RetrogeneDB ID: retro_ptro_427

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:55622335..55623091(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000042417
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DCK
• Ensembl ID: ENSPTRG00000016139
• Aliases: None
• Description: deoxycytidine kinase [Source:HGNC Symbol;Acc:2704]

Sequence

>retro_ptro_427
ATGGCCACCCCGCCCAAGAGAAGCTGCCCGTCTGTCTCAGCCAGCTCTGAGGGGACCCGCATCAAGAAAATCTCCATCGA
AGGGAACATCGCGGCAGATAAGTCAACATTTGTGAATATCCTTAAACAATTGTGTGAAGATTGGGAAGTGGTTCCTGAAC
CTGTTGCCAGACGGTGCAATGTTCAAAGTACTCAAGATGAATTTGAGGAACTTACAACGTCTCAGAAAAATGGTGGGAAT
GTTCTTCAGATGATGTGTAAGAAACCTGAACGATGGTCTTTTACTTTCCAAACATATGCCTGTCTCAGTCGAATAAGAGC
TCAGCTTGCCTCTCTGAATGGCAAGCTCAAAGATGCAGAGAAACCTGTATTATTTTTTGAACGATCTGTGTATAGTGACA
GGTATATTTTTGCATCTAATTTGTATGAATCTGAATGCATGAATGAGACAGAGTGGACAATTTATCAAGACTGGCATGAC
TGGATGAATAACCAATTTGGCCAAAGCCTTGAATTGGATGGAATCATTTATCTTCGAGCCACTCCAGAGAAATGCTTACA
TAGAATATATTTACGGGGAAGAAATGAAGAGCAAGGCATTCCTCTTGAATATTTAGAGAAGCTTCATTATAAACATGAAA
GCTGGCTCCTGCATAGGACACTGAAAACCAACTTCGATTATCTTCAAGAGGTGCCTATCTTAACACTGGATGTTAATGAA
GACTTTAAAGATAAATATGAAAGTCTGGTTGAAAAG

Alignment

ORF - retro_ptro_427 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.43 %
• Parental protein coverage: 79.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATPPKRSCPSLSASSEGTRIKKISIEGNIAAGKSTFVNILKQLCEDWEVVPEPVARWCNVQSTQDEFEE
          MATPPKRSCPS.SASSEGTRIKKISIEGNIAA.KSTFVNILKQLCEDWEVVPEPVAR.CNVQSTQDEFEE
Retrocopy MATPPKRSCPSVSASSEGTRIKKISIEGNIAADKSTFVNILKQLCEDWEVVPEPVARRCNVQSTQDEFEE

Parental  LTMSQKNGGNVLQMMYEKPERWSFTFQTYACLSRIRAQLASLNGKLKDAEKPVLFFERSVYSDRYIFASN
          LT.SQKNGGNVLQMM..KPERWSFTFQTYACLSRIRAQLASLNGKLKDAEKPVLFFERSVYSDRYIFASN
Retrocopy LTTSQKNGGNVLQMMCKKPERWSFTFQTYACLSRIRAQLASLNGKLKDAEKPVLFFERSVYSDRYIFASN

Parental  LYESECMNEIEWTIYQDWHDWMNNQFGQSLELDGIIYLRATPETCLHRMYLRGRNEEQGIPLEYLEKLHY
          LYESECMNE.EWTIYQDWHDWMNNQFGQSLELDGIIYLRATPE.CLHR.YLRGRNEEQGIPLEYLEKLHY
Retrocopy LYESECMNETEWTIYQDWHDWMNNQFGQSLELDGIIYLRATPEKCLHRIYLRGRNEEQGIPLEYLEKLHY

Parental  KHESWLLHRTLKTNFDYLQEVPILTLDVNEDFKDKYESLVEK
          KHESWLLHRTLKTNFDYLQEVPILTLDVNEDFKDKYESLVEK
Retrocopy KHESWLLHRTLKTNFDYLQEVPILTLDVNEDFKDKYESLVEK

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	0.29 RPM	9.46 RPM
SRP007412_cerebellum	0.04 RPM	7.53 RPM
SRP007412_heart	0.03 RPM	2.77 RPM
SRP007412_kidney	0.13 RPM	2.54 RPM
SRP007412_liver	0.03 RPM	1.64 RPM
SRP007412_testis	0.11 RPM	8.64 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_427 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_427 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_427 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000022606	1 retrocopy	retro_fcat_1830,
Myotis lucifugus	ENSMLUG00000005844	1 retrocopy	retro_mluc_2007,
Mus musculus	ENSMUSG00000029366	1 retrocopy	retro_mmus_2735,
Oryctolagus cuniculus	ENSOCUG00000001265	1 retrocopy	retro_ocun_1247,
Pan troglodytes	ENSPTRG00000016139	1 retrocopy	retro_ptro_427 ,
Pteropus vampyrus	ENSPVAG00000004341	1 retrocopy	retro_pvam_32,
Rattus norvegicus	ENSRNOG00000003296	1 retrocopy	retro_rnor_1026,
Xenopus tropicalis	ENSXETG00000018331	1 retrocopy	retro_xtro_9,