RetrogeneDB ID: retro_ggor_1758

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 2b:18262112..18263752(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARHGAP42
• Ensembl ID: ENSGGOG00000011397
• Aliases: None
• Description: None

Sequence

>retro_ggor_1758
AAATCTTGTATCCGACGAAAGACAGATTCAATTGACAAACACTTCTACTTCGACATACAAGTAGTTGAAAGCCATGGGAT
CATCACATTACAGGCCTTCTCAGACGCTAATAGGAAACTCTGGCTTGAAGCCACGGATGGGAAGGAAACGATTTATACTC
TGCCTGACATTATAAGCAAGAAAGAAGAAATGTATTTGAATGAAGCAGGGTTCAATTTTGTGAGAAACTGCATTCAAGCT
GTGGAAACAAGTGGTATCACCATTTTAGGCCTCTACTGAATAGGAGGAGTGAACTCCAAAGTTCAAAAACTTGTGAATAT
CATATTTTCTCCTAAATCCCCTCCTGATATTGATATTGAACTGTGGGACAATAAGACAATAATGAGTGGGCTGAAAAACT
ACCTCAGGTGCTTTGCAGCACCACTGATGACTTACAAGTTACACAAAGATTTGTATCATTGCTGTTAAATCTGATGACCA
AAACTACAGGGTGGAGGCTGTACATGCATTGGTGTGCACATTGCCAGAGAAAAACAGAGAGATGCTGGACATCTTAATAA
AACATCTGGTCAAAGTATCACTGCACAGCCAACAAAATCTCATGACTGTCTAAAATCTTGGTGTCATATTTGGCCCAACT
CTAATGAGAGCACAGGAATAAACTGTGGCTGCTATGGTGAATATTAAATTTCAGAATATTGTGTAGAAATTCTGATAGAG
CACAATGAAACAATTTTTCATACTGCTCCAGACCCAAGCATTCCTCTTCCTCAGCCTCAGTCTCGATCTGGATCCCAAAG
GACATGAGCAATCTGCCTCTCTATAGGCTCTAGGAAGCCCAGAGGGACGTGTACTCCATGCCTGGCTGAACTTGATAGTG
ACTCCTATAGCAGCAGCACAGACAGCACCCCCATGGGGAGCATCAAGTCACTCTCTTCTCTTTCCTCGGAACAAAATAGC
ACTACAAACTCAGCTTCCTGCCAGCCCAGGGAGAAATCTGGAGGGATTCCTTGGATTGCAACCCCGTCATCTTCCCATGG
ACAGAAAAGCCTTGGTCTCTGGACAACCAGTCCTGAATCAAGTTCTAGAGAAGATGCAACCAAGACAGATGCAGAATCAG
ATTGCCAGAGTGCTGCTTCGGTCACTAGCCCAGGGGATGTTTCCCCACCCATAGACCTAGTCAAGAAAGGGCCTTATGGA
CTTTCAGGACTGAAAAGAGCTTCTGCTTCTTCTCTCAGATCCATCTCTGCAGCTGAAGGAAACACCAGCTACAGTGGATC
TATTCAAAGCTTAACTTCTGTAGGTTCCAAGGAGACACCCAAAGCTTCAAACCCAGACCTGCCTCCAAAAATGTGCAGGA
GGTTAAGACTAGACACCACCTCAAGCAATGGCTATCAGCGTACTGGCTCAGTAGTGGCAGCAAAAGCTCAACTGTTTGAA
AATGTTGGTTCACCTAAGCCAGTTTCTTCTGGGCACCAAGCCAAAGCCATGTACTCCTGTAAAGCAGAGCACAGCGTGAG
TTTTCCTTCCCACAAGGAGCGATATTTTCCAGCGTGGACCCATCAGTGGAACCAGGATGGTTAAAGGCAACTTATGAAGG
CAAAACGGGACTAGTTCCAGAAAATTATGTTGTCTTCCTC

Alignment

ORF - retro_ggor_1758 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.6 %
• Parental protein coverage: 62.93 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KSCIRRKTDSIDKRFCFDIEVVERHGIITLQAFSEANRKLWLEAMDGKEPIYTLPAIISKKEEMYLNEAG
          KSCIRRKTDSIDK.F.FDI.VVE.HGIITLQAFS.ANRKLWLEA.DGKE.IYTLP.IISKKEEMYLNEAG
Retrocopy KSCIRRKTDSIDKHFYFDIQVVESHGIITLQAFSDANRKLWLEATDGKETIYTLPDIISKKEEMYLNEAG

Parental  FNFVRKCIQAVETRGITILGLYRIGGVNSKVQKLMNTTFSPKSPPDIDIDIELWDNKTITSGLKNYLRCL
          FNFVR.CIQAVET.GITILGLY.IGGVNSKVQKL.N..FSPKSPPDIDI..ELWDNKTI.SGLKNYLRC.
Retrocopy FNFVRNCIQAVETSGITILGLY*IGGVNSKVQKLVNIIFSPKSPPDIDI--ELWDNKTIMSGLKNYLRCF

Parental  AEPLMTYKLHKDF-IIAVKSDDQNYRVEAVHALVHKLPEKNREMLDILIKHLVKVSLHSQQNLMTVSNLG
          A.PLMTYKLHKD..IIAVKSDDQNYRVEAVHALV..LPEKNREMLDILIKHLVKVSLHSQQNLMTV.NLG
Retrocopy AAPLMTYKLHKDL>IIAVKSDDQNYRVEAVHALVCTLPEKNREMLDILIKHLVKVSLHSQQNLMTV*NLG

Parental  VIFGPTLMRAQEETVAAMMNIKFQNIV-VEILIEHYEKIFHTAPDPSIPLPQPQSRSGSRRTRAICLSTG
          VIFGPTLMRAQE.TVAAM.NIKFQNIV.VEILIEH.E.IFHTAPDPSIPLPQPQSRSGS.RT.AICLS.G
Retrocopy VIFGPTLMRAQE*TVAAMVNIKFQNIV<VEILIEHNETIFHTAPDPSIPLPQPQSRSGSQRT*AICLSIG

Parental  SRKPRGRYTPCLAEPDSDSYSSSPDSTPMGSIESLSSHSSEQNSTTKSASCQPREKSGGIPWIATPSSSN
          SRKPRG..TPCLAE.DSDSYSSS.DSTPMGSI.SLSS.SSEQNSTT.SASCQPREKSGGIPWIATPSSS.
Retrocopy SRKPRGTCTPCLAELDSDSYSSSTDSTPMGSIKSLSSLSSEQNSTTNSASCQPREKSGGIPWIATPSSSH

Parental  GQKSLGLWTTSPESSSREDATKTDAESDCQSVASVTSPGDVSPPIDLVKKEPYGLSGLKRASASSLRSIS
          GQKSLGLWTTSPESSSREDATKTDAESDCQS.ASVTSPGDVSPPIDLVKK.PYGLSGLKRASASSLRSIS
Retrocopy GQKSLGLWTTSPESSSREDATKTDAESDCQSAASVTSPGDVSPPIDLVKKGPYGLSGLKRASASSLRSIS

Parental  AAEGNKSYSGSIQSLTSVGSKETPKASPNPDLPPKMCRRLRLDTASSNGYQRPGSVVAAKAQLFENVGSP
          AAEGN.SYSGSIQSLTSVGSKETPKAS.NPDLPPKMCRRLRLDT.SSNGYQR.GSVVAAKAQLFENVGSP
Retrocopy AAEGNTSYSGSIQSLTSVGSKETPKAS-NPDLPPKMCRRLRLDTTSSNGYQRTGSVVAAKAQLFENVGSP

Parental  KPVSSGRQAKAMYSCKAEHS-HELSFPQGAIFSNVYPSVEPGWLKATYEGKTGLVPENYVVFL
          KPVSSG.QAKAMYSCKAEHS..E.SFPQGAIFS.V.PSVEPGWLKATYEGKTGLVPENYVVFL
Retrocopy KPVSSGHQAKAMYSCKAEHS<REFSFPQGAIFSSVDPSVEPGWLKATYEGKTGLVPENYVVFL

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	5.75 RPM
SRP007412_cerebellum	0.00 RPM	2.68 RPM
SRP007412_heart	0.00 RPM	1.06 RPM
SRP007412_kidney	0.00 RPM	14.72 RPM
SRP007412_liver	0.00 RPM	7.31 RPM
SRP007412_testis	0.00 RPM	13.47 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_1758 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1758 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000005829	1 retrocopy	retro_ecab_997,
Homo sapiens	ENSG00000165895	2 retrocopies	retro_hsap_2156, retro_hsap_2318,
Gorilla gorilla	ENSGGOG00000011397	2 retrocopies	retro_ggor_1714, retro_ggor_1758 ,
Pongo abelii	ENSPPYG00000003799	1 retrocopy	retro_pabe_2095,
Pan troglodytes	ENSPTRG00000004204	4 retrocopies	retro_ptro_1641, retro_ptro_1692, retro_ptro_3083, retro_ptro_892,