RetrogeneDB ID: retro_ptro_172

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:92893874..92894630(+)
• Located in intron of: ENSPTRG00000000956

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRKAR1A
• Ensembl ID: ENSPTRG00000009579
• Aliases: None
• Description: None

Sequence

>retro_ptro_172
GCCAAAGCCATTGAAAAGAATGTGCTGATTTCACATCTTGATGATAATGAGAGAAGTGATATATTTGATGCCATGTTTCC
AGTCTCCTTTATCACTGGAGAGACAGTGATTCTGCAAGGTGATGAAGGGGATAACTTCTAGGTGATTGAGCAAGGAGAGA
GGGATGTCTGTGTCAATGATGAATGAACAACCAGTGTTGAAGAAGGAGGGAGCTTTGGAGAATTTGTTTTGATTTATGGA
ACACCTAGAGTAGCCACTGTCAAAGCAAAGGCAAATGTGAAATGGTAGTGTATCAACCGAGGCAGCTGTAGAAGAATCCA
TATGGGAAGCACACTGAGAATGTGGAAGATGTATGAGGAATTCCTTAGTAAAGTGTCTATTTTAGAGTCTCTGGATAAGT
GAGAGCACCTTACGGTAGCTGATACATGGGAACCAGTCAAGTTTGAAGATTGGCAGAAGATTGTGGTGCAGGGAGAACCA
GGGGATTAGTTCCTTATTATTCTAGAGGGGCCAGCTGCTATGCTGCAACGTTGGTCGGAAAATGAAGAGTTTGTTGAAGT
GGGAAGATTGGGGCCTTCTGATTATTTTGGTGAATTTGCATTCCTGATGAATCACCCTCCTGCTGCCACAGTGGTTGTAC
ATGGCCCCTTGAAGTACATTAAGCTGGACCAGCCTAGATTTGAATGTGCTCTTGGCCCAGGCTCAGACCTCCTCAAACGA
AACATCCAGCAGTACAACAGTTCTGTGTCACTGTCT

Alignment

ORF - retro_ptro_172 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.16 %
• Parental protein coverage: 66.14 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AKAIEKNVLFSHLDDNERSDIFDAMFSVSFIAGETVIQQGDEGDNFYVIDQGETDVYVNNEWATSVGEGG
          AKAIEKNVL.SHLDDNERSDIFDAMF.VSFI.GETVI.QGDEGDNF.VI.QGE.DV.VN.E..TSV.EGG
Retrocopy AKAIEKNVLISHLDDNERSDIFDAMFPVSFITGETVILQGDEGDNF*VIEQGERDVCVNDE*TTSVEEGG

Parental  SFGELALIYGTPRAATVKAKTNVKLWGIDRDSYRRILMGSTLRKRKMYEEFLSKVSILESLDKWERLTVA
          SFGE..LIYGTPR.ATVKAK.NVK...I.R.S.RRI.MGSTLR..KMYEEFLSKVSILESLDK.E.LTVA
Retrocopy SFGEFVLIYGTPRVATVKAKANVKW*CINRGSCRRIHMGSTLRMWKMYEEFLSKVSILESLDK*EHLTVA

Parental  DALEPVQFEDGQKIVVQGEPGDEFFIILEGSAAVLQRRSENEEFVEVGRLGPSDYFGEIALLMNRPRAAT
          D..EPV.FED.QKIVVQGEPGD.F.IILEG.AA.LQR.SENEEFVEVGRLGPSDYFGE.A.LMN.P.AAT
Retrocopy DTWEPVKFEDWQKIVVQGEPGD*FLIILEGPAAMLQRWSENEEFVEVGRLGPSDYFGEFAFLMNHPPAAT

Parental  VVARGPLKCVKLDRPRFERVLGPCSDILKRNIQQYNSFVSLS
          VV..GPLK..KLD.PRFE..LGP.SD.LKRNIQQYNS.VSLS
Retrocopy VVVHGPLKYIKLDQPRFECALGPGSDLLKRNIQQYNSSVSLS

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	277.48 RPM
SRP007412_cerebellum	0.04 RPM	290.41 RPM
SRP007412_heart	0.06 RPM	502.45 RPM
SRP007412_kidney	0.00 RPM	213.16 RPM
SRP007412_liver	0.00 RPM	87.76 RPM
SRP007412_testis	0.11 RPM	394.77 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_172 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_172 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_172 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_267

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000108946	1 retrocopy	retro_hsap_186,
Gorilla gorilla	ENSGGOG00000016507	1 retrocopy	retro_ggor_267,
Macaca mulatta	ENSMMUG00000002194	2 retrocopies	retro_mmul_2498, retro_mmul_393,
Nomascus leucogenys	ENSNLEG00000001982	1 retrocopy	retro_nleu_996,
Pan troglodytes	ENSPTRG00000009579	1 retrocopy	retro_ptro_172 ,
Ictidomys tridecemlineatus	ENSSTOG00000012903	1 retrocopy	retro_itri_104,