RetrogeneDB ID: retro_ggor_1720

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 2b:39845417..39845945(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000024927
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NUDC
• Ensembl ID: ENSGGOG00000015314
• Aliases: None
• Description: None

Sequence

>retro_ggor_1720
AAAGGAAAACTGAAGCCCAACCTAGGCAACGGGGCAGACCTGCCCAATTACCGCTGGACCCAGAGCCTGTCGGAGCTGGA
CCTGGTGGTCCCTTTCCGTGTAAACTTCCGGCTGAAAGGGAAGGACATGGTGGTGGACATCCAGGGGCAGCATCTCCGGG
TGGGGCTCAAGGGGCAGCCAGCGATCATCGATGGGGAGCTCTACAACGAAGTGAAGGTAGGGGACAGCTCGTGGCTCATT
GAGGATGGCAAGGTGGTGACTGTGCATCTTGAGAAGATCAATAAGATGGAGTGGTGGAGCTGCTTGGTGTCCAGTGACCC
TGAGATCAATACCAAGATGATTAACCCTGAGAATTCCAAGCTGTCAGACCTGGACAATGAGACTTGCAGCATGGTGGAAA
AGATGATATATGACCAGAGACAGAAGTCCATGGGGCTGCCAATCTCAGACGAACAGAAGAAACAGGAGATTCTGAAGAAG
TTCATGGATCAGCATCTGGAGATGGATTTTTCCAAGGCCAAATTCAAC

Alignment

ORF - retro_ggor_1720 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.48 %
• Parental protein coverage: 52.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KGKLKPNLGNGADLPNYRWTQTLSELDLAVPFHVNFRLKGKDVVVDIQRRHLRVGLKGQPAIIDGELYNE
          KGKLKPNLGNGADLPNYRWTQ.LSELDL.VPF.VNFRLKGKD.VVDIQ..HLRVGLKGQPAIIDGELYNE
Retrocopy KGKLKPNLGNGADLPNYRWTQSLSELDLVVPFRVNFRLKGKDMVVDIQGQHLRVGLKGQPAIIDGELYNE

Parental  VKVEESSWLIEDGKVVTVHLEKINKMEWWSRLVSSDPEINTKKINPENSKLSDLDSETRSMVEKMMYDQR
          VKV..SSWLIEDGKVVTVHLEKINKMEWWS.LVSSDPEINTK.INPENSKLSDLD.ET.SMVEKM.YDQR
Retrocopy VKVGDSSWLIEDGKVVTVHLEKINKMEWWSCLVSSDPEINTKMINPENSKLSDLDNETCSMVEKMIYDQR

Parental  QKSMGLPTSDEQKKQEILKKFMDQHPEMDFSKAKFN
          QKSMGLP.SDEQKKQEILKKFMDQH.EMDFSKAKFN
Retrocopy QKSMGLPISDEQKKQEILKKFMDQHLEMDFSKAKFN

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	0.96 RPM	202.22 RPM
SRP007412_cerebellum	0.91 RPM	95.86 RPM
SRP007412_heart	0.19 RPM	44.25 RPM
SRP007412_kidney	0.78 RPM	94.33 RPM
SRP007412_liver	0.05 RPM	45.90 RPM
SRP007412_testis	0.00 RPM	93.24 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_1720 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1720 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2168
Pan troglodytes	retro_ptro_1655
Pongo abelii	retro_pabe_2055

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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,