RetrogeneDB ID: retro_ptro_368

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:165203910..165204336(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PACRGL
• Ensembl ID: ENSPTRG00000015945
• Aliases: None
• Description: None

Sequence

>retro_ptro_368
GGAGAGGTCATGGTAGGAGAGAGATGTAGTAACTGTGATCAAAGGAAATCACCAAGCACATGAATAAAACACAGGACTAC
AGTTCACCAAAGTACATTTTTATTTTCAAATACTTCTCCACAGTCTGCAAGAAAAGCTTATGCTCAACTAAGTGATAAAC
TTATTCCTAAAATAATTAACCTATTTGGTGAACAGTCATGAGCCCCTTCTGCATTGGAAGCTATTTACTCTAAAGGAGCT
GTTCCATGCAGATTGGCACATCATTCAGTAAAACACAGATTACAGTGGGACTGCCTCCAGAAAATCTTGCATTGGAGCCT
CTTCTTAATTATTTTAGCTGAAGATGTAAGAGATAAACATCCATATACCTTTGTGCCAAAGGAAGGTTTTAGAGAATTAC
TTTTGTTCAAATGTCGTCCTGAAAAA

Alignment

ORF - retro_ptro_368 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.07 %
• Parental protein coverage: 64.71 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GTQLKNRATGNYDQRTSSSTQIKHRNAVQGSKSSLSTSSPESARKLHPRPSDKLNPKTINPFGEQSRAPS
          G.........N.DQR.S.ST.IKHR..V..S....S..SP.SARK.....SDKL.PK.IN.FGEQS.APS
Retrocopy GEVMVGERCSNCDQRKSPST*IKHRTTVHQSTFLFSNTSPQSARKAYAQLSDKLIPKIINLFGEQS*APS

Parental  AFAAIYSKGGIPCRLVHGSVKHRLQWEC-PPESLSFDPL-LITLAEGLRETKHPYTFVSKEGFRELLLVK
          A..AIYSKG..PCRL.H.SVKHRLQW.C.PPE.L...PL.LI.LAE..R..KHPYTFV.KEGFRELLL.K
Retrocopy ALEAIYSKGAVPCRLAHHSVKHRLQWDC<PPENLALEPL>LIILAEDVRD-KHPYTFVPKEGFRELLLFK

Parental  GAPEK
          ..PEK
Retrocopy CRPEK

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	0.36 RPM	3.72 RPM
SRP007412_cerebellum	0.14 RPM	4.59 RPM
SRP007412_heart	0.00 RPM	2.71 RPM
SRP007412_kidney	0.00 RPM	5.70 RPM
SRP007412_liver	0.00 RPM	2.26 RPM
SRP007412_testis	0.00 RPM	47.53 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_368 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_368 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_368 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_488
Gorilla gorilla	retro_ggor_458

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000015625	1 retrocopy	retro_dord_96,
Homo sapiens	ENSG00000163138	1 retrocopy	retro_hsap_488,
Gorilla gorilla	ENSGGOG00000012603	1 retrocopy	retro_ggor_458,
Macropus eugenii	ENSMEUG00000009937	2 retrocopies	retro_meug_1836, retro_meug_1954,
Monodelphis domestica	ENSMODG00000000641	2 retrocopies	retro_mdom_1541, retro_mdom_1646,
Oryctolagus cuniculus	ENSOCUG00000002186	1 retrocopy	retro_ocun_258,
Pan troglodytes	ENSPTRG00000015945	1 retrocopy	retro_ptro_368 ,
Rattus norvegicus	ENSRNOG00000004140	1 retrocopy	retro_rnor_1543,
Tarsius syrichta	ENSTSYG00000001584	1 retrocopy	retro_tsyr_1866,