RetrogeneDB ID: retro_ptro_2811

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:15297706..15298677(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSIP1
• Ensembl ID: ENSPTRG00000020786
• Aliases: None
• Description: None

Sequence

>retro_ptro_2811
ACTCGCGATTTCAAACCTGGAGACCTCATCTTCGCCAAGATGAAAGGTTATCCCCACTGGTCAGCTGGAGTAGATGAAGT
TCTTGATGGAGCTGTAAAGCCACCCACAAACAAACTACCCATTTTCTTTTTTGGAACTCATGAGACTGCTTTTTTAGGAC
CAAAGGTTATATTTCCTTACTCCGAAAATAAGGAAAAGTATGGCAAACCAAACAAAAGATTTTAACGAAGGTTTATGGGG
ACAGATAACAATCCAAAAGTGAAATTTTCAAGTCAACAGGCAGCAACTAAACAATCAAACGCATCATCCAATGTTGAAGT
TGAAGAAAAAGAAACTAGTGTTTCAAAGGAAGATACCGACCATGAAGAAAAAGCCAGCAATGAGGATGTGACTAAAGCAG
TTGACGTAACTACTCCAAAAGCTGCCAGAAGAGGGAGAAAGAGAAAGGCAGAAAAACAAGTAGAAACTGAGGAGGCAGGA
GTAGTGACAACAGCAACAGCATCTGTTAATCTAAAAGTGAGTCCTAAAAGAGGACGACCTGCAGCTACAGAAGTCAAGAT
TCAAAAACCAAGAGGCAGACCCAAAATGGTAAAACAGCCCTGTCCTTCAGAGAGTGACATCATTACTGAAGAGGACAAAA
GTAAGAAAAAGGGGCAAGAGGAAAAACAACCTAAAAAGCAGCCTAAGAAGGACGAAGAGGGCCAGAAGGAAGAAGATAAG
CCAAGAAAAGAGCCAGACAAAATAGAGTAGAAGAAAGAAGTTGAGTCAAAAGGAAAAATTTAGCTAACACAGGGGTTACA
TCAACCTCCGATTCTGAAGAAGAAGGAGATGATCAAGAAGGTGAAAAGAAGAGAAAAGGTGGGAGGAACGTTCAGACTGC
TCACAGAAGGAATATGCTGAAAGGCCAAAATGAGAAAGAAGCAGCAGATCGAAAACGCAAGCAGGAAAAACAAGTGGAAA
CTGAGCACCAA

Alignment

ORF - retro_ptro_2811 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.35 %
• Parental protein coverage: 61.51 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TRDFKPGDLIFAKMKGYPHWPARVDEVPDGAVKPPTNKLPIFFFGTHETAFLGPKDIFPYSENKEKYGKP
          TRDFKPGDLIFAKMKGYPHW.A.VDEV.DGAVKPPTNKLPIFFFGTHETAFLGPK.IFPYSENKEKYGKP
Retrocopy TRDFKPGDLIFAKMKGYPHWSAGVDEVLDGAVKPPTNKLPIFFFGTHETAFLGPKVIFPYSENKEKYGKP

Parental  NKRKGFNEGLWEIDNNPKVKFSSQQAATKQSNASSDVEVEEKETSVSKEDTDHEEKASNEDVTKAVDITT
          NKR..F.......DNNPKVKFSSQQAATKQSNASS.VEVEEKETSVSKEDTDHEEKASNEDVTKAVD.TT
Retrocopy NKR--F*RRFMGTDNNPKVKFSSQQAATKQSNASSNVEVEEKETSVSKEDTDHEEKASNEDVTKAVDVTT

Parental  PKAARRGRKRKAEKQVETEEAGVVTTATASVNLKVSPKRGRPAATEVKIPKPRGRPKMVKQPCPSESDII
          PKAARRGRKRKAEKQVETEEAGVVTTATASVNLKVSPKRGRPAATEVKI.KPRGRPKMVKQPCPSESDII
Retrocopy PKAARRGRKRKAEKQVETEEAGVVTTATASVNLKVSPKRGRPAATEVKIQKPRGRPKMVKQPCPSESDII

Parental  TEEDKSKKKGQEEKQPKKQPKKDEEGQKEEDKPRKEPDKKEGKKEVES-KRKNLAKTGVTSTSDSEEEGD
          TEEDKSKKKGQEEKQPKKQPKKDEEGQKEEDKPRKEPDK.E.KKEVES.KRKNLA.TGVTSTSDSEEEGD
Retrocopy TEEDKSKKKGQEEKQPKKQPKKDEEGQKEEDKPRKEPDKIE*KKEVES<KRKNLANTGVTSTSDSEEEGD

Parental  DQEGEKKRKGGRNFQTAHRRNMLKGQHEKEAADRKRKQEEQMETEQQ
          DQEGEKKRKGGRN.QTAHRRNMLKGQ.EKEAADRKRKQE.Q.ETE.Q
Retrocopy DQEGEKKRKGGRNVQTAHRRNMLKGQNEKEAADRKRKQEKQVETEHQ

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	1.13 RPM	60.15 RPM
SRP007412_cerebellum	0.39 RPM	130.49 RPM
SRP007412_heart	0.03 RPM	19.53 RPM
SRP007412_kidney	0.00 RPM	31.46 RPM
SRP007412_liver	0.10 RPM	10.41 RPM
SRP007412_testis	0.42 RPM	166.51 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2811 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2811 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2811 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4136

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012471	1 retrocopy	retro_cjac_4069,
Homo sapiens	ENSG00000164985	1 retrocopy	retro_hsap_4136,
Mus musculus	ENSMUSG00000028484	1 retrocopy	retro_mmus_2896,
Pan troglodytes	ENSPTRG00000001474	1 retrocopy	retro_ptro_1,
Pan troglodytes	ENSPTRG00000020786	1 retrocopy	retro_ptro_2811 ,
Tupaia belangeri	ENSTBEG00000000715	1 retrocopy	retro_tbel_364,