RetrogeneDB ID: retro_pabe_81

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 14:74725415..74726294(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000005972
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: NUS1
• Ensembl ID: ENSPPYG00000025886
• Aliases: None
• Description: nuclear undecaprenyl pyrophosphate synthase 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:21042]

Sequence

>retro_pabe_81
ATGACGAGGCTGTACGAGCTGGTGTGGTGGGTGCTGCACGCGCTGCTCTATCTGCACCGCACGCTCACCTCCTGGCTCCG
CGTTGGGTTCGGCACCTGGAACTGGATCTGGCGGCGCTGCTGCCGCGCCGCCTCTGCCGCGGTCCTAGCGCCTCTCGGCT
TCACGCTCCGCCAGCCCCGGGCAGTTGGCAGGAACCGCCGTCACCACCGGCACCCGCGCGGGGGGTCGTGCCTGGCAGCC
GCCCACCACCGGATGCGCTGGCGCGCCGACGGCCGTTCCTTGGAGAAGCTGCCTGTGCATATGGGCCTGGTGATCACCCA
GGTGGAGCAGGAACCCAGCTTCTCGGACATCGCGAGCCTCGTGGTGTGGTGTATGGCCGTGGGCATCTCCTACATTAGCG
TCTACGACCACCAAGGTATTTTCAAAAGAAATAATTCCAGATTGACGGATGAAATTTTAAAACAACAGCAAGAACTTCTG
GGCCTAGATTGTTCAAAATACTCACCAGAATTTGCAAATAGTAGTGACAAAGATGATCAAGTTTTAAATTGCCATTTGGC
AGTGAAGGTGCTGTCTCCGGAAGATGGAAAAGCAGATATTTTAAGAGCTGCTCAGGACTTTTGCCAGTTAGTAGCCCAGA
AGCAAAAGAGACCCACAGATTTGGATGTAGATACGTTAGGCAGTTTACTTAGTTCAAATGGTTGTCCTGATCCTGATTTA
GTATTGAAGTTCGGTCCTGTGGACAGCACATTAGGCTTTCTTCCCTGGCACATCAGATTGACTGAGATTGTCTCTTTGCC
TTCCCACCTAAACATCAGTTATGAGGACTTTTTCTCTGCCCTTCGTCAATATGCAGCCTGTGAACAGCGTCTGGGAAAG

Alignment

ORF - retro_pabe_81 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.21 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTGLYELVWRVLHALLCLHRTLTSWLRVRFGTWNWIWRRCCRAASAAVLAPLGFTLRKPPAVGRNRRHHR
          MT.LYELVW.VLHALL.LHRTLTSWLRV.FGTWNWIWRRCCRAASAAVLAPLGFTLR.P.AVGRNRRHHR
Retrocopy MTRLYELVWWVLHALLYLHRTLTSWLRVGFGTWNWIWRRCCRAASAAVLAPLGFTLRQPRAVGRNRRHHR

Parental  HPRGGSCLAAAHHRMRWRADGRSLEKLPVHMGLVITEVEQEPSFSDIASLVVWCMAVGISYISVYDHQGI
          HPRGGSCLAAAHHRMRWRADGRSLEKLPVHMGLVIT.VEQEPSFSDIASLVVWCMAVGISYISVYDHQGI
Retrocopy HPRGGSCLAAAHHRMRWRADGRSLEKLPVHMGLVITQVEQEPSFSDIASLVVWCMAVGISYISVYDHQGI

Parental  FKRNNSRLMDEILKQQQELLGLDCSKYSPEFANSNDKDDQVLNCHLAVKVLSPEDGKADIVRAAQDFCQL
          FKRNNSRL.DEILKQQQELLGLDCSKYSPEFANS.DKDDQVLNCHLAVKVLSPEDGKADI.RAAQDFCQL
Retrocopy FKRNNSRLTDEILKQQQELLGLDCSKYSPEFANSSDKDDQVLNCHLAVKVLSPEDGKADILRAAQDFCQL

Parental  VAQKQKRPTDLDVDTLGSLLSSNGCPDPDLVLKFGPVDSTLGFLPWHIRLTEIV
          VAQKQKRPTDLDVDTLGSLLSSNGCPDPDLVLKFGPVDSTLGFLPWHIRLTEIV
Retrocopy VAQKQKRPTDLDVDTLGSLLSSNGCPDPDLVLKFGPVDSTLGFLPWHIRLTEIV

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	1.82 RPM	4.31 RPM
SRP007412_cerebellum	1.95 RPM	2.80 RPM
SRP007412_heart	1.17 RPM	2.92 RPM
SRP007412_kidney	2.78 RPM	5.87 RPM
SRP007412_liver	3.86 RPM	7.99 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_81 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_81 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_81 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000001780	1 retrocopy	retro_dnov_1639,
Erinaceus europaeus	ENSEEUG00000008948	1 retrocopy	retro_eeur_443,
Homo sapiens	ENSG00000153989	4 retrocopies	retro_hsap_1174, retro_hsap_1176, retro_hsap_1289, retro_hsap_4825,
Gorilla gorilla	ENSGGOG00000022321	4 retrocopies	retro_ggor_1012, retro_ggor_914, retro_ggor_915, retro_ggor_993,
Microcebus murinus	ENSMICG00000007831	1 retrocopy	retro_mmur_423,
Nomascus leucogenys	ENSNLEG00000013457	1 retrocopy	retro_nleu_2411,
Oryctolagus cuniculus	ENSOCUG00000011553	1 retrocopy	retro_ocun_1713,
Pongo abelii	ENSPPYG00000025886	1 retrocopy	retro_pabe_81 ,
Pan troglodytes	ENSPTRG00000018547	1 retrocopy	retro_ptro_808,
Tarsius syrichta	ENSTSYG00000003212	1 retrocopy	retro_tsyr_633,
Tursiops truncatus	ENSTTRG00000007352	2 retrocopies	retro_ttru_358, retro_ttru_684,