RetrogeneDB ID: retro_ptro_244

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:189391815..189392656(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNASEH1
• Ensembl ID: ENSPTRG00000011614
• Aliases: None
• Description: None

Sequence

>retro_ptro_244
CTGTCCCTGGCCCACGGAGTCACCTTGATAGCTGTGCGCTGCCACAGGGATTGCTGCAGCCTCAGGATGGTCTATGCTGT
GGGAAGGGCCTGCAGGACCGGGGTCTTTCTGACCTGGAATGAATGTAGAGCATAGGTGGACCTATTTCCTGCTGCCAGAT
TTAAGAAGTTTGCCACAGAAAATGAGGCCTGGGCCTTTGTCAGGAAATCTGCAAGCCCAGAAGGTTCAGAAGGGCAGAAA
AATAAACATGTACAAGAATCACAAATGAAAGCCAGCAAGGGACTCTGTGAGCCACTGAATGGAGATGGAGATAAAAGTGC
AGAGTCTTGTGCAAACCCTGTGAAGCAAATCACAGAGCCGGCGCCTCGAGTGAGCAGAGACATTTTCTTACATCGGAGGC
TTTGTCGTCGTCTACACTGATGGCTGCTGCTCCAGTAATGGGTGGAGGAGAGCACTAGTGGGAACTGATGTTTACTGGGG
GCCAGGCCATCCTTTAAATGTAGGCATTAGACTTCCTGGGTGACAGACAAACCAAAGAGCAGAAAATCATGCAGCCTGCA
ACACCATTGAACAAGCAAAGGCTGAAAACATCAATAAATTGGTTCTGTACACAGATAGTATGTTTGCTATAAATGGTATA
ACTAACTGGGTTCAAGGTAGGAAGAAGAACAGGTGGAAGACAAGTACAGGGAAATAGGTGACGAACAAAAAGGACTTTGT
GGCACTGGAGAAGCTCAGTCAAGGCATGGACATTCAGTGGATACTTGTTCCTGGTCATCCAGGGTTTATTGGCAATGAAG
AAGCTGATAGATTAGCAAGAGGAGCTAAACATTCTGAAGAC

Alignment

ORF - retro_ptro_244 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.14 %
• Parental protein coverage: 98.6 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LFLAHRVALAAFPCRRGSRGFGMFYAVRRGRKTGVFLTWNECRAQVDRFPAARFKKFATEDEAWAFVRKS
          L.LAH.V.L.A..C.R......M.YAV.R...TGVFLTWNECRA.VD.FPAARFKKFATE.EAWAFVRKS
Retrocopy LSLAHGVTLIAVRCHRDCCSLRMVYAVGRACRTGVFLTWNECRA*VDLFPAARFKKFATENEAWAFVRKS

Parental  ASPEVSEGHENQHGQESEAKASKRLREPLDGDGHESAEPYAKHMKPSVEPAPPVSRDTFSYM-GDFVVVY
          ASPE.SEG..N.H.QES..KASK.L.EPL.GDG..SAE..A...K...EPAP.VSRD.F....G..VV.Y
Retrocopy ASPEGSEGQKNKHVQESQMKASKGLCEPLNGDGDKSAESCANPVKQITEPAPRVSRDIFLHR>GFVVV-Y

Parental  TDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKTQNINKLVLYTDSMF
          TDGCCSSNG.RR...G..VYWGPGHPLNVGIRLPG.QTNQRAE.HAAC..IEQAK..NINKLVLYTDSMF
Retrocopy TDGCCSSNGWRRALVGTDVYWGPGHPLNVGIRLPG*QTNQRAENHAACNTIEQAKAENINKLVLYTDSMF

Parental  TINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQGMDIQWMHVPGHSGFIGNEEADRLAREGAKQ
          .INGITNWVQG.KKN.WKTS.GK.V.NK.DFVALE.L.QGMDIQW..VPGH.GFIGNEEADRLAR.GAK.
Retrocopy AINGITNWVQGRKKNRWKTSTGK*VTNKKDFVALEKLSQGMDIQWILVPGHPGFIGNEEADRLAR-GAKH

Parental  SED
          SED
Retrocopy SED

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	7.49 RPM
SRP007412_cerebellum	0.00 RPM	20.40 RPM
SRP007412_heart	0.00 RPM	14.51 RPM
SRP007412_kidney	0.10 RPM	9.62 RPM
SRP007412_liver	0.00 RPM	11.69 RPM
SRP007412_testis	0.00 RPM	11.38 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_244 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_244 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_244 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_300
Gorilla gorilla	retro_ggor_336
Macaca mulatta	retro_mmul_544

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008547	6 retrocopies	retro_chof_158, retro_chof_1653, retro_chof_1836, retro_chof_2224, retro_chof_485, retro_chof_843,
Callithrix jacchus	ENSCJAG00000035450	1 retrocopy	retro_cjac_3811,
Echinops telfairi	ENSETEG00000012674	1 retrocopy	retro_etel_1286,
Homo sapiens	ENSG00000171865	2 retrocopies	retro_hsap_1814, retro_hsap_300,
Macropus eugenii	ENSMEUG00000003610	1 retrocopy	retro_meug_1172,
Macaca mulatta	ENSMMUG00000014475	2 retrocopies	retro_mmul_544, retro_mmul_799,
Monodelphis domestica	ENSMODG00000014491	1 retrocopy	retro_mdom_593,
Nomascus leucogenys	ENSNLEG00000015400	2 retrocopies	retro_nleu_2399, retro_nleu_2959,
Pongo abelii	ENSPPYG00000025873	1 retrocopy	retro_pabe_18,
Pan troglodytes	ENSPTRG00000011614	1 retrocopy	retro_ptro_244 ,
Pteropus vampyrus	ENSPVAG00000002070	1 retrocopy	retro_pvam_144,
Sarcophilus harrisii	ENSSHAG00000013051	1 retrocopy	retro_shar_245,