RetrogeneDB ID: retro_pabe_1872

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 22:16441101..16442791(+)
• Located in intron of: ENSPPYG00000011600

Retrocopy information

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

Parental gene information

• Parental gene symbol: KLHL12
• Ensembl ID: ENSPPYG00000000343
• Aliases: None
• Description: kelch-like family member 12 [Source:HGNC Symbol;Acc:19360]

Sequence

>retro_pabe_1872
GGAGGCATTATGGCCCCCAAAGACATAATGACAAATACTCATGCTAAATCAATCCTCAGTTCAATGAACTCCCTCGGGAA
GAGCAATACCCTGACATTGAGAGTAGAGCAGAACGACTTCCCTGCCCATCAGATTGTGCTGGCTGCCTGTAGTGATTAAT
TCTGTGCCATGTTCACTAGTGAGCTTTCACAGAAGGGGAAACCTTATGTTGACATCCAAGGTTTGACTGCCTCTACCATG
GAAATTTTATTGGACTTTGTGTACACAGAAACAGTATATGTGACATGGAGAATGTACAAGAACTGCTTCCTGCAGCCTGC
CTGCTTCAGTTGAAAGGTGTGAAACAAGCCTGCTGTGAGTTCTTGGAAAGTCAGTTGGACCCTTCTAATTGCCTGGGTAT
TAGGGATTTTGCTGAAACCCACAACTGTGTTGACCTGACACAAGTGGCTGAGGTTTTTAGCCAGAAGAATTTTCCTGAAG
TGGTACAGCATGAAGAGTTCATTCTTCTGAGACAAGGAGAGGTGGAAAAGCTAATCAAGTGCGACGAAATTCAGGTGGAT
CCTGAAGAACCAGTCTTTGAGGTTGTCATCAGTTGGGTGAAGCATGCCAAGAAAGAGCAGAAAGAATCCTTGCCTAACCT
GCTACAGTATATGCAGATGCCCCTGCTAACCCTCAGGTATATCACAGATGTAATAGATGCTGAGCCTTTCATCCGCTGTG
GTTTACAATGCAGGGATCTGGTTGATGAAGCAAAGAAGTTTCATCTGAGGCCTGAACTTCAGAGTCAGATGCAGGGACCC
AGGACAAGGGCTCGCCTAGGAGCCAATGAAGTGTTTTTGGTGGCTGGGGGCTTCGGAAGCCAGCAGTCTCCCATCGACGC
AGTAAAGAAATATGACCCCAAGACTCAGGAGTGGAGCTTTTTGCCAAGCATCACTCATAAGAGACGTTATGTGGCCTCAG
TGTCCCTACATGACCAGATCTACGTCATTGGTGGCTATGATGGCCGTTCCCGCCTTAGTCCAGTGGAATGTCTAGACTAC
ACAGCAGATGAGGATGGGGTCTGGTATTCTGTGGCCCCTATGAATGTCCGATGAGGTCTTGCTGGAGCCACCACCCTGGG
AGATTTGATCTATGTCTCTGGAGGCTTTGATGGAAGCAGGCATCACACCAGTATGGAGCGGTATGATCCAAACATTGACC
AGTGGAGCATGCTGGGAGAGATGCAGACAGCCCGGGAAGGTGCTGGACTCGTAGTGGCCAGTGGAGTGATCCACTGTCTA
GGAGGGTATGACGGCTTGAATATCTTAAATTCAGTTGAGAAATATGACCCTCATACAGGACACTGGACTAATGTTACACC
AACGGCACCAAGCGTTCTGGTGCAGGAGTAGCCCTGCTGAATGACCGTATTTATGTGGTGGGGGGATCTGATGGTATAGC
CCATCTTTCTTCCGTTGAAGCATACAACATTTACACTGATTCCTGGACAACTGCCACCAGTATGACCACTCCACGATGCT
ACGTAGGGGCCACAGTGCTTCAGGGGAGACTTTATGCAATTGCAGGATATGATATTAAGTCCCTGCTAAGTAGCATTGAA
TGTTACGACCCTATCATCGACAGCTAGGAAGTCGTGACATCCATGGGAACCCCACGCTGTGATGCTGGTGTGTGTGTTCT
CCATGAGAAG

Alignment

ORF - retro_pabe_1872 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.33 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GGIMAPKDIMTNTHAKSILNSMNSLRKSNTSVDVTLRVEQKDFPCHRIVLAACSDYFCAMFTSELSEKGK
          GGIMAPKDIMTNTHAKSIL.SMNSL.KSNT....TLRVEQ.DFP.H.IVLAACSD.FCAMFTSELS.KGK
Retrocopy GGIMAPKDIMTNTHAKSILSSMNSLGKSNT---LTLRVEQNDFPAHQIVLAACSD*FCAMFTSELSQKGK

Parental  PYVDIQGLTASTMEILLDFVYTETVHVT-VENVQELLPAACLLQLKGVKQACCEFLESQLDPSNCLGIRD
          PYVDIQGLTASTMEILLDFVYTETV.VT..ENVQELLPAACLLQLKGVKQACCEFLESQLDPSNCLGIRD
Retrocopy PYVDIQGLTASTMEILLDFVYTETVYVT<MENVQELLPAACLLQLKGVKQACCEFLESQLDPSNCLGIRD

Parental  FAETHNCVDLMQAAEVFSQKHFPEVVQHEEFIPLSQGEVEKLIKCDEIQVDSEEPVFEAVINWVKHAKKE
          FAETHNCVDL.Q.AEVFSQK.FPEVVQHEEFI.L.QGEVEKLIKCDEIQVD.EEPVFE.VI.WVKHAKKE
Retrocopy FAETHNCVDLTQVAEVFSQKNFPEVVQHEEFILLRQGEVEKLIKCDEIQVDPEEPVFEVVISWVKHAKKE

Parental  REESLPNLLQYVRMPLLTPRYITDVIDAEPFIRCSLQCRDLVDEAKKFHLRPELRSQMQGPRTRARLGAN
          ..ESLPNLLQY..MPLLT.RYITDVIDAEPFIRC.LQCRDLVDEAKKFHLRPEL.SQMQGPRTRARLGAN
Retrocopy QKESLPNLLQYMQMPLLTLRYITDVIDAEPFIRCGLQCRDLVDEAKKFHLRPELQSQMQGPRTRARLGAN

Parental  EVLLVVGGFGSQQSPIDVVEKYDPKTQEWSFLPSITRKRRYVASVSLHDRIYVIGGYDGRSRLSSVECLD
          EV.LV.GGFGSQQSPID.V.KYDPKTQEWSFLPSIT.KRRYVASVSLHD.IYVIGGYDGRSRLS.VECLD
Retrocopy EVFLVAGGFGSQQSPIDAVKKYDPKTQEWSFLPSITHKRRYVASVSLHDQIYVIGGYDGRSRLSPVECLD

Parental  YTADEDGVWYSVAPMNVRRGLAGATTLGDMIYVSGGFDGSRRHTSMERYDPNIDQWSMLGDMQTAREGAG
          YTADEDGVWYSVAPMNVR.GLAGATTLGD.IYVSGGFDGSR.HTSMERYDPNIDQWSMLG.MQTAREGAG
Retrocopy YTADEDGVWYSVAPMNVR*GLAGATTLGDLIYVSGGFDGSRHHTSMERYDPNIDQWSMLGEMQTAREGAG

Parental  LVVASGMIYCLGGYDGLNILNSVEKYDPHTGHWTNVTPMA-TKRSGAGVALLNDHIYVVGGFDGTAHLSS
          LVVASG.I.CLGGYDGLNILNSVEKYDPHTGHWTNVTP.A.TKRSGAGVALLND.IYVVGG.DG.AHLSS
Retrocopy LVVASGVIHCLGGYDGLNILNSVEKYDPHTGHWTNVTPTA<TKRSGAGVALLNDRIYVVGGSDGIAHLSS

Parental  VEAYNIRTDSWTTVTSMTTPRCYVGATVLRGRLYAIAGYDGNSLLSSIECYDPIIDSWEVVTSMGTQRCD
          VEAYNI.TDSWTT.TSMTTPRCYVGATVL.GRLYAIAGYD..SLLSSIECYDPIIDS.EVVTSMGT.RCD
Retrocopy VEAYNIYTDSWTTATSMTTPRCYVGATVLQGRLYAIAGYDIKSLLSSIECYDPIIDS*EVVTSMGTPRCD

Parental  AGVCVLREK
          AGVCVL.EK
Retrocopy AGVCVLHEK

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	1.88 RPM	39.98 RPM
SRP007412_cerebellum	5.96 RPM	28.21 RPM
SRP007412_heart	0.81 RPM	12.97 RPM
SRP007412_kidney	1.79 RPM	27.64 RPM
SRP007412_liver	0.95 RPM	21.70 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1872 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1872 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1872 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006231	1 retrocopy	retro_cjac_2151,
Dasypus novemcinctus	ENSDNOG00000010436	1 retrocopy	retro_dnov_2190,
Echinops telfairi	ENSETEG00000007800	2 retrocopies	retro_etel_2103, retro_etel_723,
Homo sapiens	ENSG00000117153	1 retrocopy	retro_hsap_2545,
Macaca mulatta	ENSMMUG00000017849	1 retrocopy	retro_mmul_612,
Nomascus leucogenys	ENSNLEG00000018103	1 retrocopy	retro_nleu_2795,
Otolemur garnettii	ENSOGAG00000014771	1 retrocopy	retro_ogar_1552,
Pongo abelii	ENSPPYG00000000343	1 retrocopy	retro_pabe_1872 ,
Pan troglodytes	ENSPTRG00000001861	1 retrocopy	retro_ptro_1483,