RetrogeneDB ID: retro_ggor_336

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 1:190345520..190346349(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNASEH1
• Ensembl ID: ENSGGOG00000034822
• Aliases: None
• Description: None

Sequence

>retro_ggor_336
CTGTCCCTGGCCCACAGAGTCACCTTGATAGCTGTGCGCTGCCACAGGGACTGCTGCAGCCTCAGGATGGTCTATGCTGT
GGGGAGGGCCTGCAGGACCGGGGTCTTTCTGACCTGGAATGAATGTAGAGCATAGGTGGACCTATTTCCTGCTGCCAGAT
TTAAGAAGTTTGCCACAGAAAATGAGGCCTGGGACTTTGTCAGGAAATCTGCAAGCCCAGAAGTTTCAGAAGGGCAGAAA
AATAAACATGTACAAGAATCACAAATGAAAGCCAGCAAGGGACTCTGTGAGCCACTGAATGGAGATGGAGATGAAAGTGC
AGAGTCTTGTGCAAAGCCTGTGAAGCAAATCACAAAGCCGGCGCCTCGAGTGAGCAGAGACATTTTCTTACATCGGAGGC
TTTGTCGTCGTCTACACTGATGGCTGCTGCTCCAGTAATGGGTGCAGGAGAGCACTAGTGGGAACTGACATTTACTGGGG
GCCAGGCCATCCTTTAAATGTAGGCATTAGACTTCCTGGGTGACAGACAAACCAAAGAGCAGAAAATCATGCAGCCTGCA
ACACCATTGAACAAGCAAAGGCTGAAAACATCAATAAATTGGTTCTGTACACAGATAGTATGTTTGCTATAAATGGTATA
ACTAACTGGGTTCAAGGTAGGAAGAAGAACAGGTGGAAGACAAGTACAGGGAAAGAGGTGACGAACAAAGAGGACTTTGT
AGCACTGGAGAAGCTCAGTCAAGGCATGGACATTCAGTGGATACTTGTTCCTGGTCATCCAGGGTTTATTGGCAATGAAG
AAGCTGATAGATTAGCAAGAGGAGCTAAA

Alignment

ORF - retro_ggor_336 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.18 %
• Parental protein coverage: 98.23 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LFLAHKVALVAVPCRRGSRGFGMFYAVRRGRKTGVFLTWNECRAQVDRFPAARFKKFATEDEAWAFVRKS
          L.LAH.V.L.AV.C.R......M.YAV.R...TGVFLTWNECRA.VD.FPAARFKKFATE.EAW.FVRKS
Retrocopy LSLAHRVTLIAVRCHRDCCSLRMVYAVGRACRTGVFLTWNECRA*VDLFPAARFKKFATENEAWDFVRKS

Parental  ASPEVSEGRENQHGQESDAKAIKRLREPLDGDGHESAEPYAKHMKPSVEPAPPVSRDMFSYM-GDFVVVY
          ASPEVSEG..N.H.QES..KA.K.L.EPL.GDG.ESAE..AK..K....PAP.VSRD.F....G..VV.Y
Retrocopy ASPEVSEGQKNKHVQESQMKASKGLCEPLNGDGDESAESCAKPVKQITKPAPRVSRDIFLHR>GFVVV-Y

Parental  TDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKTQNINKLVLYTDSMF
          TDGCCSSNG.RR...G...YWGPGHPLNVGIRLPG.QTNQRAE.HAAC..IEQAK..NINKLVLYTDSMF
Retrocopy TDGCCSSNGCRRALVGTDIYWGPGHPLNVGIRLPG*QTNQRAENHAACNTIEQAKAENINKLVLYTDSMF

Parental  TINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQGMDIQWKMVLEHTYKLDNSYIQRSRKEGAK
          .INGITNWVQG.KKN.WKTS.GKEV.NKEDFVALE.L.QGMDIQW..V..H.....N....R....GAK
Retrocopy AINGITNWVQGRKKNRWKTSTGKEVTNKEDFVALEKLSQGMDIQWILVPGHPGFIGNEEADRLAR-GAK

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	0.05 RPM	7.62 RPM
SRP007412_cerebellum	0.00 RPM	6.62 RPM
SRP007412_heart	0.00 RPM	3.16 RPM
SRP007412_kidney	0.04 RPM	4.95 RPM
SRP007412_liver	0.00 RPM	2.82 RPM
SRP007412_testis	0.00 RPM	6.53 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_336 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_336 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_300
Pan troglodytes	retro_ptro_244
Macaca mulatta	retro_mmul_544

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 19 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,
Gorilla gorilla	ENSGGOG00000034822	2 retrocopies	retro_ggor_2175, retro_ggor_336 ,
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,
Pteropus vampyrus	ENSPVAG00000002070	1 retrocopy	retro_pvam_144,
Sarcophilus harrisii	ENSSHAG00000013051	1 retrocopy	retro_shar_245,