RetrogeneDB ID: retro_ptro_1919

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:117564853..117566332(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM214B
• Ensembl ID: ENSPTRG00000020904
• Aliases: None
• Description: family with sequence similarity 214, member B [Source:HGNC Symbol;Acc:25666]

Sequence

>retro_ptro_1919
ACATCCCCCAGGCTCTACCAGGTATTTATCTTTTCCCCTCCAGCTGGTGCCTCTGAGCTTCACAGGGCCCAGAAGCGACC
AGCCCCACCCACTAAGGGTCCTCAGGAGCTGGAGAGGGGCCCTGGGCTGGGGGCCAGAGAGGGACTACCCCCTGAAGAAC
CATCTTCTGTAGGGCTATTGGGCCCAGGGGGACTGGGGCTGGGAGTAGGTGTGGCCAGCCACCATTTCTCCCACCGTGAC
CTCTGTGTTGTGGAACAGGGAAGTAGTGCCACCTCTTCTTGGACTTCAGGGGCCTGGAGTCCCTCCTGGCCCCGATCATA
TGCTTCCTGAAATACTTTACACACCAAAGACTAGGCTTTCCCAGACCCAGGGGGACAGGGGTCCCTAGGGGAGTCCCCAG
GGCCAGCCCTCTGGGCCAGCTACACACGCTCGACACTGATTTGCAGTTTTGCACAAATAAGGGGTAAGAGCCCAGTGGCT
AGGGTGGGCAAGAGGGGGAGCCTCTGGCCTAGGGAGTCCCCTGGCATTGACAGTGGGCACAGTCTCAAGCACACACCCCC
AGCCCTGGACCTCCAGGCCCCTGCCCCACCAAGCAAAGGCTGCTTCTGCTGGAGAAGCCCCAAATGTCAGTTCTAAGGAA
GAGGGTCCAGCCCTTTGGACGTGCCAGGGAACCCTGGGCCACCCTACTGCTACCAACAGTTCTGATGCTCAAACCACACC
CTTCTGGAGCCACCTGCTGCCTGGGCCCAAGGAGCCTGTTTTGGACCCAACAGACTGCAGTCCCATGGGGCGGAGGCTGA
CAGGTGCCCATCACCTGAAGCTGAGCCCACTTTGAAGCCTCTGGAAGGGGCCAGGCCTGCTGAGCCCCCCTAGTGCCTCC
CCTGTTCCTACCCCTGCTATCAGCTGTACCCTGCTGGGCAACTTTGAGGAATCATTGCGGCAAGGACGCTTTGCACCATC
TGGCCACATTGAGGGCTTCACAGCAGAGACTGGAGCTAGTGGGTCCTACTGCCCCCACCATGTCACACTGCCTGTCACTG
TCACCTTCTTTGAGGTTTCTGAGCAAAATGCCCCCACCCACTTCCTGGGCTTTGTGGATCTGAACCTCCTGGGGAGGAAG
AGTTACAGCGTGCCCAAAGTGGGCACCATACAAGTAACATTTAACCCCAACCAGACTGTGGTGAAGATGTTCCTGGTGAC
CTTCGACTTCTTGGACATGGCTGCTGCCACATGCCCCTCCTGTGCCATTGCCTCTTTTTGGTGCCTGTGGGTGAGGAGAA
AAATGCTAACCCCACCCACTGCCTCCTCTGCTACTCGCTGCACCTTGGGTTCTGGAGCTCCCCCTCAGGCCTCTTAAGCC
TGAATGGAGATCTCTGCCGGCTTTTTTCCTGCTAGAGCCTGGAGCTGGACGCAGGGCTCCCCTACGAACTTCAGGCTGTG
ACTGGGGCCTTTCTTAACCCACGTTATTCACTTTTGCCC

Alignment

ORF - retro_ptro_1919 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.16 %
• Parental protein coverage: 92.19 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TSPGVYQVSIFSPPAGTSEPHRALKRQAPPTEGPRELKRGPGLGAREGLPPEEPSTVGLLGPEGPGLGLG
          TSP..YQV.IFSPPAG.SE.HRA.KR.APPT.GP.EL.RGPGLGAREGLPPEEPS.VGLLGP.G.GLG.G
Retrocopy TSPRLYQVFIFSPPAGASELHRAQKRPAPPTKGPQELERGPGLGAREGLPPEEPSSVGLLGPGGLGLGVG

Parental  VASQHFSHRGLCVVEQRSSVTSSWTSGAWSPPCPPSNAPCNTLHTRDWASPDPGGQGSLGESPGPAPPGQ
          VAS.HFSHR.LCVVEQ.SS.TSSWTSGAWSP..P.S.A..NTLHT.D.A.PDPGGQGSLGESPGPA....
Retrocopy VASHHFSHRDLCVVEQGSSATSSWTSGAWSPSWPRSYAS*NTLHTKD*AFPDPGGQGSLGESPGPALWAS

Parental  LHTFDTDLHSLAQIGGKSPVAGVGNGGSLWPRESPGPANGHSPEHTPPG-PGPPGPCPTKRRLL-PAGEA
          ..T..T...S.AQI.GKSPVA.VG..GSLWPRESPG...GHS..HTPP..PGPPGPCPTK.RLL..AGEA
Retrocopy -YTRSTLICSFAQIRGKSPVARVGKRGSLWPRESPGIDSGHSLKHTPPA<PGPPGPCPTKQRLL<SAGEA

Parental  PDVSSEEEGPAPRRRRGSLGHPTAANSSDAKATPFWSHLLPGPKEPVLDPTDCGPMGRRLKGARRLKLSP
          P.VSS.EEGPA.....G.LGHPTA.NSSDA..TPFWSHLLPGPKEPVLDPTDC.PMGRRL.GA..LKLSP
Retrocopy PNVSSKEEGPALWTCQGTLGHPTATNSSDAQTTPFWSHLLPGPKEPVLDPTDCSPMGRRLTGAHHLKLSP

Parental  LRSLRKGPGLLSPPSASPVPTPAVSRTLLGNFEESLLRGRFAPSGHIEGFTAEIGASGSYCPQHVTLPVT
          L.SL.KGPGLLSPPSASPVPTPA.S.TLLGNFEESL..GRFAPSGHIEGFTAE.GASGSYCP.HVTLPVT
Retrocopy L*SLWKGPGLLSPPSASPVPTPAISCTLLGNFEESLRQGRFAPSGHIEGFTAETGASGSYCPHHVTLPVT

Parental  VTFFDVSEQNAPAPFLGIVDLNPLGRKGYSVPKVGTVQVTLFNPNQTVVKMFLVTFDFSDMPAA-HMTFL
          VTFF.VSEQNAP..FLG.VDLN.LGRK.YSVPKVGT.QVT.FNPNQTVVKMFLVTFDF.DM.AA.HM..L
Retrocopy VTFFEVSEQNAPTHFLGFVDLNLLGRKSYSVPKVGTIQVT-FNPNQTVVKMFLVTFDFLDMAAA<HMPLL

Parental  RHRLFLVPVGEEGNANPTHRLLCYLLHLRFRSSRSGRLSLHGDIRLLFSRRSLELDTGLPYELQAVTEAP
          .H.LFLVPVGEE.NANPTH.LLCY.LHL.F.SS.SG.LSL.GD...LFS..SLELD.GLPYELQAVT.A.
Retrocopy CHCLFLVPVGEEKNANPTHCLLCYSLHLGFWSSPSGLLSLNGDLCRLFSC*SLELDAGLPYELQAVTGAF

Parental  HNPRYSPLP
          .NPRYS.LP
Retrocopy LNPRYSLLP

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	28.99 RPM
SRP007412_cerebellum	0.00 RPM	28.61 RPM
SRP007412_heart	0.00 RPM	11.72 RPM
SRP007412_kidney	0.00 RPM	20.01 RPM
SRP007412_liver	0.00 RPM	13.49 RPM
SRP007412_testis	0.00 RPM	6.96 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1919 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1919 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1919 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2831
Gorilla gorilla	retro_ggor_1966
Pongo abelii	retro_pabe_2200
Macaca mulatta	retro_mmul_1504

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009210	1 retrocopy	retro_cjac_1357,
Homo sapiens	ENSG00000005238	1 retrocopy	retro_hsap_2831,
Gorilla gorilla	ENSGGOG00000003218	1 retrocopy	retro_ggor_1966,
Microcebus murinus	ENSMICG00000005528	1 retrocopy	retro_mmur_1580,
Macaca mulatta	ENSMMUG00000011862	1 retrocopy	retro_mmul_1504,
Nomascus leucogenys	ENSNLEG00000004530	1 retrocopy	retro_nleu_1207,
Pongo abelii	ENSPPYG00000019101	1 retrocopy	retro_pabe_2200,
Pan troglodytes	ENSPTRG00000020904	1 retrocopy	retro_ptro_1919 ,