RetrogeneDB ID: retro_ptro_2402

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:152461068..152461787(+)
• Located in intron of: ENSPTRG00000018709

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDCL2
• Ensembl ID: ENSPTRG00000016073
• Aliases: None
• Description: phosducin-like 2 [Source:HGNC Symbol;Acc:29524]

Sequence

>retro_ptro_2402
ATGCAGGACCCCAACGCAGACACTGAGTGGAATGACATCTTACGCAAAAAGGGTTTCTTACCCGCCAAGGAAAGAATTGG
AAGGATTGGAAGAGGAGGCAGAAGAGGAGCAGCGCATCCTCCAGCAGTCAGTGGTGAAAACATATGAAGATATGACTTTG
GAAGAGCTGGAGGATCGTGAAGACGAGTTTAATGAGGAGGATGAATGTGCTATTGAAATGTACAGACGGCAGAGACTGGC
TGAGTGGAAAGCAACTAAACTGAAGAATAAATTTGGAGAAGTTTTGGAGATCTCAGGGAAGGATTATGTTCAAGAAGTTA
CCAAAGCTGGCGAGGGCTTGTGGGTCATCTTGCACCTTTACAAACAAGGAATTCCCCTCTGTGCCCTGATAAATCAGCAC
CTCAGTGGACTTGCCAGGAAGTTTCCTGATGTCAAATTTATCAAAGCCATTTCAACAACCTGCATACCCAATTATCCTGA
TAGGAATCTGCCAACAATATTTGTTTACCTGGAAGGAGATATCAAGGCTCAGTTTATTGGTCCTCTGAGTGTTTGGCGGC
ATGAACCTGACAAGAGATGAGTTGGAATGGAAACTGTCTGAATCTGGAGCAATAATGACAGACCTGGAGGAAAACCCTAA
GAAGCCGATTGAAGACGTGTTGCTGTCCTCAGTGCGGCGCTCTGTCCTCATGAAGAGGGACAGCGATTCCGAGGGTGAC

Alignment

ORF - retro_ptro_2402 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.43 %
• Parental protein coverage: 98.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MQDPNEDTEWNDILRDFGILP-PKEESK--DEIEEMVLRLQKEAMVKPFEKMTLAQLKEAEDEFDEEDMQ
          MQDPN.DTEWNDILR..G.LP.P..E.....E..E...R......VK..E.MTL..L...EDEF.EED..
Retrocopy MQDPNADTEWNDILRKKGFLP>PRKELEGLEEEAEEEQRILQQSVVKTYEDMTLEELEDREDEFNEEDEC

Parental  AIETYRKKRLQEWKALKKKQKFGELREISGNQYVNEVTNAEEDVWVITHLYRSSIPMCLLVNQHLSLLAR
          AIE.YR..RL.EWKA.K.K.KFGE..EISG..YV.EVT.A.E..WVI.HLY...IP.C.L.NQHLS.LAR
Retrocopy AIEMYRRQRLAEWKATKLKNKFGEVLEISGKDYVQEVTKAGEGLWVILHLYKQGIPLCALINQHLSGLAR

Parental  KFPETKFVKAIVNSCIQHYHDNCLPTIFVYKNGQIEAKFIGIIEC-GGINLKLEELEWKLAEVGAIQTDL
          KFP..KF.KAI...CI..Y.D..LPTIFVY..G.I.A.FIG.....GG.NL...ELEWKL.E.GAI.TDL
Retrocopy KFPDVKFIKAISTTCIPNYPDRNLPTIFVYLEGDIKAQFIGPLSV>GGMNLTRDELEWKLSESGAIMTDL

Parental  EENPRKDIVDMMVSSIRNTSIHDDSDSSNSD
          EENP.K.I.D...SS.R..........S..D
Retrocopy EENPKKPIEDVLLSSVRRSVLMKRDSDSEGD

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	2.84 RPM	0.00 RPM
SRP007412_cerebellum	2.08 RPM	0.00 RPM
SRP007412_heart	5.10 RPM	0.06 RPM
SRP007412_kidney	3.95 RPM	0.00 RPM
SRP007412_liver	3.60 RPM	0.00 RPM
SRP007412_testis	4.95 RPM	45.53 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2402 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2402 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2402 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3535

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012692	3 retrocopies	retro_chof_1554, retro_chof_562, retro_chof_737,
Echinops telfairi	ENSETEG00000000666	1 retrocopy	retro_etel_1568,
Gorilla gorilla	ENSGGOG00000007908	1 retrocopy	retro_ggor_2890,
Monodelphis domestica	ENSMODG00000020680	2 retrocopies	retro_mdom_1048, retro_mdom_993,
Pan troglodytes	ENSPTRG00000016073	7 retrocopies	retro_ptro_148, retro_ptro_1810, retro_ptro_1865, retro_ptro_2402 , retro_ptro_2690, retro_ptro_2784, retro_ptro_675,