RetrogeneDB ID: retro_ptro_3239

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:80327512..80330264(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HK2
• Ensembl ID: ENSPTRG00000012104
• Aliases: None
• Description: None

Sequence

>retro_ptro_3239
ATGGTTGCCTCGCATTTGCTTGCCTACTTCTTCAAGGAGCTCAACCATGACCAAGTGCAGAAGGTTGACCAGTATCTCTA
CCACATGCACCTCTCTGATGAGACCCTCTTGGAGATCTCTAAGCGGTTCCGCAAGGAGATAGAGAAAGGGCTTGGATCCA
CCACTCACCCCACTGCAGCAGTGAAGATGCTGCCCACCTTTGTGAGGTCCACTTCAGATGGGACAGAACACGGAGAGTTC
CTGGCTCTGGACCTTGGAGGGACCAACTTCCGTATGCTTTAGGTGAAAGTAACGGACAATGGGCTCCGGAAGGTGGAGAT
GGAGAACCAGATCTATGCCATCCCCGAGGACGTCATGCGAGGCAGTGACACCGAGCTGTTTGACCACATTGCCGAATGGC
TGGCTAACTTCATGGATAAGCTACAAATCAAAGACAAGAAGCTCCCATTGGGTTTTACCTTCTCGTTCCCCTGCCGCCAG
ACTAAACTAGACGAGAGTTTCCTGGTCTCATGGACCAAGGGATTCAAGTCCAGTGGAGTGGAAGGCAGAGACGTTGTGGC
TCTGATCCGGAAGGCCATCCAGAGGAGAGGGGACTTTGATATCGACATTGTGGCTGTGGTGAATGACACAGTTGGGACCA
TGATGACCTGTGGTCATGACGACCACAACTGTGAGATTGGTCTCATTGTGGGCACTGGCAGCAACGCCTGCCACATGGAA
GAGATGCGCCACATCGAGATGGTAGAAGGCGACGAGGGGCAGATGTGTATCAATATCGAGTGGGGGGCCTTCGGGGACGA
TGGCTTGCTCAATGACATTCGCACTGAGTTTGACCAGGAGATTGACATGGGCTCACTGAACCTGGGGAAGCAACTGTTTG
AGAAGGTGATCAGTGCGATGTACATGGGGGAGCTGATGAGGTTTATCCTGGTGAAGATGGCCAAGGAGGAGCTGCTCTTT
AGGGGGAAGCTCAGCCCAGAGCTTCTCAATACCGGTCACTTTGAGACCAAAGACATCTCAGACACTGAAGGGGAGAAGGA
TGGCATCCGGAAGGCCCGTGAGGTCCTGATGCGGTTGGGCATGGACCCGACTCAGGAGGACTGCGTGGCCACTCACCGGA
TCTGTCAGATCGTGTCCACACACTCCGCCAGCCTGTGCACAGCCACCCTGGCCCCCGTGCTGCAGCGCATCAAGGAGAAC
AAAGGCGAGGAGCAGCTTCGCTCTACTATTGGGGTCGACGGTTCCGTCTACAAGAAACACCCCCATTTTGCCAAGCGTCT
ACATAAGACCGTGTGGCGGCTGTTGCCCGACTGCTATGTCTGCTTCCTCCGCTCCGAGGATGGCAGTGGCAAAGGTGCAG
CCATGGTGACAGCAGTGGCTTACCGGCTGGCCGATCAACACCGTGCCCGCCAGAAGACACTAGAGCCTCTGCAGCTGAGC
CATGACCAGCTGTTGGAGGTCAAGAGGAGGATGAAGGTAGAAATGGAGCGAGGTCTGAGCAAGGAGACTCACGCCAGTGC
CCCCGTCAAGATGCTTCCCACCTACGTGTGTGCCACCCCTGACGGCACAGAGAAAGGGGACTTCTTGGCCTTGGACCTTG
GAGGAACAAATTTCCGGGTCCTGCTGGTCTGTGTTCGGAATGGGAAGTGGAGTGGAGTGGAGATGCACAACAAGATCTAT
GCCATCCCGCAGGAGGTCATGCATGGCACCGGGGACGAGCTCTTTGACCACATTGTCCAGTGCATCGCGGACTTCCTGGA
GTACATGGGCATGAAGGGCGTGTGCCTGCCTCTGGGTTTTACCTTCTCCTTCCCCTGCCAGCAGAACAGCCTGGACGAGA
GCATCCTCCTCTAGTGGACAAAAGGCTTCAAGGAATCTGGCTGCGAGGGCGAGGACGTGGTGACCCTGCTGAAGGAAGCG
ATCCACCGGCGAGAGGAGTTTGACCTGGATGTGATTGCTGTGGTGAACGACACAGTCAGAACTATGATGACCTGTGGCTT
TGAAGACCCTCACTGTGAAGTTGGCCTCATCGGTTGGCACGGGCAGCAATGTCTGCTACATGGAAGAGATGAGCAATGTG
GAACTGGTGGAAGGAGAAGAGGGGCGGATGTGTGTGAACATGGAATGGGGGGCCTTTGGGGACAATGGATGCCTAGATGA
CTTCCACACAGAATTTGATGTGGCTGTGGATGAGCTTTCACTCAACCCCGGCAAGCAGAGGTTCGAGAAAATGATCAATG
GAATGTACCTGGGTGAGATTGTCGGTAACATTCTCATCGATTTCACCAAGCGTGGGCTGCTCTTCTGAGGCCACATCTCA
GAGCTACTCAAGAAAAGGGGCATCTTTGAAACCAAGTTCTTGTCTCAGATTGAGAGTGACTGCCTGGCCCTGCTGCAAGT
CCGAGCCATTCTGCAACACTTAGGGCTTGAGAGCACCTGTGACGACAGCATCATTGTTAAGGAGGTGTGCACCGTGGTGG
CCCGGCGGGCAGCCCAGCTCTGTGGTGCAGGCATGGCCGCTGTGGTGGACAAGATACGAGAAAACCGTGGGCTGGACACT
GTCAAAGTGACAGTGGGTGTGGATGGGACCCTCTGCAAGCTACATCCTCACTTTGCCAAAGTCATGCATGAGACAGTGAA
GGACCTGGCTCCGAAATGTGATGTGTCTTTCCTGCAGTCAGAGGATGGCAGCGGGAAGGGGGCGGCGCTCATTACTGCTG
CGTTCTGCCGCATCCGTGAGGCTGGACAGCGA

Alignment

ORF - retro_ptro_3239 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.25 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MIASHLLAYFFTELNHDQVQKVDQYLYHMRLSDETLLEISKRFRKEMEKGLGATTHPTAAVKMLPTFVRS
          M.ASHLLAYFF.ELNHDQVQKVDQYLYHM.LSDETLLEISKRFRKE.EKGLG.TTHPTAAVKMLPTFVRS
Retrocopy MVASHLLAYFFKELNHDQVQKVDQYLYHMHLSDETLLEISKRFRKEIEKGLGSTTHPTAAVKMLPTFVRS

Parental  TPDGTEHGEFLALDLGGTNFRVLWVKVTDNGLQKVEMENQIYAIPEDIMRGSGTQLFDHIAECLANFMDK
          T.DGTEHGEFLALDLGGTNFR.L.VKVTDNGL.KVEMENQIYAIPED.MRGS.T.LFDHIAE.LANFMDK
Retrocopy TSDGTEHGEFLALDLGGTNFRML*VKVTDNGLRKVEMENQIYAIPEDVMRGSDTELFDHIAEWLANFMDK

Parental  LQIKDKKLPLGFTFSFPCHQTKLDESFLVSWTKGFKSSGVEGRDVVALIRKAIQRRGDFDIDIVAVVNDT
          LQIKDKKLPLGFTFSFPC.QTKLDESFLVSWTKGFKSSGVEGRDVVALIRKAIQRRGDFDIDIVAVVNDT
Retrocopy LQIKDKKLPLGFTFSFPCRQTKLDESFLVSWTKGFKSSGVEGRDVVALIRKAIQRRGDFDIDIVAVVNDT

Parental  VGTMMTCGYDDHNCEIGLIVGTGSNACYMEEMRHIDMVEGDEGRMCINMEWGAFGDDGSLNDIRTEFDQE
          VGTMMTCG.DDHNCEIGLIVGTGSNAC.MEEMRHI.MVEGDEG.MCIN.EWGAFGDDG.LNDIRTEFDQE
Retrocopy VGTMMTCGHDDHNCEIGLIVGTGSNACHMEEMRHIEMVEGDEGQMCINIEWGAFGDDGLLNDIRTEFDQE

Parental  IDMGSLNPGKQLFEKMISGMYMGELVRLILVKMAKEELLFGGKLSPELLNTGRFETKDISDIEGEKDGIR
          IDMGSLN.GKQLFEK.IS.MYMGEL.R.ILVKMAKEELLF.GKLSPELLNTG.FETKDISD.EGEKDGIR
Retrocopy IDMGSLNLGKQLFEKVISAMYMGELMRFILVKMAKEELLFRGKLSPELLNTGHFETKDISDTEGEKDGIR

Parental  KAREVLMRLGLDPTQEDCVATHRICQIVSTRSASLCAATLAAVLQRIKENKGEERLRSTIGVDGSVYKKH
          KAREVLMRLG.DPTQEDCVATHRICQIVST.SASLC.ATLA.VLQRIKENKGEE.LRSTIGVDGSVYKKH
Retrocopy KAREVLMRLGMDPTQEDCVATHRICQIVSTHSASLCTATLAPVLQRIKENKGEEQLRSTIGVDGSVYKKH

Parental  PHFAKRLHKTVRRLVPGCDVRFLRSEDGSGKGAAMVTAVAYRLADQHRARQKTLEHLQLSHDQLLEVKRR
          PHFAKRLHKTV.RL.P.C.V.FLRSEDGSGKGAAMVTAVAYRLADQHRARQKTLE.LQLSHDQLLEVKRR
Retrocopy PHFAKRLHKTVWRLLPDCYVCFLRSEDGSGKGAAMVTAVAYRLADQHRARQKTLEPLQLSHDQLLEVKRR

Parental  MKVEMERGLSKETHASAPVKMLPTYVCATPDGTEKGDFLALDLGGTNFRVLLVRVRNGKWGGVEMHNKIY
          MKVEMERGLSKETHASAPVKMLPTYVCATPDGTEKGDFLALDLGGTNFRVLLV.VRNGKW.GVEMHNKIY
Retrocopy MKVEMERGLSKETHASAPVKMLPTYVCATPDGTEKGDFLALDLGGTNFRVLLVCVRNGKWSGVEMHNKIY

Parental  AVPQEVMHGTGDELFDHIVQCIADFLEYMGMKGVSLPLGFTFSFPCQQNSLDESILLKWTKGFKASGCEG
          A.PQEVMHGTGDELFDHIVQCIADFLEYMGMKGV.LPLGFTFSFPCQQNSLDESILL.WTKGFK.SGCEG
Retrocopy AIPQEVMHGTGDELFDHIVQCIADFLEYMGMKGVCLPLGFTFSFPCQQNSLDESILL*WTKGFKESGCEG

Parental  EDVVTLLKEAIHRREEFDLDVVAVVNDTVGTMMTCGFEDPHCEVGLI-VGTGSNACYMEEMRNVELVEGE
          EDVVTLLKEAIHRREEFDLDV.AVVNDTV.TMMTCGFEDPHCEVGLI.VGTGSN.CYMEEM.NVELVEGE
Retrocopy EDVVTLLKEAIHRREEFDLDVIAVVNDTVRTMMTCGFEDPHCEVGLI>VGTGSNVCYMEEMSNVELVEGE

Parental  EGRMCVNMEWGAFGDNGCLDDFRTEFDVAVDELSLNPGKQRFEKMISGMYLGEIVRNILIDFTKRGLLFR
          EGRMCVNMEWGAFGDNGCLDDF.TEFDVAVDELSLNPGKQRFEKMI.GMYLGEIV.NILIDFTKRGLLF.
Retrocopy EGRMCVNMEWGAFGDNGCLDDFHTEFDVAVDELSLNPGKQRFEKMINGMYLGEIVGNILIDFTKRGLLF*

Parental  GRISERLKTRGIFETKFLSQIESDCLALLQVRAILQHLGLESTCDDSIIVKEVCTVVARRAAQLCGAGMA
          G.ISE.LK.RGIFETKFLSQIESDCLALLQVRAILQHLGLESTCDDSIIVKEVCTVVARRAAQLCGAGMA
Retrocopy GHISELLKKRGIFETKFLSQIESDCLALLQVRAILQHLGLESTCDDSIIVKEVCTVVARRAAQLCGAGMA

Parental  AVVDKIRENRGLDALKVTVGVDGTLYKLHPHFAKVMHETVKDLAPKCDVSFLQSEDGSGKGAALITAVAC
          AVVDKIRENRGLD..KVTVGVDGTL.KLHPHFAKVMHETVKDLAPKCDVSFLQSEDGSGKGAALITA..C
Retrocopy AVVDKIRENRGLDTVKVTVGVDGTLCKLHPHFAKVMHETVKDLAPKCDVSFLQSEDGSGKGAALITAAFC

Parental  RIREAGQR
          RIREAGQR
Retrocopy RIREAGQR

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	4.92 RPM
SRP007412_cerebellum	0.00 RPM	7.60 RPM
SRP007412_heart	0.00 RPM	9.91 RPM
SRP007412_kidney	0.00 RPM	8.21 RPM
SRP007412_liver	0.00 RPM	15.32 RPM
SRP007412_testis	0.53 RPM	189.27 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3239 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3239 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3239 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_3781

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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	ENSG00000159399	1 retrocopy	retro_hsap_4864,
Nomascus leucogenys	ENSNLEG00000001062	1 retrocopy	retro_nleu_1997,
Pongo abelii	ENSPPYG00000012260	1 retrocopy	retro_pabe_3781,
Pan troglodytes	ENSPTRG00000012104	1 retrocopy	retro_ptro_3239 ,