RetrogeneDB ID: retro_ptro_312

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:76404625..76405793(-)
• Located in intron of: ENSPTRG00000000871

Retrocopy information

• Ensembl ID: ENSPTRG00000040641
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DLST
• Ensembl ID: ENSPTRG00000006543
• Aliases: None
• Description: dihydrolipoamide S-succinyltransferase (E2 component of 2-oxo-glutarate complex) [Source:HGNC Symbol;Acc:2911]

Sequence

>retro_ptro_312
ATGCTGTCCCGGTCCCACTGTGTGTCCCGGGCGTTCAGCCACTTGCTCTCTGCCTTCCAGAAGGGGAACTGCCCTCTAGG
GAGACATTCCCTGCCTGGGGTCTCCTTATGCCAGGGACCAGGTTACCCTAACAGCAGGAAGGTTGTCATTAACAACAGTG
TCTTCAGTGTTCGCTTCTTCAGAACTACAACTGTATGCAAGGATGACTTGGTTACAGTCAAAACCCCAGCGTTTGCAGAA
CCTGTCACAGAGGGAGATGTCAGGTGGGAGAAAGCTGTTGGAGACACAGTTGCAGAAGATGAAGTGGTTTGTGAGATTGA
AACTGACAAGACATTGGTGCAGGTTCCATCACCAGCAAATGGCATGATTGAAGCTCTTTTCGTACCTGATGGGGGAAAAG
TCGAAGGAGGCACTCCGCTTTTCACACTCGGGAAAACTGGTGCTGCTCCTGCTAAGGCCAAGCTGGCTGAAGCTCCTGCT
GCTGCAGCCCCAAAAGCAGAACCTATAGCAGCGGCAGTTCCTCCCCGTGCAGCACCCATACCCACTCAGATGCCACCTGT
GCCCTCGCCCTCACAACCTCCTTCTAGCAAACCTGTGTCTGCAGTAAAACCCACTGCTGTCCCACCACTAGCTGAGCCAG
GAGCTGGCAAAGGTCTGCATTCAGAACATCGGGAGAAAATGAACAGGATGCGGCAGTGCATTGCTCAGCGTCTGAAGGAG
GCCCAGAATACATGTGCCAATGCTGACAATTTTTAATGAGATTGACGTGAGTAACATCCAGAAGATGAGGGCTCGGCACA
AAGAGGCTTTTTTGAAGAAACATAACCTCAAACTAGGCTTCATGTCGGCATTTGTGAAGGCCTCAGCCTTTGCCTTGCAG
GAACAGCCTGTTGTAAATGCAGTGATTGACGATATAACCAAAGAGGTGGTATACAGGGATTATATTGACATCAGTGTTGC
AGTGGCCACCCCACAGGGTCTGGTGGTTCCAGTCATCAGGAATGTGGAAGCTATGAATTATGCAGATATTGAACAGACCA
TCACTGAACTGGGAGAGAAGGCCCAAAAGAATGAACTTGCCATTGAAGATATGGATGGCGGTACCTTCACCATTAGCAAC
GGAGGTGTTTTTGGCTCACTCTTTGGAACACCCATTATCAACCCCCCT

Alignment

ORF - retro_ptro_312 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.08 %
• Parental protein coverage: 85.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLSRSRCVSRAFSRSLSAFQKGNCPLGRRSLPGVSLCQGPGYPNSRKVVINNSVFSVRFFRTTAVCKDDL
          MLSRS.CVSRAFS..LSAFQKGNCPLGR.SLPGVSLCQGPGYPNSRKVVINNSVFSVRFFRTT.VCKDDL
Retrocopy MLSRSHCVSRAFSHLLSAFQKGNCPLGRHSLPGVSLCQGPGYPNSRKVVINNSVFSVRFFRTTTVCKDDL

Parental  VTVKTPAFAESVTEGDVRWEKAVGDTVAEDEVVCEIETDKTSVQVPSPANGVIEALLVPDGGKVEGGTPL
          VTVKTPAFAE.VTEGDVRWEKAVGDTVAEDEVVCEIETDKT.VQVPSPANG.IEAL.VPDGGKVEGGTPL
Retrocopy VTVKTPAFAEPVTEGDVRWEKAVGDTVAEDEVVCEIETDKTLVQVPSPANGMIEALFVPDGGKVEGGTPL

Parental  FTLRKTGAAPAKAKPAEAPAAAAPKAEPTAAAVPPPAAPIPTQMPPVPSPSQPPSGKPVSAVKPTVAPPL
          FTL.KTGAAPAKAK.AEAPAAAAPKAEP.AAAVPP.AAPIPTQMPPVPSPSQPPS.KPVSAVKPT..PPL
Retrocopy FTLGKTGAAPAKAKLAEAPAAAAPKAEPIAAAVPPRAAPIPTQMPPVPSPSQPPSSKPVSAVKPTAVPPL

Parental  AEPGAGKGLRSEHREKMNRMRQRIAQRLKEAQNTCA-MLTTFNEIDMSNIQGMRARHKEAFLKKHNLKLG
          AEPGAGKGL.SEHREKMNRMRQ.IAQRLKEAQNTCA.MLT.FNEID.SNIQ.MRARHKEAFLKKHNLKLG
Retrocopy AEPGAGKGLHSEHREKMNRMRQCIAQRLKEAQNTCA>MLTIFNEIDVSNIQKMRARHKEAFLKKHNLKLG

Parental  FMSAFVKASAFALQEQPVVNAVIDDTTKEVVYRDYIDISVAVATPRGLVVPVIRNVEAMNFADIERTITE
          FMSAFVKASAFALQEQPVVNAVIDD.TKEVVYRDYIDISVAVATP.GLVVPVIRNVEAMN.ADIE.TITE
Retrocopy FMSAFVKASAFALQEQPVVNAVIDDITKEVVYRDYIDISVAVATPQGLVVPVIRNVEAMNYADIEQTITE

Parental  LGEKARKNELAIEDMDGGTFTISNGGVFGSLFGTPIINPP
          LGEKA.KNELAIEDMDGGTFTISNGGVFGSLFGTPIINPP
Retrocopy LGEKAQKNELAIEDMDGGTFTISNGGVFGSLFGTPIINPP

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	0.39 RPM	59.65 RPM
SRP007412_cerebellum	0.65 RPM	63.70 RPM
SRP007412_heart	0.26 RPM	128.01 RPM
SRP007412_kidney	0.65 RPM	251.03 RPM
SRP007412_liver	0.36 RPM	56.17 RPM
SRP007412_testis	0.11 RPM	51.95 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_312 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_312 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_312 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_407
Gorilla gorilla	retro_ggor_403

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000009316	1 retrocopy	retro_cpor_1089,
Homo sapiens	ENSG00000119689	1 retrocopy	retro_hsap_407,
Gorilla gorilla	ENSGGOG00000011591	1 retrocopy	retro_ggor_403,
Nomascus leucogenys	ENSNLEG00000016330	1 retrocopy	retro_nleu_1006,
Oryctolagus cuniculus	ENSOCUG00000015606	1 retrocopy	retro_ocun_322,
Pan troglodytes	ENSPTRG00000006543	1 retrocopy	retro_ptro_312 ,
Tursiops truncatus	ENSTTRG00000001915	1 retrocopy	retro_ttru_681,
Xenopus tropicalis	ENSXETG00000013264	1 retrocopy	retro_xtro_46,