RetrogeneDB ID: retro_ptro_1416

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 20:13050814..13051438(-)
• Located in intron of: ENSPTRG00000013255

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC84
• Ensembl ID: ENSPTRG00000004360
• Aliases: None
• Description: None

Sequence

>retro_ptro_1416
CCCCAGGATTATGCACGATTCAAAAAATCCCTGGTGGAAGACTTGGGTTCCTATGAAGAAAAAGAGGATGAGGTGACCAA
GGAGATGGCAGCTCAGATCTGTGAGGTGGAACAGAGCTGGCAGGAGGTGGTTCAGTCTGTCCTAGAGGTTGGTTTCCCTC
GGAGGATCCAGAACCCCTCAGCCAGTGCCGGGCACTTTAGTCCCTGGAAGCTGGAAAAGGATGAACAGCCAGGTAGCTTC
CAGCTCACAGCAGGCCTCCAACTTGGACCTGCCACAGCTCCAGAGCTTGACTGGATGGAGACAGGACTATCTCTGATATT
CATTGGTCATCAGGATATACCAGGAGTTGGTAACATCCACTCAGGTGCCACACCTCCCTGGATGATCCAAGATGAAGAAT
GCATCTCTGGGAACCAACAAACAGGACCGTCCTATAAAGAATTTATTAAAGAAAAGGAAAAAGAGAAGTTGAAGGAACTT
TCCCCAAACTGAGTTGGGGCCAACTTTAATCACAGCTCGAGGACCAGTGCAGGCTGGCTGCCCTCTTTGGACCGTGTCTG
GAATAATGGATACTGTTGGCAGTTCAGGCGTCAACTCAGAACTGAAGCTGCAACAATGAACAAG

Alignment

ORF - retro_ptro_1416 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.27 %
• Parental protein coverage: 61.14 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PQDYARFKKSMVKGLDSYEEKEDEVIKEMAAQIREVEQSRQEVVRSVLE---PQAVPDPEEGSSAPRSWK
          PQDYARFKKS.V..L.SYEEKEDEV.KEMAAQI.EVEQS.QEVV.SVLE...P.....P.........WK
Retrocopy PQDYARFKKSLVEDLGSYEEKEDEVTKEMAAQICEVEQSWQEVVQSVLEVGFPRRIQNPSASAGHFSPWK

Parental  GMNSQVASSLQQPSNLDLPP--APELDWMETGPSLTFIGHQDIPGVGNIHSGATPPWMIQDEEYIAGNQE
          ........S.Q....L.L.P..APELDWMETG.SL.FIGHQDIPGVGNIHSGATPPWMIQDEE.I.GNQ.
Retrocopy LEKDEQPGSFQLTAGLQLGPATAPELDWMETGLSLIFIGHQDIPGVGNIHSGATPPWMIQDEECISGNQQ

Parental  IGPSYEEFLKEKEKQKLKKLPPDRVGANFDHSSRTSAGWLPSFGRVWNNGRRWQSRHQFKTEAAAMKK
          .GPSY.EF.KEKEK.KLK.L.P..VGANF.HSSRTSAGWLPS..RVWNNG..WQ.R.Q..TEAA.M.K
Retrocopy TGPSYKEFIKEKEKEKLKELSPN*VGANFNHSSRTSAGWLPSLDRVWNNGYCWQFRRQLRTEAATMNK

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	0.02 RPM	9.67 RPM
SRP007412_cerebellum	0.00 RPM	10.75 RPM
SRP007412_heart	0.00 RPM	2.54 RPM
SRP007412_kidney	0.00 RPM	7.90 RPM
SRP007412_liver	0.03 RPM	5.07 RPM
SRP007412_testis	0.00 RPM	3.16 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1416 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1416 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1416 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2451
Gorilla gorilla	retro_ggor_1527
Pongo abelii	retro_pabe_1802

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000186166	1 retrocopy	retro_hsap_2451,
Gorilla gorilla	ENSGGOG00000023065	1 retrocopy	retro_ggor_1527,
Nomascus leucogenys	ENSNLEG00000007378	1 retrocopy	retro_nleu_205,
Pongo abelii	ENSPPYG00000003948	1 retrocopy	retro_pabe_1802,
Pan troglodytes	ENSPTRG00000004360	1 retrocopy	retro_ptro_1416 ,