RetrogeneDB ID: retro_pabe_3109

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:148328716..148330389(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLUD1
• Ensembl ID: ENSPPYG00000002827
• Aliases: None
• Description: glutamate dehydrogenase 1 [Source:HGNC Symbol;Acc:4335]

Sequence

>retro_pabe_3109
ATGTACCGCTACGTGGGCGAAGCGCTGCTGCTGTCCCGGGCCGGGCGGCTGCCCTGGGCTCCGCGGCCACCGACTCGGCT
GGGTTGCTGGGCCGGGCCCGGGGACAGCCCGCCGCCGCCCCGGAGCCGGGGCTCGCATTGGCCGCCCGGCGCCACTACAG
CGACGCGGTGGCCGACCGCGAGGACGACCCCAACTTCCTCAAGATGGTGGAGGGCTTCTTCTATCGCGGCGCCAGCATCG
TGGAGGACAAGCTGGTGGAGGACCTGAGGACCCGGGAGAGCGAGGAGCAGAAGCGGAACCGGGTGCGCGGCATCCTGCGG
ATCATCAAGCCCTGCAACCATGTGCTGAGTCTCTCCTTCCCCATCCGGCGCGACGACGGCTCCTGGGAGGTCATCTAAGG
CTACCGGGCCCAGCACAGCCAGCACCGCACACCCTGCAAGGGAGGTATCCGTTACAGCACTGATGTGAGTGTAGATGAAG
TAAAAACTTTGGCTTCTCTGGTGACATACAAGTGTGCAGTGGTTGATGTGCCGTTTGGGGGTGCTAAAGCTGGTGTTAAG
ATCAATCCCAAGAACTATACCGATAATGAATTGGAAAAGATCACAAGGAGGTTCACCATGGAACTAGCAAAGAAGGGCTT
TATTGGTCCTGGCATTGATGTGCCTGCTCCAGACATGAGCACAGGTGAGCGGGAGATGTCCTGGATCGCTGATACCTATG
TCAGCACCATAGGGCACTACGATATTAATGCACACGCCTGTGTTACTGGTAAACCCATCAGCCAAGAGGGCGTGCATGGA
CGCATCTCTGCTACTGGCCGTGGTGTCTTCCATAGGATTGAAAACTTCATCAGTGAAGCTTCTTACATGAGCATTTTAGG
AATGACACCAGGGTTTGGAGATAAAACATTTGTTGTTCAGGGATTTGGTAATGTGGGCCTACACTCTATGAGATATTTAC
ATCGTTTTGGTGCTAAGTGTATTGCTGTTGGTGAGTCTGATGGGAGTATATGGAATCCAGATGGTATTGACCTAAAGGAA
CTGGAAGACTTCAGATTGCAACATGGGTCCATTCTGGGCTTCCCCAAGGCAAAGCCCTATGAAGGAAGCATCTTGGAGGC
CGACTGTGACATACTGATCCCGGCTGCCGGTGAGAAGCAGTTGACCAAATCCAGCGCAGCCAGAGTCAAAGCCAAGATCA
TTGCTGAAGGTGCCAACGGGCCAATCACTCCAGAAGCTGACAAGGTCTTCCTGGAGAGAAACATTATGGTTATTCCAGAT
CTCTACTTGAATGCTGGAGGAGTGACAGTATCTTACTTTGAGTGGCTGAAGAATCTAAATCATGTCAGCTATGGCCGTTT
GACCTTCAAATATGAAAGGGATCCTAACTACCACTTGCTCATGTCTGTTCAAGAGAGTTTAGAAAGAAAATTTGGAAAGC
ACGGTGGAACTATTCCCATTGTACCCACAGCAGAGTTCCGAGACAGGATATCGGGTGCATCTGAGAAAGACATCATGCAC
TCTGGCTTGGCGTACACAATGGAGCATTCTTCCAGGCAAATTATGCGCACACACATGAAGTATAACCTGGGATTGGACCT
CAGAACAGCTGCCTATGTCAATGCCATTGAGAAAGTCTTCAAAGTGTACAGTGAAGCTGGTGTGAGCTTCACA

Alignment

ORF - retro_pabe_3109 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.1 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MYRYLGEALLLSRAG-PAALGSASADSAALLGRARGQPAAAPQPGLALAARRHYSEAVADREDDPNFFKM
          MYRY.GEALLLSRAG..AALGSA..DSA.LLGRARGQPAAAP.PGLALAARRHYS.AVADREDDPNF.KM
Retrocopy MYRYVGEALLLSRAG<AAALGSAATDSAGLLGRARGQPAAAPEPGLALAARRHYSDAVADREDDPNFLKM

Parental  VEGFFDRGASIVEDKLVEDLRTRESEEQKRNRVRGILRIIKPCNHVLSLSFPIRRDDGSWEVIEGYRAQH
          VEGFF.RGASIVEDKLVEDLRTRESEEQKRNRVRGILRIIKPCNHVLSLSFPIRRDDGSWEVI.GYRAQH
Retrocopy VEGFFYRGASIVEDKLVEDLRTRESEEQKRNRVRGILRIIKPCNHVLSLSFPIRRDDGSWEVI*GYRAQH

Parental  SQHRTPCKGGIRYSTDVSVDEVKALASLMTYKCAVVDVPFGGAKAGVKINPKNYTDNELEKITRRFTMEL
          SQHRTPCKGGIRYSTDVSVDEVK.LASL.TYKCAVVDVPFGGAKAGVKINPKNYTDNELEKITRRFTMEL
Retrocopy SQHRTPCKGGIRYSTDVSVDEVKTLASLVTYKCAVVDVPFGGAKAGVKINPKNYTDNELEKITRRFTMEL

Parental  AKKGFIGPGIDVPAPDMSTGEREMSWIADTYASTIGHYDINAHACVTGKPISQGGIHGRISATGRGVFHG
          AKKGFIGPGIDVPAPDMSTGEREMSWIADTY.STIGHYDINAHACVTGKPISQ.G.HGRISATGRGVFH.
Retrocopy AKKGFIGPGIDVPAPDMSTGEREMSWIADTYVSTIGHYDINAHACVTGKPISQEGVHGRISATGRGVFHR

Parental  IENFINEASYMSILGMTPGFGDKTFVVQGFGNVGLHSMRYLHRFGAKCIAVGESDGSIWNPDGIDPKELE
          IENFI.EASYMSILGMTPGFGDKTFVVQGFGNVGLHSMRYLHRFGAKCIAVGESDGSIWNPDGID.KELE
Retrocopy IENFISEASYMSILGMTPGFGDKTFVVQGFGNVGLHSMRYLHRFGAKCIAVGESDGSIWNPDGIDLKELE

Parental  DFKLQHGSILGFPKAKPYEGSILEADCDILIPAASEKQLTKSNAPRVKAKIIAEGANGPTTPEADKIFLE
          DF.LQHGSILGFPKAKPYEGSILEADCDILIPAA.EKQLTKS.A.RVKAKIIAEGANGP.TPEADK.FLE
Retrocopy DFRLQHGSILGFPKAKPYEGSILEADCDILIPAAGEKQLTKSSAARVKAKIIAEGANGPITPEADKVFLE

Parental  RNIMVIPDLYLNAGGVTVSYFEWLKNLNHVSYGRLTFKYERDSNYHLLMSVQESLERKFGKHGGTIPIVP
          RNIMVIPDLYLNAGGVTVSYFEWLKNLNHVSYGRLTFKYERD.NYHLLMSVQESLERKFGKHGGTIPIVP
Retrocopy RNIMVIPDLYLNAGGVTVSYFEWLKNLNHVSYGRLTFKYERDPNYHLLMSVQESLERKFGKHGGTIPIVP

Parental  TAEFQDRISGASEKDIVHSGLAYTMERSARQIMRTAMKYNLGLDLRTAAYVNAIEKVFKVYNEAGVTFT
          TAEF.DRISGASEKDI.HSGLAYTME.S.RQIMRT.MKYNLGLDLRTAAYVNAIEKVFKVY.EAGV.FT
Retrocopy TAEFRDRISGASEKDIMHSGLAYTMEHSSRQIMRTHMKYNLGLDLRTAAYVNAIEKVFKVYSEAGVSFT

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	0.11 RPM	112.24 RPM
SRP007412_cerebellum	0.00 RPM	77.34 RPM
SRP007412_heart	0.00 RPM	38.26 RPM
SRP007412_kidney	0.03 RPM	142.63 RPM
SRP007412_liver	0.15 RPM	303.14 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3109 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3109 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3109 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007540	2 retrocopies	retro_btau_1413, retro_btau_1741,
Canis familiaris	ENSCAFG00000016095	1 retrocopy	retro_cfam_747,
Choloepus hoffmanni	ENSCHOG00000001101	1 retrocopy	retro_chof_2002,
Callithrix jacchus	ENSCJAG00000011633	1 retrocopy	retro_cjac_2830,
Dipodomys ordii	ENSDORG00000009767	1 retrocopy	retro_dord_400,
Equus caballus	ENSECAG00000007371	2 retrocopies	retro_ecab_886, retro_ecab_919,
Echinops telfairi	ENSETEG00000019638	2 retrocopies	retro_etel_141, retro_etel_2024,
Homo sapiens	ENSG00000148672	1 retrocopy	retro_hsap_31,
Gorilla gorilla	ENSGGOG00000015770	1 retrocopy	retro_ggor_2954,
Loxodonta africana	ENSLAFG00000012059	1 retrocopy	retro_lafr_504,
Microcebus murinus	ENSMICG00000016526	1 retrocopy	retro_mmur_524,
Monodelphis domestica	ENSMODG00000002756	1 retrocopy	retro_mdom_124,
Nomascus leucogenys	ENSNLEG00000011658	1 retrocopy	retro_nleu_36,
Otolemur garnettii	ENSOGAG00000003641	1 retrocopy	retro_ogar_2757,
Procavia capensis	ENSPCAG00000008662	1 retrocopy	retro_pcap_11,
Pongo abelii	ENSPPYG00000002827	3 retrocopies	retro_pabe_3109 , retro_pabe_3213, retro_pabe_79,
Pan troglodytes	ENSPTRG00000002711	4 retrocopies	retro_ptro_3162, retro_ptro_3283, retro_ptro_3285, retro_ptro_3290,
Ictidomys tridecemlineatus	ENSSTOG00000012843	1 retrocopy	retro_itri_737,
Tarsius syrichta	ENSTSYG00000001578	1 retrocopy	retro_tsyr_313,
Tursiops truncatus	ENSTTRG00000008145	1 retrocopy	retro_ttru_950,