RetrogeneDB ID: retro_ptro_1641

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:130786588..130788226(+)
• 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_1641
AAATCTTGTATCCGACGAAAGACAGATTCAATTGACAAACACTTCTGCTTCGACATACAAGTAGTTGAAAGCCATGGGAT
CATCACATTACAGGCCTTCTCAGAAGCTAATAGGAAACTCTGGCTTGAAGCCATGGATGGGAAGGAACCAATTTATACTG
TGCCTGACATTATAAGCAAGAAAGAAGAAATGTATTTGAATGAAGCAGGGTTCAATTTTGTGAGAAACTGCATTCAACCT
GTGGAAACAAGCGGTATCACCCTTTTAGGCCTCTACTGAATAGGAGGAGTGAACCCCAAAGTTCAAAAACTTGTGAATAT
CATATTTTCTCCTAAATCCCCTCCTGATATTGATATTGAACTGTGGGACAATAAGACAATGAGTGGGCTGAAAAACCACC
TCAGGTGCTTTGCAGCACCACTGATGACTTACAAGTTACACAAAGATTTGTATCATTGCTGTTAAATCTGATGACCAAAA
CTACAGGGTGGAGGCTGTACATGCATTGGTGTGCAAATTGCCAGAGAAAAACAGAGAGATGCTGGACATCTTAATAAAAC
ATCTGGTCAAAGTATCACTGCACAGCCAACAAAATCTCATAACTGTCTCAAATCTTGGTGTCATATTTGGCCCAACTCTA
ATGAGAGCACAAGAATAAACTGTAGCTGCTATGGTGAATATTAAGTTTCAGAATATTGTGTTAGAAATTCTTACAGAGCA
TGATGAAACGATGTTTCATACTGCTCCAGACCCAAGCACTCCTCTTCCTCAGCCTCAGTCTCGATCTGGATCCCAAAAGA
CACAAGCAATCTGCCTCTCTACAGGCTCTAGGAAGCCCAGAGGGACGTGTACTCCATGCCTGGCTGAACCTGATAGTGAC
TCCTATAGAAGCAGCCCAGACAGCACCCCCATGAGGAGCAACAAGTCACTCTCTTCTCTTTCCTCAGAACAAAATAGCAC
TACAAAGTCAGCTTCCTGCCAGCCCAGGGAGAAATCTGGAGGGATTCCTTGGATTGCAACCCCGTCATCTTCCCATGGAC
AGAAAAGCCTTGGTCGCTGGACAACCAGTCCTGAATCAATTTCTAGAGAAGATGCAACCAAGACAGATGCAGAATCAGAT
TGCCAGAGTGTTGCTTCGGTCACTAGCCCAGGGGATGTTTTCCCCACCCATAGACCTAGTCAAGAAAGGGCCTTATGGGC
TTTCAGGACTGAAAAGAGCTTCTGCTTCTTCTCTCAGATCCATCTCTGCAGCTGAAGGAAACACCAGCTACAGTGGATCT
ATTCAAAGCTTAACTTCTGTAGGTTCCAAGGAGACACCCAAAGCTTCAAACCCAGACCTGCCTCCAAAAATGTGCAGGAG
GTTAAGACTAGACATCGCCTCAAGCAATGGCTATCAGCGTCCTGGCTCAGTAGTGGCAGCAAAAGCTCAACTGTTTGAAA
ATGTTGGTTCACCTAAGCCAGTTTCTTCTGGGCACCAAGCCAAAGCCATGTACTCCTGTAAAGCAGAGCACAGCATGAGT
TTTCCTTCCCACAAGGAGTGATATTTTCCAGCGTGGCCAATCAGTGGAACCAGGATGGTTAAAGGCAACTTATGAAGGCA
AAATGGGACTAGTTCCAGAAAATTATGTTGTCTTCCTC

Alignment

ORF - retro_ptro_1641 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.17 %
• Parental protein coverage: 62.93 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KSCIRRKTDSIDKRFCFDIEVVERHGIITLQAFSEANRKLWLEAMDGKEPIYTLPAIISKKEEMYLNEAG
          KSCIRRKTDSIDK.FCFDI.VVE.HGIITLQAFSEANRKLWLEAMDGKEPIYT.P.IISKKEEMYLNEAG
Retrocopy KSCIRRKTDSIDKHFCFDIQVVESHGIITLQAFSEANRKLWLEAMDGKEPIYTVPDIISKKEEMYLNEAG

Parental  FNFVRKCIQAVETRGITILGLYRIGGVNSKVQKLMNTTFSPKSPPDIDIDIELWDNKTITSGLKNYLRCL
          FNFVR.CIQ.VET.GIT.LGLY.IGGVN.KVQKL.N..FSPKSPPDIDI..ELWDNKT..SGLKN.LRC.
Retrocopy FNFVRNCIQPVETSGITLLGLY*IGGVNPKVQKLVNIIFSPKSPPDIDI--ELWDNKTM-SGLKNHLRCF

Parental  AEPLMTYKLHKDF-IIAVKSDDQNYRVEAVHALVHKLPEKNREMLDILIKHLVKVSLHSQQNLMTVSNLG
          A.PLMTYKLHKD..IIAVKSDDQNYRVEAVHALV.KLPEKNREMLDILIKHLVKVSLHSQQNL.TVSNLG
Retrocopy AAPLMTYKLHKDL>IIAVKSDDQNYRVEAVHALVCKLPEKNREMLDILIKHLVKVSLHSQQNLITVSNLG

Parental  VIFGPTLMRAQEETVAAMMNIKFQNIVVEILIEHYEKIFHTAPDPSIPLPQPQSRSGSRRTRAICLSTGS
          VIFGPTLMRAQE.TVAAM.NIKFQNIV.EIL.EH.E..FHTAPDPS.PLPQPQSRSGS..T.AICLSTGS
Retrocopy VIFGPTLMRAQE*TVAAMVNIKFQNIVLEILTEHDETMFHTAPDPSTPLPQPQSRSGSQKTQAICLSTGS

Parental  RKPRGRYTPCLAEPDSDSYSSSPDSTPMGSIESLSSHSSEQNSTTKSASCQPREKSGGIPWIATPSSSNG
          RKPRG..TPCLAEPDSDSY.SSPDSTPM.S..SLSS.SSEQNSTTKSASCQPREKSGGIPWIATPSSS.G
Retrocopy RKPRGTCTPCLAEPDSDSYRSSPDSTPMRSNKSLSSLSSEQNSTTKSASCQPREKSGGIPWIATPSSSHG

Parental  QKSLGLWTTSPESSSREDATKTDAESDCQSVASVTSPGDV-SPPIDLVKKEPYGLSGLKRASASSLRSIS
          QKSLG.WTTSPES.SREDATKTDAESDCQSVASVTSPGDV.SPPIDLVKK.PYGLSGLKRASASSLRSIS
Retrocopy QKSLGRWTTSPESISREDATKTDAESDCQSVASVTSPGDV>SPPIDLVKKGPYGLSGLKRASASSLRSIS

Parental  AAEGNKSYSGSIQSLTSVGSKETPKASPNPDLPPKMCRRLRLDTASSNGYQRPGSVVAAKAQLFENVGSP
          AAEGN.SYSGSIQSLTSVGSKETPKAS.NPDLPPKMCRRLRLD.ASSNGYQRPGSVVAAKAQLFENVGSP
Retrocopy AAEGNTSYSGSIQSLTSVGSKETPKAS-NPDLPPKMCRRLRLDIASSNGYQRPGSVVAAKAQLFENVGSP

Parental  KPVSSGRQAKAMYSCKAEHS-HELSFPQGAIFSNVY-PSVEPGWLKATYEGKTGLVPENYVVFL
          KPVSSG.QAKAMYSCKAEHS.HE.SFPQG.IFS.V...SVEPGWLKATYEGK.GLVPENYVVFL
Retrocopy KPVSSGHQAKAMYSCKAEHS<HEFSFPQGVIFSSVA<QSVEPGWLKATYEGKMGLVPENYVVFL

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	0.07 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	0.11 RPM	44.26 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1641 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1641 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1641 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,