RetrogeneDB ID: retro_pabe_2064

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:68692935..68693556(+)
• Located in intron of: ENSPPYG00000012977

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_2064
GAGAATCATGAGGCCCAGCTCAAGAATGGCAGCCTTGACTCCCCAGGGAAGCAGGAGACTGAGGAAGATGAGGAGGAGAA
AGATGAGAAGGACAAAGGAAAACTGAAGCCCAACCTAGGCAACAGGGCAGACTTGCCTGATTACCGCTGGACCAAGACCC
TGTCTTAGCTAGACCTGGCGATCCCTTTCCGTGTGAACTTCCAGCTGAAAGGGAAGGACGTAGTGGTGGACATCCAGTGG
CAGCACCTCCAGGTGGGGCTCAAGAGGCAGCCAGCGATCATCGATGGGGAGTTCTACAACGAAGTGAAGGCGGAGGAGAG
CTCGTGGCTCATTGAGGACGGCAAGGTGGTGACTGTGCATCTGGAGAAGATCAATACGTTGGAGTGGTGGAGCCGCTTGG
TGTCCAGTGACCCTGAGATCAATACCAAGAAGATTAACCCTGAGAATTCCAAGCTGTCATACCTGGACAGTGAGACTCAC
ATCATGGTGGAAAAGATGATCTATGACCAGTGACAGAAGTCCGTGGGACTGCCAACCTCAGACGAACAGAAGAAACAGGA
GATTCTGAAGAAGTTCATGGATCAGCATCCGGAGATGGATTTTTCCAAGGCTAAATTCAAC

Alignment

ORF - retro_pabe_2064 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.06 %
• Parental protein coverage: 62.35 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ENHEAQLKNGSLDSPGKQETEEDEEEEDEKDKGKLKPNLGNGADLPNYRWTQTLSELDLAVPFRVNFRLK
          ENHEAQLKNGSLDSPGKQET.............KLKPNLGN.ADLP.YRWT.TLS.LDLA.PFRVNF.LK
Retrocopy ENHEAQLKNGSLDSPGKQETXXXXXXXXXXXXXKLKPNLGNRADLPDYRWTKTLS*LDLAIPFRVNFQLK

Parental  GKDVVVDIQRRHLRVGLKGQPAIIDGELYNEVKVEESSWLIEDGKVVTVHLEKINKMEWWSRLVSSDPEI
          GKDVVVDIQ..HL.VGLK.QPAIIDGE.YNEVK.EESSWLIEDGKVVTVHLEKIN..EWWSRLVSSDPEI
Retrocopy GKDVVVDIQWQHLQVGLKRQPAIIDGEFYNEVKAEESSWLIEDGKVVTVHLEKINTLEWWSRLVSSDPEI

Parental  NTKKINPENSKLSDLDSETRSMVEKMMYDQRQKSMGLPTSDEQKKQEILKKFMDQHPEMDFSKAKFN
          NTKKINPENSKLS.LDSET..MVEKM.YDQ.QKS.GLPTSDEQKKQEILKKFMDQHPEMDFSKAKFN
Retrocopy NTKKINPENSKLSYLDSETHIMVEKMIYDQ*QKSVGLPTSDEQKKQEILKKFMDQHPEMDFSKAKFN

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	265.17 RPM
SRP007412_cerebellum	0.00 RPM	137.53 RPM
SRP007412_heart	0.03 RPM	69.96 RPM
SRP007412_kidney	0.10 RPM	155.56 RPM
SRP007412_liver	0.03 RPM	115.03 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2064 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2064 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2064 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2183
Pan troglodytes	retro_ptro_1661
Gorilla gorilla	retro_ggor_1730

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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,