RetrogeneDB ID: retro_ptro_675

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:22954235..22954820(+)
• Located in intron of: None

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_675
CCCAACACAGACACTGAGTGGAATGACATCTTAGCAAAAAGGGCATCTTGCCCCCCAAGGAAAGTCTGAAAGAATTGGAA
AACAAGGCAGAAGAGGAGCAGCGCATCCTCCAGCAGTCAGTGGTGAAAATGTATGAAGATATGACTTTGGAAGAGCTGGA
GGATCATGAAGACAAATTTAATGAGGAGGATGAACATGCTATTGAAATGTACAGACAGCTGAGACTATCTGAGTGGAAAG
CAACTAAACTGAAGAATAAATCTGGAGAAGTTTTGGAGATCTCAGGAAAGGATTATGTTCAAGAAGTTACCAAAGCTGGT
GAGAGTTTGCGGGTAATCTTGCACCTTTAAAAACAAGGAATTTCCCCTCTGTGCCCTGATAAATCAGCACCTTGGTGGAC
TTGCCAGGAAGTTCCCTGGTGTCAAATTTATCAAAGCCATTTCAACAACCTGCATACCCAATTAACCTGTTAGGAATCTG
CCCATGATATTTGTTTACCTGGAAGGAGATATCAAGGCTCAGTTTATCAGTCCTCTGGTGTTTGGCGGCATGAACCTGTC
GAGAGATGAGTTGGAGTGGAAACTG

Alignment

ORF - retro_ptro_675 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.81 %
• Parental protein coverage: 80.08 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PNEDTEWNDILRDF-GILPPKEESKD--EIEEMVLRLQKEAMVKPFEKMTLAQLKEAEDEFDEEDMQAIE
          PN.DTEWNDIL....GILPPKE..K......E...R......VK..E.MTL..L...ED.F.EED..AIE
Retrocopy PNTDTEWNDILAKR<GILPPKESLKELENKAEEEQRILQQSVVKMYEDMTLEELEDHEDKFNEEDEHAIE

Parental  TYRKKRLQEWKALKKKQKFGELREISGNQYVNEVTNAEEDVWVITHLYRSSI-PMCLLVNQHLSLLARKF
          .YR..RL.EWKA.K.K.K.GE..EISG..YV.EVT.A.E...VI.HL....I.P.C.L.NQHL..LARKF
Retrocopy MYRQLRLSEWKATKLKNKSGEVLEISGKDYVQEVTKAGESLRVILHL*KQGI>PLCALINQHLGGLARKF

Parental  PETKFVKAIVNSCIQHYHDNCLPTIFVYKNGQIEAKFIGIIECGGINLKLEELEWKL
          P..KF.KAI...CI.......LP.IFVY..G.I.A.FI.....GG.NL...ELEWKL
Retrocopy PGVKFIKAISTTCIPN*PVRNLPMIFVYLEGDIKAQFISPLVFGGMNLSRDELEWKL

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	0.00 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.06 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	45.53 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_675 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_675 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_675 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1132

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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 ,