RetrogeneDB ID: retro_ggor_2023

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 4:39781271..39782163(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WDR5
• Ensembl ID: ENSGGOG00000004997
• Aliases: None
• Description: None

Sequence

>retro_ggor_2023
TCTCTAAAGTTCACCCTTGCTGGCCGCACCAAAGCAGTGTCCTCCGTGAAATTCAGCCCGAATGGAGAGTGGCTGGCAAG
TTCATCTGCTGATAAACTCATTAAAATTTGGGGGACTCATATGATGGGAAATCTGAGAAAACCGTCTGGTCACAAGCTGG
GAATATCTGATGCAGCCTGGTCGTCAGATTCTAACCTTTTTGTTTCCGCCTCAGATGACAAAACCTTGAAGATACGGGAC
GTGAGCTCGGGAAAGTGTCTGAAAACCCTGAAGGGACACAGTAATTACGTCTTTTGCTGTAACTTCAATCTCCAGTCCAG
CCTTACTGTCTCAGGATCCTTTGATGAAAGTGTGAGGATATGGGTTGTGAAAACAGGGAAGTGCCACAAGACTGCTAGCT
CACTCGGATCCAGTCTCGGCCATTCATTTTAATCGTGATGGATTCTTGATAGTTTCAAGTAGCTATGATGGTCTCTGTCA
CATCTGGGACACCGCCTCAGGCCAGTGCCTGAAAACGCTCACTGATTATGACAACCCCTGGTGTCTTTTGTGAAGCTCTC
CCCGAAGGGCGGATACAGCCTGGCTGCCACGCTGGACAACACTCAAGCTCTGGGACTACAGCAAGGGGAAGTGCCTGAAG
ACATACACTGGCCACAAGAACGAGAAATACTGCATATTTGCCAATTTCTCTGTTACTGGCGGGAAGTGGATTGTGTCTGG
CTCTGAGGATAACCTTCTTTACATCTGGAACCTTCAGACAAAAGAGATTGTACAGAAATTACAAGGCCACACAGATGTTG
TGATCTCAACAGCTTGTCACCCAACAGAAAACATCATCACCTCTGCCGCGCTAGAAAATGACAAAACAATTAAACTGTGG
AAGAGTGACTGT

Alignment

ORF - retro_ggor_2023 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.67 %
• Parental protein coverage: 89.52 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKFEKTISGHKLGISDVAWSSDSNLLVSA
          .LKFTLAG.TKAVSSVKFSPNGEWLASSSADKLIKIWG..........SGHKLGISD.AWSSDSNL.VSA
Retrocopy SLKFTLAGRTKAVSSVKFSPNGEWLASSSADKLIKIWGTHMMGNLRKPSGHKLGISDAAWSSDSNLFVSA

Parental  SDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFNPQSNLIVSGSFDESVRIWDVKT-GKCLKTLPAHSDPV
          SDDKTLKI.DVSSGKCLKTLKGHSNYVFCCNFN.QS.L.VSGSFDESVRIW.VKT.G.....L.AHSDPV
Retrocopy SDDKTLKIRDVSSGKCLKTLKGHSNYVFCCNFNLQSSLTVSGSFDESVRIWVVKT>GSATRLL-AHSDPV

Parental  SAVHFNRDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVSFVKFSPNGKYILAATLDNTLKLWDYS
          SA.HFNRDG.LIVSSSYDGLC.IWDTASGQCLKT...D...P......SP............TLKLWDYS
Retrocopy SAIHFNRDGFLIVSSSYDGLCHIWDTASGQCLKT-LTDYDNPWCLL*SSPRRADTAWLPRWTTLKLWDYS

Parental  KGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQGHTDVVISTACHPTEN
          KGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNL.YIWNLQTKEIVQKLQGHTDVVISTACHPTEN
Retrocopy KGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLLYIWNLQTKEIVQKLQGHTDVVISTACHPTEN

Parental  IIASAALENDKTIKLWKSDC
          II.SAALENDKTIKLWKSDC
Retrocopy IITSAALENDKTIKLWKSDC

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	0.58 RPM	34.00 RPM
SRP007412_cerebellum	1.65 RPM	49.92 RPM
SRP007412_heart	0.06 RPM	10.54 RPM
SRP007412_kidney	0.12 RPM	29.36 RPM
SRP007412_liver	0.00 RPM	24.48 RPM
SRP007412_testis	0.10 RPM	79.98 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_2023 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2023 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1975

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011179	1 retrocopy	retro_amel_29,
Bos taurus	ENSBTAG00000047031	1 retrocopy	retro_btau_299,
Canis familiaris	ENSCAFG00000019830	1 retrocopy	retro_cfam_128,
Callithrix jacchus	ENSCJAG00000010123	1 retrocopy	retro_cjac_1,
Cavia porcellus	ENSCPOG00000014790	1 retrocopy	retro_cpor_12,
Dipodomys ordii	ENSDORG00000015010	1 retrocopy	retro_dord_7,
Equus caballus	ENSECAG00000017389	1 retrocopy	retro_ecab_82,
Echinops telfairi	ENSETEG00000015731	1 retrocopy	retro_etel_15,
Felis catus	ENSFCAG00000005712	1 retrocopy	retro_fcat_119,
Homo sapiens	ENSG00000196363	1 retrocopy	retro_hsap_11,
Gorilla gorilla	ENSGGOG00000004997	2 retrocopies	retro_ggor_171, retro_ggor_2023 ,
Gorilla gorilla	ENSGGOG00000014802	1 retrocopy	retro_ggor_440,
Loxodonta africana	ENSLAFG00000011192	1 retrocopy	retro_lafr_55,
Microcebus murinus	ENSMICG00000008085	1 retrocopy	retro_mmur_34,
Myotis lucifugus	ENSMLUG00000002236	1 retrocopy	retro_mluc_11,
Macaca mulatta	ENSMMUG00000014159	1 retrocopy	retro_mmul_190,
Mustela putorius furo	ENSMPUG00000012184	1 retrocopy	retro_mputfur_2,
Mus musculus	ENSMUSG00000026917	1 retrocopy	retro_mmus_132,
Otolemur garnettii	ENSOGAG00000008960	1 retrocopy	retro_ogar_86,
Procavia capensis	ENSPCAG00000013476	1 retrocopy	retro_pcap_43,
Pan troglodytes	ENSPTRG00000023653	2 retrocopies	retro_ptro_18, retro_ptro_1975,
Pteropus vampyrus	ENSPVAG00000001666	1 retrocopy	retro_pvam_112,
Rattus norvegicus	ENSRNOG00000008212	1 retrocopy	retro_rnor_258,
Sus scrofa	ENSSSCG00000024912	1 retrocopy	retro_sscr_1,
Ictidomys tridecemlineatus	ENSSTOG00000015899	1 retrocopy	retro_itri_117,
Drosophila melanogaster	FBgn0040066	1 retrocopy	retro_dmel_69,