RetrogeneDB ID: retro_ptro_1810

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:104886733..104887442(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000012286
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_ptro_1810
ATGCAGGACCCCAACGCAGACACTGAGTGGAATGACATCTTAACGCAAAAAGGGTATCTTACCCCCCAAGGAAAGTCTGA
AAGAATTGGAAGAGGAGGCAGAAGAGGAGCAGTGCATCCTCCAGCAGTCAGTGGTGAAAACATATGAAGATATGACTTTG
GAAGAGCTGGAGGATCATGAAGATGAGTTTAATGAGGAGGATGAATGTGCTATTGAAATGTGCAGACGGCAGAGACTGGC
TGAGTGGAAAGCAACTAAATTGAAGAATAAATTTTGAGAAGTTTTGGAGATCTCAGGGAAGGATTATGTTCAAGAAGTTA
CCAAAGCTGGTGAGGGCTTGTGGGTCATCTTGCACCTTTACAAACAAGGAATTCCCCTCTGTGCCCTGATAAATCAGAAC
CTCGGTGGACTTGCCAGGAAGTTTCCTGATGTCAAATTTATCAAAGCCATTTCAACAACCTGCATACCCAATTATCCTGA
TAGGAATCTGCCCACGATATTTGTTTACCTGGAAGGAGATATCAAGGCTCAGTTTATTGGTCCTCTGGTGTTTGGTGGCA
TGAACCTGACAAGAGATGAGTTGGAATGGAAACTGTCTGAATCTGGAGCAATTATGATGGACCTGGAGGAAAACCCTAAG
AAGCCGATTGAAGATGTATTGCTGTCCTCAGTGCGGCACTCTGTCCTCATGAGGAGGGACAGCGATTCT

Alignment

ORF - retro_ptro_1810 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.98 %
• Parental protein coverage: 96.68 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MQDPNEDTEWNDIL-RDFGILPPKE---ESKDEIEEMVLRLQKEAMVKPFEKMTLAQLKEAEDEFDEEDM
          MQDPN.DTEWNDIL.R..GILPPKE...E...E.EE....LQ....VK..E.MTL..L...EDEF.EED.
Retrocopy MQDPNADTEWNDIL>RKKGILPPKESLKELEEEAEEEQCILQ-QSVVKTYEDMTLEELEDHEDEFNEEDE

Parental  QAIETYRKKRLQEWKALKKKQKFGELREISGNQYVNEVTNAEEDVWVITHLYRSSIPMCLLVNQHLSLLA
          .AIE..R..RL.EWKA.K.K.KF.E..EISG..YV.EVT.A.E..WVI.HLY...IP.C.L.NQ.L..LA
Retrocopy CAIEMCRRQRLAEWKATKLKNKF*EVLEISGKDYVQEVTKAGEGLWVILHLYKQGIPLCALINQNLGGLA

Parental  RKFPETKFVKAIVNSCIQHYHDNCLPTIFVYKNGQIEAKFIGIIECGGINLKLEELEWKLAEVGAIQTDL
          RKFP..KF.KAI...CI..Y.D..LPTIFVY..G.I.A.FIG....GG.NL...ELEWKL.E.GAI..DL
Retrocopy RKFPDVKFIKAISTTCIPNYPDRNLPTIFVYLEGDIKAQFIGPLVFGGMNLTRDELEWKLSESGAIMMDL

Parental  EENPRKDIVDMMVSSIRNTSI-HDDSDS
          EENP.K.I.D...SS.R.......DSDS
Retrocopy EENPKKPIEDVLLSSVRHSVLMRRDSDS

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	0.70 RPM	0.00 RPM
SRP007412_cerebellum	0.50 RPM	0.00 RPM
SRP007412_heart	0.67 RPM	0.06 RPM
SRP007412_kidney	0.68 RPM	0.00 RPM
SRP007412_liver	0.46 RPM	0.00 RPM
SRP007412_testis	3.48 RPM	45.53 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1810 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1810 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1810 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2684

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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,