RetrogeneDB ID: retro_ptro_1700

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:146997178..146997870(-)
• Located in intron of: ENSPTRG00000012509

Retrocopy information

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

Parental gene information

• Parental gene symbol: SFXN4
• Ensembl ID: ENSPTRG00000002990
• Aliases: None
• Description: None

Sequence

>retro_ptro_1700
TTTCTTCAGTGGACACAATTATTAGATCTTAAAAATCTGGTCATTTCAATTGAGAAAATAGAGGCAACTACTCTTTGTAA
ATAAAGAGGCATCCAGGCCTGACTTGGAGGACCCAATGATACAAGAAACTTTGAAGAGCAGTCTCTCAACAGGGCATCAT
GACAGCAGCAAACTGAACCCTGCCTTTTTCAGCCTATAGCTATATTGCCTTTCATGATGCCCATGGTATTTCTGTAGATG
ATGCCAGCAAAAGGGAGAAAGTCCATGGTTTTACCCCAGGTTTCTTATAAACTTACATATAATTATAGCACACAGCATTA
TCAGCAGAAATGCAAACTGTAATCATTGCCAAAGAGTATATTACTAGGGGAAGGAGTAATTGCTTCTTCAATCTTCTTTG
GAATAATCCCTCATTTGGGCCCAAATGAAGTATGCCCAGGATAATCTTTAGATGAAAAAAACCTGACCTATCATCTTTCT
CAACCAAGTCAATGGAATGAATGTTTTTGCATTCCAAAGTTTTGGGCCCATTCAAGGGATCAAGGTAATGGGCAAGGAAG
GCAATGTCATGGACCATCTCAGAAGAGCTGGGAAAAAGGCTGTTAAAGAAACAGCAATATCCAGGGAAGCGCTGTTTGGG
ACATTAGCTTTTATTCCGATGTCTTCAACTATTTTTTAAAAAGACACAGTAC

Alignment

ORF - retro_ptro_1700 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.24 %
• Parental protein coverage: 69.44 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  FLQWTELLDPTNVFISVESIENS-RQLLCTNEDASSPASADQRIQEAWKRSLATVHPDSSNLIPK-LFRP
          FLQWT.LLD..N....V.SIE...RQLL..N..AS.P...D..IQE..K.SL.T.H.DSS.L.P..LF.P
Retrocopy FLQWTQLLDLKNL---VISIEKI>RQLLFVNKEASRPDLEDPMIQETLKSSLSTGHHDSSKLNPA<LFQP

Parental  AAFLPFMAPTVFLSMTPLKGIKSVILPQVFLCAYMAAFNSINGNRSYTCK--PLERSLLMA-GAVASSTF
          .A.LPFM.P.VFL.M.P.KG.KS..LPQV....Y....N.........CK...L..S.L...G..ASS.F
Retrocopy IAILPFMMPMVFL*MMPAKGRKSMVLPQV---SYKLTYNYSTQHYQQKCKL*SLPKSILLGEGVIASSIF

Parental  LGVIPQ-FVQMKYGLTGPWIKRLLPVIFLVQASGMNVYMSRSLESIKGIAVMDKEGNVLGHSRIAGTKAV
          .G.IP....QMKY.......K...P.IFL.Q..GMNV....S...I.GI.VM.KEGNV..H.R.AG.KAV
Retrocopy FGIIPH>WAQMKYAQDNL*MKKT*PIIFLNQVNGMNVFAFQSFGPIQGIKVMGKEGNVMDHLRRAGKKAV

Parental  RETLASRIVLFGTSALIP-EVFTY-FFKRTQY
          .ET..SR..LFGT.A.IP..VF.Y.FFK.TQY
Retrocopy KETAISREALFGTLAFIP<DVFNY<FFKKTQY

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	8.26 RPM
SRP007412_cerebellum	0.00 RPM	10.58 RPM
SRP007412_heart	0.03 RPM	14.98 RPM
SRP007412_kidney	0.00 RPM	17.23 RPM
SRP007412_liver	0.10 RPM	10.77 RPM
SRP007412_testis	0.00 RPM	18.44 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1700 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1700 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1700 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000004492	1 retrocopy	retro_dord_644,
Pan troglodytes	ENSPTRG00000002990	1 retrocopy	retro_ptro_1700 ,