RetrogeneDB ID: retro_pabe_3781

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:78416879..78419567(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HK2
• Ensembl ID: ENSPPYG00000012260
• Aliases: None
• Description: hexokinase 2 [Source:HGNC Symbol;Acc:4923]

Sequence

>retro_pabe_3781
GTTGACCAGTATCTCTACCACATGCGCCTCTCTGATGAGACCCTCTTGGAGATCTCTAAGCGGTTCTGCAAGGAGATAGA
GAAAGGGCTTGGATCCACCACTCACCCCACTGCAGCAGTGAAGATGCTGCCCACCTTTGTGAGGTCCACTTCAGATGGGA
CAGAACACGGAGAGTTCCTGGCTCTGGACCTTGGAGGGACCAACTTCCGTGTGCTTTGGGTGAAAGTAACGGACAATGGG
CTCCAGAAGGTGGAGATGGAGAACCAGATCTATGCCATCCCCGAGGACATCATGCGAGGCAGTGACACCCAGCTGTTTGA
CCACGTTGACGAATGCCTGGCTAACTTCATGGATAAGCTACAAATCAAAGACAAGAAGCTCCCATTGGGTTTTACCTTCT
CGTTCCCCTGCCGCCAGACTAAACTAGACGAGAGTTTCCTGGTCTCATGGACCAAGGGATTCAAGTCCAGTGGAGTGGAA
GGCAGAGACGTTGTGGCTCTGATCCGGAAGGCCATCCAGAGGAGAGGGGACTTTGATATCGACATTGTGGCTGTGGTGAA
TGACACAGTTGGGACCATGATGACCTGTGGTTATGATGACCACAACTGTGAAATTGGTCTCATTGTGGGCACGGGCAGCA
ACGCCTGCTACATGGAAGAGATGCGCCACATCGACATGGTGGAAGGCGATGAGGGGCAGATGTGTATCAATATGGAGTGG
GGGGCCTTCGGGGACGATGGCTAGCTCAATGACATTTGCACTGAGTTTGACCAGGAGATTGACATGGGCTTACTGAACCT
GGGGAAGCAACTGTTTGAGAAGATGATCAGTGGGATGTACATGGGGGAGCTGGTGAGGTTTCTCCTGGTGAAGATGGCCA
AGGAGGAGCTGCTCTTTAGGGGGAAGCTCAGCCCAGAGCTTCTCAACACCGGTCGCTTTGAGACCAAAGAAATCTCAGAC
ACTGAAGGGGAGAAGGATGGCATCCGGAAGGCCCGTGAGGTCCTGATGCGGTTGGGCATGGACCCAACTCAGGAGGACTG
CGTGGCCACTCACCGGATCTGCCAGATCGTGTCCACACACTCCGCCAGCCTGTGCACAGCCACCCTGGCTGCCGTGCCGC
AGCGCATCAAGGAGAACACAGGCGAGGAGCAGCTTCGCTCTACTATTGGGGTCGACGGCTCCATCTACAAGAAACACCCC
CATTTTGCCAAGCGTCTACATAAGACCGTGTGGCGGCTGGTGCCCGACTGCTATGTCTGCTTCCTCCGCTCCGAGGATGG
CAGTGGCAAAGGTGCAGCCATGGTGACAGCAGTGGCTTACCGGCTGGCCGATCAACACCGTGCCCGCCAGAAGACACTAG
AGCCTCTGCAGCTGAGCCATGACCAGCTGTTGGAGGTCAAGAGGAGGATGAAGGTAGAAATGGAGCGAGGTCTGAGCAAG
GAGACTCACGCCAGTGCCCCTGTCAAGATGCTGCCCACCTACGTGTGTGCCACCCCTGACGGCACAGAGAAAGGGGACTT
CTTGGCCTTGGACCTTGGAGGAACAAATTTCCGGGTCCTGCTGGTCTGTGTTCGGAATGGGAAGTGGGGTGGAGTGGAGA
TGCACAACAAGATCTACGCCATCCCGTAGGAGGTCATGCATGGCACTGGGGACGAGCTCTTTGACCACATTGTCCAGTGC
ATCGTGGACTTCCTCGAGTACATGGGCATGAAGGGCGTGTCCCTGCCTCTGGGTTTTACCTTCTCCTTCCCCTGCCAGCA
GAACAGCCTGGACGAGAGCATTCTCCTCTAGTGGACAAAAGGCTTCAAGGAATCTGGCTGCGAGGGCGAGGACGTGGTGA
CCCTGCTGAAGGAAGTGATCCACCGGCGAGAGGAGTTTGACCTGGATGTGATTGCTGTGGTGAACGACACAGTCAGAACT
ATGATGACCTGTGGCTTTGAAGACCCTCACTGTGAAGCTGGCCTCATCGTTGGCATGGGCAGCAATGCCTGCTACATGGA
AGAGATGCACAATGTGGAACTGGTGGAAAGAGAAGAGGGGCGGATGTGTGTGAACATGGAATGGGGGGCCTTTGGGGACA
ATGGATGCCTAGATGACTTCCGCACAGAATTTGATGTGGCTGTGGATGAGCTTTCACTCAACCCCGGCAAGCAGAAGTTC
GAGAAAATGATTAATGGAATGTACCTGGATGAGACTGTCGGTAACATTCTCATCGATTTCACCAAGCGTGGGCTGCTTTT
CCGAGGCCACATCTCAGAGCTACTCAAGACAAGGGGCATCTTTGAAACCAAGTTCTTGTCTCAGATTGAGAGTGACTGCC
TGGCCCTGCTGCAAGTCCGTGCCATTCTGCAACACTTAGGGCTTTAGAGCACCTGTGACGACAGCATCATTGTTAAGGAG
GTGTGCACCTTGGTGGCCCGGGGGGCAGCCCAGCTCTGTGGCGCAGGCATGGCCGCTGTGATGGACAAGATACGAGAAAA
CCGTGGGCTGGACGCTCTCAAAGTGACAGCGGGTGTGGATGGGACCCTCTACAAGCTACATCCTCACTTTGCCAAAGTCA
TGCATGAGACAGTGAAGGACCTGGCTTCGAAATGTGATGTGTCTTTCCTGCAGTCAGAGGATGACAGTGGGAAGGGGGCG
CTTCTCATCACTGCTGTGTCCTGCCACATCCGTGAGGCTGGACAGCGA

Alignment

ORF - retro_pabe_3781 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.42 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VDQYLYHMRLSDETLLEISKRFRKEMEKGLGATTHPTAAVKMLPTFVRSTPDGTEHGEFLALDLGGTNFR
          VDQYLYHMRLSDETLLEISKRF.KE.EKGLG.TTHPTAAVKMLPTFVRST.DGTEHGEFLALDLGGTNFR
Retrocopy VDQYLYHMRLSDETLLEISKRFCKEIEKGLGSTTHPTAAVKMLPTFVRSTSDGTEHGEFLALDLGGTNFR

Parental  VLWVKVTDNGLQKVEMENQIYAIPEDIMRGSGTQLFDHIAECLANFMDKLQIKDKKLPLGFTFSFPCHQT
          VLWVKVTDNGLQKVEMENQIYAIPEDIMRGS.TQLFDH..ECLANFMDKLQIKDKKLPLGFTFSFPC.QT
Retrocopy VLWVKVTDNGLQKVEMENQIYAIPEDIMRGSDTQLFDHVDECLANFMDKLQIKDKKLPLGFTFSFPCRQT

Parental  KLDESFLVSWTKGFKSSGVEGRDVVALIRKAIQRRGDFDIDIVAVVNDTVGTMMTCGYDDHNCEIGLIVG
          KLDESFLVSWTKGFKSSGVEGRDVVALIRKAIQRRGDFDIDIVAVVNDTVGTMMTCGYDDHNCEIGLIVG
Retrocopy KLDESFLVSWTKGFKSSGVEGRDVVALIRKAIQRRGDFDIDIVAVVNDTVGTMMTCGYDDHNCEIGLIVG

Parental  TGSNACYMEEMRHIDMVEGDEGRMCINMEWGAFGDDGSLNDIRTEFDQEIDMGSLNPGKQLFEKMISGMY
          TGSNACYMEEMRHIDMVEGDEG.MCINMEWGAFGDDG.LNDI.TEFDQEIDMG.LN.GKQLFEKMISGMY
Retrocopy TGSNACYMEEMRHIDMVEGDEGQMCINMEWGAFGDDG*LNDICTEFDQEIDMGLLNLGKQLFEKMISGMY

Parental  MGELVRLILVKMAKEELLFGGKLSPELLNTGRFETKDISDIEGEKDGIRKAREVLMRLGLDPTQEDCVAT
          MGELVR..LVKMAKEELLF.GKLSPELLNTGRFETK.ISD.EGEKDGIRKAREVLMRLG.DPTQEDCVAT
Retrocopy MGELVRFLLVKMAKEELLFRGKLSPELLNTGRFETKEISDTEGEKDGIRKAREVLMRLGMDPTQEDCVAT

Parental  HRICQIVSTRSASLCAATLAAVLQRIKENKGEERLRSTIGVDGSVYKKHPHFAKRLHKTVRRLVPDCDVR
          HRICQIVST.SASLC.ATLAAV.QRIKEN.GEE.LRSTIGVDGS.YKKHPHFAKRLHKTV.RLVPDC.V.
Retrocopy HRICQIVSTHSASLCTATLAAVPQRIKENTGEEQLRSTIGVDGSIYKKHPHFAKRLHKTVWRLVPDCYVC

Parental  FLRSEDGSGKGAAMVTAVAYRLADQHRARQKTLEPLQLSHDQLLEVKRRMKVEMERGLSKETHASAPVKM
          FLRSEDGSGKGAAMVTAVAYRLADQHRARQKTLEPLQLSHDQLLEVKRRMKVEMERGLSKETHASAPVKM
Retrocopy FLRSEDGSGKGAAMVTAVAYRLADQHRARQKTLEPLQLSHDQLLEVKRRMKVEMERGLSKETHASAPVKM

Parental  LPTYVCATPDGTEKGDFLALDLGGTNFRVLLVRVRNGKWGGVEMHNKIYAIPQEVMHGTGDELFDHIVQC
          LPTYVCATPDGTEKGDFLALDLGGTNFRVLLV.VRNGKWGGVEMHNKIYAIP.EVMHGTGDELFDHIVQC
Retrocopy LPTYVCATPDGTEKGDFLALDLGGTNFRVLLVCVRNGKWGGVEMHNKIYAIP*EVMHGTGDELFDHIVQC

Parental  IADFLEYMGMKGVSLPLGFTFSFPCQQNSLDESILLKWTKGFKASGCEGEDVVTLLKEAIHRREEFDLDV
          I.DFLEYMGMKGVSLPLGFTFSFPCQQNSLDESILL.WTKGFK.SGCEGEDVVTLLKE.IHRREEFDLDV
Retrocopy IVDFLEYMGMKGVSLPLGFTFSFPCQQNSLDESILL*WTKGFKESGCEGEDVVTLLKEVIHRREEFDLDV

Parental  VAVVNDTVGTMMTCGFEDPHCEVGLIVGTGSNACYMEEMRNVELVEGEEGQMCVNMEWGAFGDNGCLDDF
          .AVVNDTV.TMMTCGFEDPHCE.GLIVG.GSNACYMEEM.NVELVE.EEG.MCVNMEWGAFGDNGCLDDF
Retrocopy IAVVNDTVRTMMTCGFEDPHCEAGLIVGMGSNACYMEEMHNVELVEREEGRMCVNMEWGAFGDNGCLDDF

Parental  RTEFDVAVDELSLNPGKQRFEKMISGMYLGEIVRNILIDFTKRGLLFRGRISERLKTRGIFETKFLSQIE
          RTEFDVAVDELSLNPGKQ.FEKMI.GMYL.E.V.NILIDFTKRGLLFRG.ISE.LKTRGIFETKFLSQIE
Retrocopy RTEFDVAVDELSLNPGKQKFEKMINGMYLDETVGNILIDFTKRGLLFRGHISELLKTRGIFETKFLSQIE

Parental  SDCLALLQVRAILQHLGLESTCDDSIIVKEVCTVVARRAAQLCGAGMAAVVDKIRENRGLDTLKVTVGVD
          SDCLALLQVRAILQHLGL.STCDDSIIVKEVCT.VAR.AAQLCGAGMAAV.DKIRENRGLD.LKVT.GVD
Retrocopy SDCLALLQVRAILQHLGL*STCDDSIIVKEVCTLVARGAAQLCGAGMAAVMDKIRENRGLDALKVTAGVD

Parental  GTLYKLHPHFAKVMHETVKDLAPKCDVSFLQSEDGSGKGAALITAVACRIREAGQR
          GTLYKLHPHFAKVMHETVKDLA.KCDVSFLQSED.SGKGA.LITAV.C.IREAGQR
Retrocopy GTLYKLHPHFAKVMHETVKDLASKCDVSFLQSEDDSGKGALLITAVSCHIREAGQR

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	0.06 RPM	8.63 RPM
SRP007412_cerebellum	0.00 RPM	2.31 RPM
SRP007412_heart	0.03 RPM	6.59 RPM
SRP007412_kidney	0.00 RPM	6.30 RPM
SRP007412_liver	0.06 RPM	13.13 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3781 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3781 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3781 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_3239

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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,