RetrogeneDB ID: retro_ptro_3083

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL395150.1:6731..8369(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARHGAP42
• Ensembl ID: ENSPTRG00000004204
• Aliases: None
• Description: None

Sequence

>retro_ptro_3083
AAATCTTGTATCCGACGAAAGACAGATTCAATTGACAAACACTTCTGCTTCGACATACAAGTAGTTGAAAGGCATGAGAT
CATCACATTACAGGCCTTCTCAGACGCTAATAGGAAACTCTGGCTTGAAGCCATGGATGGGAAGGAAACGATTTATACTC
TGCCTGACATTATAAGCAAGAAAGAAGAAAGGTATTTGAATGAAGCAGGGTTCAATTTTGTGAGAAACTGCATTCAAGCT
GTGGAAACAAGCAGTATCACCGTTTTAGGCCTCTACTGAATAGGAAGAGTGAATTCCAAAGTTCAAAAACTTGTGAATAT
CATATTTTCTCCTAAATCCCCTCCTGATATTGATATTGAACTGTGGGACAATAAGACAATGAGTGGCCTGAAAAACTACC
TCAGGTGCTTTGCAGCACCACTGATGACTTACAAGTTACACAAAGATTTGTATCATTGCTGTTAAATCTGATGACCAAAA
CTACAGGGTGGAGGCTGTACATGCATTGGTGTGCAAATTGCCAGAGAAAAACAGAGAGATGCTGGACATCTTAATAAAAC
ATCTGGTCAAAGTATCACTGCACAGCCAACAAAATCTCATGACTATCTCAAATCTTGGTGTCATATTTCTCCCAACTCTA
ATGAGAGCACAAGAATAAACTGTACCTGCTATGGTGAATATTAAATTTCAGAATATTGTGTTGGAAATTCTTACAGAGCA
TGATGAAACGATTTTTCATACTGCTCCAGACCCAAGCATTCCTCTTCCTCAGCCTCAGTCTCGATCTGGATCCCAAAGGA
CATGAGCAATCTGCCTCTCTACAGGCTCTAGGTAGCCCAGAGGGACGTGTACTCCATGCCTGGCTGAACCTGACAGTGAC
TCCTATAGCAGCAGCCCAGACAGCACCCCCATGGGGAGCATCAAGTCACTCTCTTATCTTTCCTCAGAACAAAATAGCAC
TACAAAGTCAGCTTCCTGCCAGCCCAGGGAGAAATCTGGAGGGATTCCTTGGATTGCAACCCTTTCATCTTCCCATGGAC
AGAAAAGCCTTGGTCTCTGGACAACCAGTCGTGAATCAAGTTCTAGAGAAGATGCAACCAAGACAGATGCAGAATCGGAT
TGCCAGAGTGCTGCTTCGGTCACTAGCCCAGGGGATGTTTCCCCACCCATAGACCTAGTCAAGAAAGGGCCTTATGGACT
TTCAGGACTGAAAAGAGCTTCTGCTTCTTCTCTCAGATCCATCTCTGCAGCTGAAGGAAACATGAGCTACAGTGGATCTA
TTCAAAGCTTAACTTCTGTAGGTTCCAAGAAGACACCCAAAGCTTCAAACCCAGACCTGCCTCCAAAAATGTGCAGCAGG
TTAAGACTAGACACCACCGCAAGCAATAGCTATCAGCGTACTGGCTCAGTAGTGGCAGCAAAAGCTCAACTGTTTGAAAA
TGTTGGTTCACCTAAGCCAGTTTCTTCTGGGCACCAAGCCAAAGCCATGTACTCCTGTAAAGCAGAGCACAGCATGAGTT
TTCCTTCCCACAAGGAGCGATATTTTCCAGCGTGGACCCATCAGTGGAACCAGGATGGTTAAAGGCAACTTATGAAGGCA
AAACGGGACTAGTTCCAGAAAATTATGTTGTCTTCCTC

Alignment

ORF - retro_ptro_3083 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.13 %
• Parental protein coverage: 62.93 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KSCIRRKTDSIDKRFCFDIEVVERHGIITLQAFSEANRKLWLEAMDGKEPIYTLPAIISKKEEMYLNEAG
          KSCIRRKTDSIDK.FCFDI.VVERH.IITLQAFS.ANRKLWLEAMDGKE.IYTLP.IISKKEE.YLNEAG
Retrocopy KSCIRRKTDSIDKHFCFDIQVVERHEIITLQAFSDANRKLWLEAMDGKETIYTLPDIISKKEERYLNEAG

Parental  FNFVRKCIQAVETRGITILGLYRIGGVNSKVQKLMNTTFSPKSPPDIDIDIELWDNKTITSGLKNYLRCL
          FNFVR.CIQAVET..IT.LGLY.IG.VNSKVQKL.N..FSPKSPPDIDI..ELWDNKT..SGLKNYLRC.
Retrocopy FNFVRNCIQAVETSSITVLGLY*IGRVNSKVQKLVNIIFSPKSPPDIDI--ELWDNKTM-SGLKNYLRCF

Parental  AEPLMTYKLHKDF-IIAVKSDDQNYRVEAVHALVHKLPEKNREMLDILIKHLVKVSLHSQQNLMTVSNLG
          A.PLMTYKLHKD..IIAVKSDDQNYRVEAVHALV.KLPEKNREMLDILIKHLVKVSLHSQQNLMT.SNLG
Retrocopy AAPLMTYKLHKDL>IIAVKSDDQNYRVEAVHALVCKLPEKNREMLDILIKHLVKVSLHSQQNLMTISNLG

Parental  VIFGPTLMRAQEETVAAMMNIKFQNIVVEILIEHYEKIFHTAPDPSIPLPQPQSRSGSRRTRAICLSTGS
          VIF.PTLMRAQE.TV.AM.NIKFQNIV.EIL.EH.E.IFHTAPDPSIPLPQPQSRSGS.RT.AICLSTGS
Retrocopy VIFLPTLMRAQE*TVPAMVNIKFQNIVLEILTEHDETIFHTAPDPSIPLPQPQSRSGSQRT*AICLSTGS

Parental  RKPRGRYTPCLAEPDSDSYSSSPDSTPMGSIESLSSHSSEQNSTTKSASCQPREKSGGIPWIATPSSSNG
          R.PRG..TPCLAEPDSDSYSSSPDSTPMGSI.SLS..SSEQNSTTKSASCQPREKSGGIPWIAT.SSS.G
Retrocopy R*PRGTCTPCLAEPDSDSYSSSPDSTPMGSIKSLSYLSSEQNSTTKSASCQPREKSGGIPWIATLSSSHG

Parental  QKSLGLWTTSPESSSREDATKTDAESDCQSVASVTSPGDVSPPIDLVKKEPYGLSGLKRASASSLRSISA
          QKSLGLWTTS.ESSSREDATKTDAESDCQS.ASVTSPGDVSPPIDLVKK.PYGLSGLKRASASSLRSISA
Retrocopy QKSLGLWTTSRESSSREDATKTDAESDCQSAASVTSPGDVSPPIDLVKKGPYGLSGLKRASASSLRSISA

Parental  AEGNKSYSGSIQSLTSVGSKETPKASPNPDLPPKMCRRLRLDTASSNGYQRPGSVVAAKAQLFENVGSPK
          AEGN.SYSGSIQSLTSVGSK.TPKAS.NPDLPPKMC.RLRLDT..SN.YQR.GSVVAAKAQLFENVGSPK
Retrocopy AEGNMSYSGSIQSLTSVGSKKTPKAS-NPDLPPKMCSRLRLDTTASNSYQRTGSVVAAKAQLFENVGSPK

Parental  PVSSGRQAKAMYSCKAEHS-HELSFPQGAIFSNVYPSVEPGWLKATYEGKTGLVPENYVVFL
          PVSSG.QAKAMYSCKAEHS.HE.SFPQGAIFS.V.PSVEPGWLKATYEGKTGLVPENYVVFL
Retrocopy PVSSGHQAKAMYSCKAEHS<HEFSFPQGAIFSSVDPSVEPGWLKATYEGKTGLVPENYVVFL

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	1.84 RPM
SRP007412_cerebellum	0.00 RPM	2.04 RPM
SRP007412_heart	0.00 RPM	6.82 RPM
SRP007412_kidney	0.00 RPM	9.05 RPM
SRP007412_liver	0.00 RPM	6.32 RPM
SRP007412_testis	0.00 RPM	44.26 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3083 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3083 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3083 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 11 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	ENSPTRG00000002365	1 retrocopy	retro_ptro_2448,
Pan troglodytes	ENSPTRG00000004204	4 retrocopies	retro_ptro_1641, retro_ptro_1692, retro_ptro_3083 , retro_ptro_892,