopy	retro_ggor_947,
Pan troglodytes	ENSPTRG00000001759	1 retrocopy	retro_ptro_833 ,