RetrogeneDB ID: retro_pabe_2989

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:113040512..113041173(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OAT
• Ensembl ID: ENSPPYG00000002737
• Aliases: None
• Description: ornithine aminotransferase, mitochondrial [Source:RefSeq peptide;Acc:NP_001125904]

Sequence

>retro_pabe_2989
TTTTCAACTACCACAGTTATTCCCATGAATACAAGAATGGAGGCTGCAGAGACTGCCTGTAAACTAGCTCATAGGTGGGG
CTATACCATGAAGGACATTCAGAAATACAAGCAAAGTTGTTTTTGCAGCTGGAAACTTTTGGGGTAGGACGTTGTCTGCT
ATGTCCAGTTCCACAGACCCAACCAGTTATGATGGTTTGGGGCCGTTTATGCTGGGATTTGACATCATTCCCTATAATGA
TCTGCCTGCACAGGAGCATGCTTTTCAGGATCCGAATGTGGCTGCGTTCATGGTTGAACCAATTTAGGGTGAAGCGAGTG
TTGTTGTTCTGGATCCAGGTTACCTAATGGGAGTGCAAGAACTCCACACCAGGCACCAGGTTCTGTTTATTGCTGGTGAA
ATACAGACAAGATTAGCCAGAACTGGTAGACGGCTGGCTGTTGAACGTGCAAATGTCAGACCTGATATAGTCTTCCTCGG
AAAGGCCCTTTCTGGGGGCTTATCCCCTATGTCTGCAGTGCTGTGTGATGATGATATATTGCTGACCATTAAGCCAGGGG
AACATGGGTCCACATACGTTGGCAACCCATTAGGCTGCTGAGTGGCTATCACAGCCCTTGAGGTTTTAGACCTTGCTGAA
AATGCAGAAAGAATGGGTATT

Alignment

ORF - retro_pabe_2989 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.76 %
• Parental protein coverage: 51.03 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FNYHKVLPMNTGVEAGETACKLARKWGYTVKGIQKYK-AKI-IFAAGNFWGRTLSAISSSTDPTSYDGFG
          F....V.PMNT..EA.ETACKLA..WGYT.K.IQKYK.AK...FAAGNFWGRTLSA.SSSTDPTSYDG.G
Retrocopy FSTTTVIPMNTRMEAAETACKLAHRWGYTMKDIQKYK<AKL<VFAAGNFWGRTLSAMSSSTDPTSYDGLG

Parental  PFMPGFDIIPYNDLPALERALQDPNVAAFMVEPIQGEAGVVVPDPGYLMGVRELCTRHQVLFIADEIQTG
          PFM.GFDIIPYNDLPA.E.A.QDPNVAAFMVEPI.GEA.VVV.DPGYLMGV.EL.TRHQVLFIA.EIQT.
Retrocopy PFMLGFDIIPYNDLPAQEHAFQDPNVAAFMVEPI*GEASVVVLDPGYLMGVQELHTRHQVLFIAGEIQTR

Parental  LARTGRWLAVDYENVRPDIVLLGKALSGGLYPVSAVLCDDDIMLTIKPGEHGSTYGGNPLGCRVAIAALE
          LARTGR.LAV...NVRPDIV.LGKALSGGL.P.SAVLCDDDI.LTIKPGEHGSTY.GNPLGC.VAI.ALE
Retrocopy LARTGRRLAVERANVRPDIVFLGKALSGGLSPMSAVLCDDDILLTIKPGEHGSTYVGNPLGC*VAITALE

Parental  VLEEENLAENADKLGL
          VL....LAENA...G.
Retrocopy VLD---LAENAERMGI

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	94.99 RPM
SRP007412_cerebellum	0.00 RPM	72.35 RPM
SRP007412_heart	0.00 RPM	14.57 RPM
SRP007412_kidney	0.00 RPM	51.18 RPM
SRP007412_liver	0.00 RPM	322.42 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2989 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2989 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2989 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012633	1 retrocopy	retro_cjac_2462,
Homo sapiens	ENSG00000065154	1 retrocopy	retro_hsap_4828,
Gorilla gorilla	ENSGGOG00000000848	1 retrocopy	retro_ggor_3010,
Macropus eugenii	ENSMEUG00000005655	1 retrocopy	retro_meug_613,
Mus musculus	ENSMUSG00000030934	1 retrocopy	retro_mmus_3475,
Nomascus leucogenys	ENSNLEG00000000482	2 retrocopies	retro_nleu_2176, retro_nleu_503,
Pongo abelii	ENSPPYG00000002737	2 retrocopies	retro_pabe_2989 , retro_pabe_3754,
Pan troglodytes	ENSPTRG00000003028	1 retrocopy	retro_ptro_3213,
Sus scrofa	ENSSSCG00000010734	1 retrocopy	retro_sscr_1181,
Tursiops truncatus	ENSTTRG00000004225	1 retrocopy	retro_ttru_87,