RetrogeneDB ID: retro_ptro_1692

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:131927814..131929452(-)
• Located in intron of: ENSPTRG00000012461

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_1692
AAATCTTGTATCCGACGAAAGACAGATTCAATTGACAAACACTTCTGCTTCGACATACAAGTAGTTGAAAGGCATGGGAT
CATCACATTACAGGCCTTCTCAGACGCTAATAGGAAACTCTGGCTTGAAGCCATGGATGGGAAGGAAATGATTTATACTC
TGCCTGACATTATAAGCAAGAAAGAAGAAAGGTATTTGAATGAAGCAGGGTTCAATTTTGTGAGAAACTGCATTCAAGCT
GTGGAAACAAGCAGTATCACCGTTTTAGGCCTCTACTGAATAGGAGGAGTGAATTCCAAAGTTCAAAAACTTGTGAATAT
CATATTTTCTCCTAAATCCCCTCCTGATATTGATATTGAACTGTGGGACAATAAGACAATGAGTGGGCTGAAAAACTACC
TCAGGTGCTTTGCAGCACCACTGATGACTTACAAGTTACACAAAGATTTGTATCATTGCTGTTAAATCTGATGACCAAAA
CTACAGGGTGGAGGCTGTACATGCATTGGTGTGCAAATTGCCAGAGAAAAACAGAGAGATGCTGGACATCTTAATAAAAC
ATCTGGTCAAAGTATCACTGCACAGCCAACAAAATCTCATGACTATCTCAAATCTTGGTGTCATATTTCTCCCAACTCTA
ATGAGAGCACAAGAATAAACTGTAGCTGCTATGGTGAATATTAAATTTCAGAATATTGTGTTAGAAATTCTTACAGAGCA
CGATGAAACGATTTTTCATACTGCTCCAGACCCAAGCATTCCTCTTCCTCAGCCTCAGTCTCGATCTGGATCCCAAAGGA
CATGAGCAATCTGCCTCTCTACAGGCTCTAGGAAGCCCAGAGGGACGTGTACTCCATGGCTGGCTGAAACTGACAGTGAC
TCCTATAGCAGCAGCCCAGACAGCACCCCCATGGGGAGCATCAAGTCACTCTCTTATCTTTCCTCAGAACAAAATAGCAC
TACAAAGTCAGCTTCCTGCCAGCCCAGGGAGAAATCTGGAGGGATTCCTTGGATTGCAACCCTTTCATCTTCCCATGGAC
AGAAAAGCCTTGGTCTCTGGACAACCAGTCCTGAATCAAGTTCTAGAGAAGATGCAACCAAGACAGATGCAGAATCAGAT
TGCCAGAGTGCTGCTTCGGTCACTAGCCCAGGGGATGTTTCCCCACCCATAGACCTAGTCAAGAAAGGGCCTTATGGACT
TTCAGGACTGAAAAGAGCTTCTGCTTCTTCTCTCAGATCCATCTCTGCAGCTGAAGGAAACATGAGCTACAGTGGATCTA
TTCAAAGCTTAACTTCTGTAGGTTCCAAGGAGACACCCAAAGCTTCAAACCCAGACCTGCCTCCAAAAATGTGCAGCAGG
TTAAGACTAGACACCACTGCAAGCAATAGCTATCAGCGTACTGGCTCAGTAGTGGCAGCAAAAGCTCAACTGTTTGAAAA
TGTTGGTTCACCTAAGCCAGTTTCTTCTGGGCACCAAGCCAAAGCCATGTACTCCTGTAAAGCAGAGCACAGCATGAGTT
TTCCTTCCCACAAGGAGCGATATTTTCCAGCGTGGACCCATCAGTGGAACCAGGATGGTTAAAGGCAACTTATGAAGGCA
AAACGGGATTAGTTCCAGAAAATTATGTTGTCTTCCTC

Alignment

ORF - retro_ptro_1692 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.86 %
• Parental protein coverage: 62.93 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KSCIRRKTDSIDKRFCFDIEVVERHGIITLQAFSEANRKLWLEAMDGKEPIYTLPAIISKKEEMYLNEAG
          KSCIRRKTDSIDK.FCFDI.VVERHGIITLQAFS.ANRKLWLEAMDGKE.IYTLP.IISKKEE.YLNEAG
Retrocopy KSCIRRKTDSIDKHFCFDIQVVERHGIITLQAFSDANRKLWLEAMDGKEMIYTLPDIISKKEERYLNEAG

Parental  FNFVRKCIQAVETRGITILGLYRIGGVNSKVQKLMNTTFSPKSPPDIDIDIELWDNKTITSGLKNYLRCL
          FNFVR.CIQAVET..IT.LGLY.IGGVNSKVQKL.N..FSPKSPPDIDI..ELWDNKT..SGLKNYLRC.
Retrocopy FNFVRNCIQAVETSSITVLGLY*IGGVNSKVQKLVNIIFSPKSPPDIDI--ELWDNKTM-SGLKNYLRCF

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

Parental  VIFGPTLMRAQEETVAAMMNIKFQNIVVEILIEHYEKIFHTAPDPSIPLPQPQSRSGSRRTRAICLSTGS
          VIF.PTLMRAQE.TVAAM.NIKFQNIV.EIL.EH.E.IFHTAPDPSIPLPQPQSRSGS.RT.AICLSTGS
Retrocopy VIFLPTLMRAQE*TVAAMVNIKFQNIVLEILTEHDETIFHTAPDPSIPLPQPQSRSGSQRT*AICLSTGS

Parental  RKPRGRYTPCLAEPDSDSYSSSPDSTPMGSIESLSSHSSEQNSTTKSASCQPREKSGGIPWIATPSSSNG
          RKPRG..TP.LAE.DSDSYSSSPDSTPMGSI.SLS..SSEQNSTTKSASCQPREKSGGIPWIAT.SSS.G
Retrocopy RKPRGTCTPWLAETDSDSYSSSPDSTPMGSIKSLSYLSSEQNSTTKSASCQPREKSGGIPWIATLSSSHG

Parental  QKSLGLWTTSPESSSREDATKTDAESDCQSVASVTSPGDVSPPIDLVKKEPYGLSGLKRASASSLRSISA
          QKSLGLWTTSPESSSREDATKTDAESDCQS.ASVTSPGDVSPPIDLVKK.PYGLSGLKRASASSLRSISA
Retrocopy QKSLGLWTTSPESSSREDATKTDAESDCQSAASVTSPGDVSPPIDLVKKGPYGLSGLKRASASSLRSISA

Parental  AEGNKSYSGSIQSLTSVGSKETPKASPNPDLPPKMCRRLRLDTASSNGYQRPGSVVAAKAQLFENVGSPK
          AEGN.SYSGSIQSLTSVGSKETPKAS.NPDLPPKMC.RLRLDT..SN.YQR.GSVVAAKAQLFENVGSPK
Retrocopy AEGNMSYSGSIQSLTSVGSKETPKAS-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	0.04 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_1692 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1692 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1692 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,