RetrogeneDB ID: retro_ptro_2110

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:168615400..168618079(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NOL8
• Ensembl ID: ENSPTRG00000021109
• Aliases: None
• Description: None

Sequence

>retro_ptro_2110
ACACGGAAAGATGACCATGGAAACCCACAGAAAGTCTTTGCATATATCAGCATCAGTGTAGCAGAAGCAGACCTGAAAAA
ATGCATATCCATTTTAAATAAAACAAAATGGAAAGGTAGAACATTACAAATTCAACTAGCAAAAGAAAGCTTTTTGCACA
GATTGGCCCAAGAGAAAGAAGAAGCAAAAGCTAAGAAAGGAAAATCAACAACAGGTAACATCAACTTGTTAGAAAAGATA
GGAGGAGTGGAATTCCATATGAAAGCTGCGCCAGGGACAGAAGTGCCAGGGTATAAGAATTGGGTTGTGAGCAAATTTGG
AAAAGTGTTACTTGTTCTTCACCTTAAAATTTATCATAAATGTAAAATTATAAAATATGATCCCTCAAAATACTGCCACA
ACCTAAAGAAGATAGGGGAGGATTTCACAAACACCATTCCTATATCCAGCCTGACTTGGGAACTGGAAGGAGGGAATGAC
CCTATGAGTAAGAAATGGTGAGGAGACTTCTCTGACTTTCATGGCCCTCCCAAGAAGATGATAAAAGTGCAGAGGGATGA
GAGTTCCACTGGGTCTCTGGCCATGAGTCCAAGGCCCAGGTGGGTAATAGAGAGACCACCCTTAACACAGCAACAAGCTG
CACAAAAAAAGAACTTCTAATTCCACTACTCCTAAATCATCTCCTGTACCTGTTTCTGATACTCAGAAACTTTAAAATCT
ACCTTTTAGGACTTCTGGATTGGAAACTGCCAAGAAGAGAAGTGGCATTTCTGATGATTATATTGATTCTAAAGATGAAT
TAAGAATGATGGTTGCAAAAGAGGAAAACTTACAGAGAACTACACAATCCTCAATAAATGAATCTGAAACTGATCCCTTT
GAAGTTGTAAGAGATAACTTCAAATCAGGAGTTCACAAATTGCATTCTTCAACAGGTTTAGGTATCAAAAATAATGCCTC
TTGCCATGACAGTGATGATGATATTACGAGAAATGATTGTGAGTATGACTCAGGAGATACAGATGAAATCATTGTGATGA
AAAAAAATGTTGCTAAGGTCAAAAACAGTACAGAATTTTCACAAATGGAAAAATCTACAGACAAGAAAACTTCCTTCAAA
AATAGAGAAAACTGTGAGCTTCTGATCACTGTATTAAAGTACAAGAAAGAAAAGGCAATGTAGAGTCAGCCCTCGGTCAT
GGATTAAAGGCTCTTAATCGCAAATCTCCCTCTCGCTCCAATAGCAATGAAGATGCTGATTCTGCATCAGAATTAGCTGA
CTCTGAAGGAGACAAGGAGTATAATGCCATGATGAAAAACCGCCTTCGTGTGAATCTCACTTTAGCTGATTTGGAACAAT
TGGCTGGCGTGAACAGAAGGTTTCCGATGAAGATACTGAGAGTGACGGACCAGAAACCACCACACAATGCAAGTTTGACA
GAGGCTCCAACAGCCCCAAGACTCCCACTGGCCTCCACGGATGCAGACACTGTATTTGTCCTGAGGACACTGTGGCTTCC
CTGTTAGAAGGAGAGGAGAGCACCTGTGGCAAACAGAAACCAAAGGAAAACAACTGAAAGCCAGAATTCCAGGTTTTCAA
GGGAGTAGGCTGTTTATATGAAAAAGGAGTCAATAAAAAAATCCTTGAAAGACAATGTTGCCTCTAACAATATTAATAAA
GATCAGAATTCCATGAAACATGTGGATCCCAGGATCACATCCATGGAAGATGGGTCCCCATATGTTAATGGCTCATCGGG
TGAACTGACTCTGTGCCAACATGCAAAGAAGGTGAATGGCCCAACTATATTCAGCCTCAAAAAAGATAGAACACTTCTGA
GAGCCAGGATTGCAAGGCAGTGTCCACTAGCAGTTCTGAAAAGAGAAGTAAGAATTCTATTTCTAGTTTATTGCCATTAA
AAGGTAAGAAGTCCTTAAGTCTTAGTGCAAAGACTCACAACATAGGCTTTGACAAAGACAGCTGCCATAGTACCACAAGA
CAGAAGCTTCAGAGGAAGAGAGGTCTGACTCAAGCAGCCTCACATCTCTTGAGAAATCACCAAAGGTCTCATCCAAGGAC
ACTCAGGAAATCAAAACTGATTTCTCACTTTCTATTAGTAATTCGTCAGATCTGAGTGCTAAGGATAAGCATGCTGAAGA
CGATGAGAAGCATTTGGCAGCCTTGGAAGTCAGGCAAAAAGCAAAAGAATGCAGAAGAAGCTGGTGGATAATGCTCTGGC
AAATTTGGATGGTCATCCAGAGGATAAACTAACGCACATCATCTTCGGTTCTGACAGTGAATGTGAAACAGAGGAGATAT
CGACTCAGGAGCAGAGACATCCAGGAGAGGAATGGGTGAAAGAGTCTATGGGTAAAACATTGGGGAAGCTGCCTGATAGC
AGTGATGATGAGGAATCTGATTCTGAAGATGACAGTAACAGGTTCAAAATTAAACCTCAGTTTGAGGGCAGAGCTGGACA
GAAGCTCATGGATTTACAGTCGCACTTTGGCACTGATGACAGATTCTGCATGAATTCTCGATTTCTAGAAAGTGACAGTG
AAGACGAACAGGAAGAGGTAAATGAAAAGAAACCCGCTAGGAAGAAGAGCTTGCTGAAGAAAAAAGAAAGCCTGGATGTT
GTACAAAGTGTTTTGAAAATCAACTTAAGCAATTCTACA

Alignment

ORF - retro_ptro_2110 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.55 %
• Parental protein coverage: 76.39 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 10

Retrocopy - Parental Gene Alignment:

Parental  TRKDDQGNPQKVFAYINISVAEADLKKCMSVLNKTKWKGGTLQIQLAKESFLHRLAQEREAAKAKKEEST
          TRKDD.GNPQKVFAYI.ISVAEADLKKC.S.LNKTKWKG.TLQIQLAKESFLHRLAQE.E.AKAKK..ST
Retrocopy TRKDDHGNPQKVFAYISISVAEADLKKCISILNKTKWKGRTLQIQLAKESFLHRLAQEKEEAKAKKGKST

Parental  TGNANLLEKTGGVDFHMKAVPGTEVPGHKNWVVSKFGRVLPVLHLKNQHKRKVIKYDPSKYCHNLKKIGE
          TGN.NLLEK.GGV.FHMKA.PGTEVPG.KNWVVSKFG.VL.VLHLK..HK.K.IKYDPSKYCHNLKKIGE
Retrocopy TGNINLLEKIGGVEFHMKAAPGTEVPGYKNWVVSKFGKVLLVLHLKIYHKCKIIKYDPSKYCHNLKKIGE

Parental  DFSNTIPISSLTWELEGGNDPMSKKRRGEFSDFHGPPKKIIKVQKDESSTGSLAMSTRPRRVIERPPLTQ
          DF.NTIPISSLTWELEGGNDPMSKK..G.FSDFHGPPKK.IKVQ.DESSTGSLAMS.RPR.VIERPPLTQ
Retrocopy DFTNTIPISSLTWELEGGNDPMSKKW*GDFSDFHGPPKKMIKVQRDESSTGSLAMSPRPRWVIERPPLTQ

Parental  QQASQK-RTCDSITPSKSSPVPVSDTQKLKNLPFKTSGLETAKKRNSISDDDTDSEDELRMMIAKEENLQ
          QQA.QK.RT..S.TP.KSSPVPVSDTQKL.NLPF.TSGLETAKKR..ISDD..DS.DELRMM.AKEENLQ
Retrocopy QQAAQK>RTSNSTTP-KSSPVPVSDTQKL*NLPFRTSGLETAKKRSGISDDYIDSKDELRMMVAKEENLQ

Parental  RSTQPSINESENDPFEVVRDDFKSGVHKLHSLIGLGIKNHVSCHDSDDDIMRNDREYDSGDTDEIIAMKK
          R.TQ.SINESE.DPFEVVRD.FKSGVHKLHS..GLGIKN..SCHDSDDDI.RND.EYDSGDTDEII.M..
Retrocopy RTTQSSINESETDPFEVVRDNFKSGVHKLHSSTGLGIKNNASCHDSDDDITRNDCEYDSGDTDEIIVMXX

Parental  NVAKVKNSTEFSQMEKST-KKTSFKNRENCEL-SDHCIKLQKRKSNVESALSHGLKSLNHKSPSHSSSSE
          .VAKVKNSTEFSQMEKST.KKTSFKNRENCEL.SDHCIK.Q.RK.NVESAL.HGLK.LN.KSPS.S.S.E
Retrocopy XVAKVKNSTEFSQMEKSTDKKTSFKNRENCEL<SDHCIKVQERKGNVESALGHGLKALNRKSPSRSNSNE

Parental  DADSASELADSEGGEEYNAMMKNCLRVNLTLADLEQLAG-SDLKVPNEDTESDGPETTTQCKFHRGSKSP
          DADSASELADSEG..EYNAMMKN.LRVNLTLADLEQLAG....KV..EDTESDGPETTTQCKF.RGS.SP
Retrocopy DADSASELADSEGDKEYNAMMKNRLRVNLTLADLEQLAG<REQKVSDEDTESDGPETTTQCKFDRGSNSP

Parental  KTPTGLRRGRQCIRPAEIVAFLLEGEENTCGKQKPKENNLKPKFQAFKGVGCLYEK-ESMKKSLKDSVAS
          KTPTGL...R.CI.P...VA.LLEGEE.TCGKQKPKENN.KP.FQ.FKGVGCLYEK.ES.KKSLKD.VAS
Retrocopy KTPTGLHGCRHCICPEDTVASLLEGEESTCGKQKPKENN*KPEFQVFKGVGCLYEK>ESIKKSLKDNVAS

Parental  NNINKDQNSMKHEDPSIISMEDGSPYVNGSLGEVTPCQHAKKANGP-NYIQPQKRQTTFESQDRKAVSPS
          NNINKDQNSMKH.DP.I.SMEDGSPYVNGS.GE.T.CQHAKK.NGP.NYIQPQKR..T.ESQD.KAVS.S
Retrocopy NNINKDQNSMKHVDPRITSMEDGSPYVNGSSGELTLCQHAKKVNGP<NYIQPQKR*NTSESQDCKAVSTS

Parental  SSEKRSKNPISR--PLEGKKSLSLSAKTHNIDFDKDSCHSTT-KTEASQEERSDSSSLTSLKKSPKVSSK
          SSEKRSKN.IS...PL.GKKSLSLSAKTHNI.FDKDSCHSTT.KTEAS.EERSDSSSLTSL.KSPKVSSK
Retrocopy SSEKRSKNSISSLLPLKGKKSLSLSAKTHNIGFDKDSCHSTT<KTEASEEERSDSSSLTSLEKSPKVSSK

Parental  DTREIKTDFSLSISNSSDLSAKDKHAEDNEKRLAALEARQKAKE-VQKKLVHNALANLDGHPEDKPTHII
          DT.EIKTDFSLSISNSSDLSAKDKHAED.EK.LAALE.RQKAKE..QKKLV.NALANLDGHPEDK.THII
Retrocopy DTQEIKTDFSLSISNSSDLSAKDKHAEDDEKHLAALEVRQKAKE<MQKKLVDNALANLDGHPEDKLTHII

Parental  FGSDSECETEETSTQEQSNPGEEWVKESMGKTSGKLFDSSDDEESDSEDDSNRFKIKPQFEGRAGQKLMD
          FGSDSECETEE.STQEQ..PGEEWVKESMGKT.GKL.DSSDDEESDSEDDSNRFKIKPQFEGRAGQKLMD
Retrocopy FGSDSECETEEISTQEQRHPGEEWVKESMGKTLGKLPDSSDDEESDSEDDSNRFKIKPQFEGRAGQKLMD

Parental  LQSHFGTDDRFRMDSRFLETDSEEEQEEVNEKKTAE-EEELAEEK-KKA-LNVVQSVLQINLSNST
          LQSHFGTDDRF.M.SRFLE.DSE.EQEEVNEKK.A..EEELAEEK.KKA.L.VVQSVL.INLSNST
Retrocopy LQSHFGTDDRFCMNSRFLESDSEDEQEEVNEKKPAR<EEELAEEK<KKA<LDVVQSVLKINLSNST

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	0.05 RPM	13.23 RPM
SRP007412_cerebellum	0.04 RPM	20.18 RPM
SRP007412_heart	0.00 RPM	15.21 RPM
SRP007412_kidney	0.00 RPM	19.56 RPM
SRP007412_liver	0.00 RPM	13.36 RPM
SRP007412_testis	0.11 RPM	34.46 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2110 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2110 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2110 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3121
Pongo abelii	retro_pabe_2577

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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	ENSG00000198000	1 retrocopy	retro_hsap_3121,
Nomascus leucogenys	ENSNLEG00000016357	1 retrocopy	retro_nleu_773,
Pongo abelii	ENSPPYG00000019375	1 retrocopy	retro_pabe_2577,
Pan troglodytes	ENSPTRG00000021109	1 retrocopy	retro_ptro_2110 ,