RetrogeneDB ID: retro_ggor_403

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 1:77979852..77981021(-)
• Located in intron of: ENSGGOG00000024342

Retrocopy information

• Ensembl ID: ENSGGOG00000024667
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DLST
• Ensembl ID: ENSGGOG00000011591
• Aliases: None
• Description: None

Sequence

>retro_ggor_403
ATGCTGTCCCGGTCCCACTGTGTGTCCCGGGCGTTCAGCCGCTCGCTCTCTGCCTTCCAGAAGGGGAACTGCCCTCTAGG
GAGACGTTCCCTGCCTGGGGTCTCCTTATGCCAGGGACCAGGTTACCCTAACAGCAGGAAGGTTGTCATTAACAACAGTG
TCTTCAGTGTTCGCTTCTTCAGAACTACAACTGTATGCAAGGATGACTTGGTTACAGTCAAAACCCCAGCGTTTGCAGAA
CCTGTCACAGAGGGAGATGTCAGGTGGAAGAAAGCTGTTGGAGACACAGTTGCAGAAGATGAAGTGGTTTGTGAGATTGA
AACTGACAAGACATTGGTGCAGGTTCCATCACCAGCAAATGGCGTGATTGAAGCTCTTTCCGTACCTGATGGGGGAAAAG
TCGAAGGAGGCACTCCGCTTTTCACACTCAGGAAAACTGGTGCTGCTCCTGCTAAGGCCAAGCCGGCTGAAGCTCCTGCT
GCTGCAGCCCCAAAAGCAGAACCTATAGCAGCGGCAGTTCCTCCCCCTGCAGCACCCATACCCACTCGGATGCCACCAGT
GCCCTCGCCCTCACAACCTCCTTCTAGCAAACCTGTGTCTGCAGTAAAACCCACTGCTGTCCCACCACTTAGCTGAGCCA
GGAGCTGGCAAAGGTCTGCATTCAGAACATCGGGAGAAAATGAACAGGATGCGGCAGTGCATTGCTCAGCGTCTGAAAGA
GGCCCAGAATACATGTGCCAATGCTGACAATTTTTAATGAGATTGACATGAGTAACATCCAAAAGATGAGGGCTCGGCAC
AAAGAGGCTTTTTTGAAGAAACATAACCTCAAACTAGGCTTCATGTCGGCATTTGTGAAGGCCTCAGCCTTTGCCTTGCA
GGAACAGCCTGTTGTAAATGCAGTGATTGACGATATAACCAAAGAGGTGGTATATAGGGATTATATTGACATCAGTGTTG
CAGTGGCCACCCCACAGGGTCTGGTGGTTCCAGTCATCAGGAATGTGGAAGCTATGAATTATGCAGATATTGAACAGACC
ATCACTGAACTGGGAGAGAAGGCCCGAAAGAATGAACTTGCCATTGAAGATATGGATGGTGGTACCTTCACCATTAGCAA
TGGAGGTGTTTTTGGCTCACTCTTTGGAACACCCATTATCAACCCCCCT

Alignment

ORF - retro_ggor_403 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.86 %
• Parental protein coverage: 85.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MLSRSRCVSRAFSRSLSAFQKGNCPLGRRSLPGVSLCQGPGYLNSRKVVINNSVFSVRFFRATAVCKDDL
          MLSRS.CVSRAFSRSLSAFQKGNCPLGRRSLPGVSLCQGPGY.NSRKVVINNSVFSVRFFR.T.VCKDDL
Retrocopy MLSRSHCVSRAFSRSLSAFQKGNCPLGRRSLPGVSLCQGPGYPNSRKVVINNSVFSVRFFRTTTVCKDDL

Parental  VTVKTPAFAESVTEGDVRWEKAVGDTVAEDEVVCEIETDKTSVQVPSPANGVIEALLVPDGGKVEGGTPL
          VTVKTPAFAE.VTEGDVRW.KAVGDTVAEDEVVCEIETDKT.VQVPSPANGVIEAL.VPDGGKVEGGTPL
Retrocopy VTVKTPAFAEPVTEGDVRWKKAVGDTVAEDEVVCEIETDKTLVQVPSPANGVIEALSVPDGGKVEGGTPL

Parental  FTLRKTGAAPAKAKPAEAPAAAAPKAEPTAAAVPPAAAPIPTQMPPVPSPSQPPSGKPVSAVKPTVAPP-
          FTLRKTGAAPAKAKPAEAPAAAAPKAEP.AAAVPP.AAPIPT.MPPVPSPSQPPS.KPVSAVKPT..PP.
Retrocopy FTLRKTGAAPAKAKPAEAPAAAAPKAEPIAAAVPPPAAPIPTRMPPVPSPSQPPSSKPVSAVKPTAVPP>

Parental  LAEPGAGKGLRSEHREKMNRMRQRIAQRLKEAQNTCA-MLTTFNEIDMSNIQEMRARHKEAFLKKHNLKL
          LAEPGAGKGL.SEHREKMNRMRQ.IAQRLKEAQNTCA.MLT.FNEIDMSNIQ.MRARHKEAFLKKHNLKL
Retrocopy LAEPGAGKGLHSEHREKMNRMRQCIAQRLKEAQNTCA>MLTIFNEIDMSNIQKMRARHKEAFLKKHNLKL

Parental  GFMSAFVKASAFALQEQPVVNAVIDDTTKEVVYRDYIDISVAVATPRGLVVPVIRNVEAMNFADIERTIT
          GFMSAFVKASAFALQEQPVVNAVIDD.TKEVVYRDYIDISVAVATP.GLVVPVIRNVEAMN.ADIE.TIT
Retrocopy GFMSAFVKASAFALQEQPVVNAVIDDITKEVVYRDYIDISVAVATPQGLVVPVIRNVEAMNYADIEQTIT

Parental  ELGEKARKNELAIEDMDGGTFTISNGGVFGSLFGTPIINPP
          ELGEKARKNELAIEDMDGGTFTISNGGVFGSLFGTPIINPP
Retrocopy ELGEKARKNELAIEDMDGGTFTISNGGVFGSLFGTPIINPP

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	0.67 RPM	47.81 RPM
SRP007412_cerebellum	1.85 RPM	45.39 RPM
SRP007412_heart	0.59 RPM	83.52 RPM
SRP007412_kidney	4.33 RPM	188.17 RPM
SRP007412_liver	8.57 RPM	39.78 RPM
SRP007412_testis	0.41 RPM	55.63 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_403 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_403 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_407
Pan troglodytes	retro_ptro_312

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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,