RetrogeneDB ID: retro_ggor_1730

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 2b:66481027..66481554(+)
• Located in intron of: ENSGGOG00000011071

Retrocopy information

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

Parental gene information

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

Sequence

>retro_ggor_1730
AAAGGAAAACTGAAGCCCAACCTAGGCAACAGGGCAGACCTGCCTGATTACCGCTGGACCAAGACCCTGTCGGAGCTGGA
CCTGGCGGTCCCTTTCCGTGTGGACTTCCAGCGGAAAGGGAAGGATGTGGTGGTGGCATCCAGCGGCGGCACCTCCAGGT
GGGGCTCAAGGGGCAGCCAGCGATCATCGATGGGGAGCTCTACAACGAAGTGAAGGCGGAGGAGAGCTCGTGGCTCATTG
AGGATGGCAAGGTGGTGACTGTGCATCTGGAGAAGATCAAGAAGATGGAGTGGTGGAGCCGCTTGGTATCCAGTGACCCT
GAGATCAATACCAAGAAGATTAACCCTGAGAATTCCAAGCTGTCAGACCTGGACAGTGAGACTCACATCATGGTGGAAAA
GACGATCTATGACCAGTGACAGAAGTCCATGGGGCTGCCAACCTCAGACAAACAGAAGAAACAGGAGATTCTGAAGAAGT
TCATGGATCAGCATCCGGAGATAGATTTTTCCAAGGCTAAATTCAAC

Alignment

ORF - retro_ggor_1730 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.27 %
• Parental protein coverage: 52.38 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KGKLKPNLGNGADLPNYRWTQTLSELDLAVPFHVNFRLKGKDVVV-DIQRRHLRVGLKGQPAIIDGELYN
          KGKLKPNLGN.ADLP.YRWT.TLSELDLAVPF.V.F..KGKDVVV..IQRRHL.VGLKGQPAIIDGELYN
Retrocopy KGKLKPNLGNRADLPDYRWTKTLSELDLAVPFRVDFQRKGKDVVV<GIQRRHLQVGLKGQPAIIDGELYN

Parental  EVKVEESSWLIEDGKVVTVHLEKINKMEWWSRLVSSDPEINTKKINPENSKLSDLDSETRSMVEKMMYDQ
          EVK.EESSWLIEDGKVVTVHLEKI.KMEWWSRLVSSDPEINTKKINPENSKLSDLDSET..MVEK..YDQ
Retrocopy EVKAEESSWLIEDGKVVTVHLEKIKKMEWWSRLVSSDPEINTKKINPENSKLSDLDSETHIMVEKTIYDQ

Parental  RQKSMGLPTSDEQKKQEILKKFMDQHPEMDFSKAKFN
          .QKSMGLPTSD.QKKQEILKKFMDQHPE.DFSKAKFN
Retrocopy *QKSMGLPTSDKQKKQEILKKFMDQHPEIDFSKAKFN

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	8.20 RPM	202.22 RPM
SRP007412_cerebellum	3.55 RPM	95.86 RPM
SRP007412_heart	1.13 RPM	44.25 RPM
SRP007412_kidney	2.90 RPM	94.33 RPM
SRP007412_liver	1.53 RPM	45.90 RPM
SRP007412_testis	2.80 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_1730 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1730 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2183
Pan troglodytes	retro_ptro_1661
Pongo abelii	retro_pabe_2064

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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,