RetrogeneDB ID: retro_pabe_2055

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:41819015..41819772(+)
• Located in intron of: ENSPPYG00000012851

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUDC
• Ensembl ID: ENSPPYG00000001673
• Aliases: None
• Description: nuclear distribution C homolog (A. nidulans) [Source:HGNC Symbol;Acc:8045]

Sequence

>retro_pabe_2055
CAGAAGGCCCGGTGGGAGAAGAGAGCCCGGGAGAAGGCGGAGCGGGTGGCCAGGCTGGCCAAGGAAGCCAAGTCAGAGAC
CTCGGGGCCCCAGATAAAGGCAGACAGGCAGAGAGGCTGCAGCTAGAGATTGACCAGAAAAAGGATGCGGAGAATCATGA
GGCCCAGCTCAAGAACGGCAGCCTTGACTCCCCAGGAAAGCAGGAGAAGAAGGAGGAAGATGAGGAGGACAAAGAAAAAC
TGAAGCCCAACCTAGGCAACAGGGCAGACCTGCCCAATTACCGCTGGACCCAGAGCCTGTCGGAGCTGGACCTGGCGGTC
CCTTTCCGTGTAAACTTCCAGCTGAAAGGGAAGGACATGGTGGTGGACATCCAGGGGCAGCACCTCCGGGTGGGGCTCAG
GCGGCAGCCAGCGATCATCGATGGGGAGCTCTACAACGAAGTGAAGGTAGAGGAGAGCTCGTGGCTCATTGAGGACGGCA
AGGTGGTGACTGTGCCTCTTGAGAAGATCAATAAGATGGAGTGGTGGAGCTGCTTGGTGTCCAGTGACCCAGAGATCAAT
ACCAAGATGATTAACCCTGAGAATTCCAAGCTGTCAGACCTGGACAGTGAGACTCGCGGCATGGTGGAAAAGATGATGTA
TGACCAGAGACAGAAGTCCATGGGGCTGCCAATCTCAGACGAACAGAAGAAACAGGAGATTCTGAAGAAGTTCATGGATA
ACATCTGGAGATGGATTTTTCCAAGGCCAAATTCAAC

Alignment

ORF - retro_pabe_2055 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.77 %
• Parental protein coverage: 78.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KRARQEAERREKAERAARLAKEAKSETSGPQIKELTDE-EAERLQLEIDQKKDAENHEAQLKNGSLDSPG
          ..AR.E...REKAE...R.A..AK...S............AERLQLEIDQKKDAENHEAQLKNGSLDSPG
Retrocopy QKARWEKRAREKAE---RVARLAKEAKSETSGPQIKAD<QAERLQLEIDQKKDAENHEAQLKNGSLDSPG

Parental  KQETEEDEEEEDEKDKGKLKPNLGNGADLPNYRWTQTLSELDLAVPFRVNFRLKGKDVVVDIQRRHLRVG
          K........EEDE.DK.KLKPNLGN.ADLPNYRWTQ.LSELDLAVPFRVNF.LKGKD.VVDIQ..HLRVG
Retrocopy K----QEKKEEDEEDKEKLKPNLGNRADLPNYRWTQSLSELDLAVPFRVNFQLKGKDMVVDIQGQHLRVG

Parental  LKGQPAIIDGELYNEVKVEESSWLIEDGKVVTVHLEKINKMEWWSRLVSSDPEINTKKINPENSKLSDLD
          L..QPAIIDGELYNEVKVEESSWLIEDGKVVTV.LEKINKMEWWS.LVSSDPEINTK.INPENSKLSDLD
Retrocopy LRRQPAIIDGELYNEVKVEESSWLIEDGKVVTVPLEKINKMEWWSCLVSSDPEINTKMINPENSKLSDLD

Parental  SETRSMVEKMMYDQRQKSMGLPTSDEQKKQEILKKFMDQ-HPEMDFSKAKFN
          SETR.MVEKMMYDQRQKSMGLP.SDEQKKQEILKKFMD..H.EMDFSKAKFN
Retrocopy SETRGMVEKMMYDQRQKSMGLPISDEQKKQEILKKFMDN<HLEMDFSKAKFN

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	0.55 RPM	265.17 RPM
SRP007412_cerebellum	0.97 RPM	137.53 RPM
SRP007412_heart	0.12 RPM	69.96 RPM
SRP007412_kidney	0.60 RPM	155.56 RPM
SRP007412_liver	0.15 RPM	115.03 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2055 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2055 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2055 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2168
Pan troglodytes	retro_ptro_1655
Gorilla gorilla	retro_ggor_1720

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000001291	1 retrocopy	retro_eeur_526,
Homo sapiens	ENSG00000090273	2 retrocopies	retro_hsap_2168, retro_hsap_2183,
Gorilla gorilla	ENSGGOG00000015314	2 retrocopies	retro_ggor_1720, retro_ggor_1730,
Microcebus murinus	ENSMICG00000015671	1 retrocopy	retro_mmur_457,
Mus musculus	ENSMUSG00000028851	1 retrocopy	retro_mmus_3181,
Nomascus leucogenys	ENSNLEG00000009404	2 retrocopies	retro_nleu_2545, retro_nleu_312,
Pongo abelii	ENSPPYG00000001673	2 retrocopies	retro_pabe_2055 , retro_pabe_2064,
Pan troglodytes	ENSPTRG00000000395	2 retrocopies	retro_ptro_1655, retro_ptro_1661,
Pteropus vampyrus	ENSPVAG00000004408	1 retrocopy	retro_pvam_434,
Rattus norvegicus	ENSRNOG00000007399	2 retrocopies	retro_rnor_2009, retro_rnor_2108,