RetrogeneDB ID: retro_ggor_1150

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 15:29809058..29810484(+)
• Located in intron of: ENSGGOG00000011600

Retrocopy information

• Ensembl ID: ENSGGOG00000024060
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DCAF13
• Ensembl ID: ENSGGOG00000015124
• Aliases: None
• Description: None

Sequence

>retro_ggor_1150
ACATTAACTAAAACAGTTAAAAAAAAAATCAGGCAGTGGACAGAACTCACAGCGAAGAGCTCGTGGAGTCCGGCCAGAAG
AGCAACCAAGATGAGGATGAAGATACTGAGCCAGAATCTGGACAATTATGTCTGTGAAACCAAGTTGGACTTACAGAGAG
TTCCAAGAAACTATGATCCTACTTTACATCCTTTTGAGGTCCCATGAGAATATGTAAGAGCTTTAAATGCTACCAAAATG
GAATGAGTATTTGCAAAACCATTCCTTGCTTTGCTGGATGGTCACCAAGATGGAGTCAGTTGCTTGGCAAAGCATCCAAA
GAACCTGGCTACTGTCCTTTCTGGGGCGTGTGATGGAGAGGTTAGAATTTGGAACCTGACTCAACAGAAATGTATCCGTA
CAATACAAGCACATGAAGGCTTTGTATAAGGAATACTTACTCACTTTTGTGGGACTTCTTTTTTCACCGTTGGTGGTGAC
AAAACTGTGAAACAATGGAAAATGGATGGGCCAGGCTATGGAGATGAGGAAGAACCATTACATACAACATTAGGAAAGAC
AGTGTATACTGGGGTTTATCATCACTGTAAAGAAGCTGTTTTTGCCACATGTGATCAGCAAGTAGACATTTGGGATGAAC
AAAGAACTAATCCTGTATGTTCAATGACCTGGGGATTTGACAGTGTAAGTAGTGTTAAATTTAACCCAATCGAGACATTT
CTCTTGGGAAGTTTGTGCGTCTGACAGGAATATAGTACTGTACGACATGAGGCAAGCTACTCCTTTGAAAAAGGTTATAT
TAGATATGAGAACAAATACAGTTTGTTGGAACCCTATGGAAGCTTTCATTTTTACGGCAGCAAATGAAGACTATAACTTA
CATACTTTTGATATGTGTGCACTGGACACTCCTGTAATGTTCCATATGGATCATGTATCTGCAGTGCTTGACATGGATTA
CCCTCCCACTGGGAAAGAGTTTGTGTCTGCTAGTTTCGATAAAGCTATTTGTATCTTTCCTATAGACAAAAGTTGAAGCA
GGGAGGTATATCACACAAAGCGAATGCAACATGTTATCTGTGTAAAATGGACTTCTGACAGCAAGTATATTATGTGTGGA
TCTGATGAAATGAACATTTGCCTGTGGAAAGCTAATGCTTCTGAAAAATTTGGTGTGCTTACATCATGAGAAAAAGCAGC
TAAGGATTATAACTAGAAATTGAAGGAGAAATTTCAGCATCATCCTCATATAAAATGTATAGCTTGTCATTGACATCTAC
CAAAATCTATCTACAGCCAGATTCAGGAACAGCGCATCATGAAAGAAGCTCGTCGAAGAAAGGAAGTGAATCGTATTAAA
CGCAGCAAGCCTGGATCTGTGCCAATTGTGTCAGAGAAGAAGAAACACGTAGGGGCAGTTGTAAAA

Alignment

ORF - retro_ggor_1150 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87. %
• Parental protein coverage: 80.81 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SLGKAEVACGRRWRAELVAKSSWSPAGRATEMKVKMLSRNPDNYVRETKLDLQRVPRNYDPALHPFEVPR
          .L.K......R.W..EL.AKSSWSPA.RAT.M..K.LS.N.DNYV.ETKLDLQRVPRNYDP.LHPFEVP.
Retrocopy TLTKTVXXXXRQW-TELTAKSSWSPARRATKMRMKILSQNLDNYVCETKLDLQRVPRNYDPTLHPFEVP*

Parental  EYVRALNATKLERVFAKPFLASLDGHRDGVNCLAKHPKNLATVLSGACDGEVRIWNLTQRNCIRTIQAHE
          EYVRALNATK.E.VFAKPFLA.LDGH.DGV.CLAKHPKNLATVLSGACDGEVRIWNLTQ..CIRTIQAHE
Retrocopy EYVRALNATKME*VFAKPFLALLDGHQDGVSCLAKHPKNLATVLSGACDGEVRIWNLTQQKCIRTIQAHE

Parental  GFVRGICTRFCGTSFFTVGDDKTVKQWKMDGPGYGDEEEPLHTILGKTVYTGIDHHWKEAVFATCGQQVD
          GFV.GI.T.FCGTSFFTVG.DKTVKQWKMDGPGYGDEEEPLHT.LGKTVYTG..HH.KEAVFATC.QQVD
Retrocopy GFV*GILTHFCGTSFFTVGGDKTVKQWKMDGPGYGDEEEPLHTTLGKTVYTGVYHHCKEAVFATCDQQVD

Parental  IWDEQRTNPICSMTWGFDSISSVKFNPIETFLLGS-CASDRNIVLYDMRQATPLKKVILGMRTNTICWNP
          IWDEQRTNP.CSMTWGFDS.SSVKFNPIETFLLGS.CASDRNIVLYDMRQATPLKKVIL.MRTNT.CWNP
Retrocopy IWDEQRTNPVCSMTWGFDSVSSVKFNPIETFLLGS>CASDRNIVLYDMRQATPLKKVILDMRTNTVCWNP

Parental  MEAFIFTAANEDYNLYTFDMRALDTPVMVHMDHVSAVLDVDYSPTGKEFVSASFDKSIRIFPVDKSRSRE
          MEAFIFTAANEDYNL.TFDM.ALDTPVM.HMDHVSAVLD.DY.PTGKEFVSASFDK.I.IFP.DKS.SRE
Retrocopy MEAFIFTAANEDYNLHTFDMCALDTPVMFHMDHVSAVLDMDYPPTGKEFVSASFDKAICIFPIDKS*SRE

Parental  VYHTKRMQHVICVKWTSDSKYIMCGSDEMNIRLWKANASEKLGVLTSREKAAKDYNQKLKEKFQHYPHIK
          VYHTKRMQHVICVKWTSDSKYIMCGSDEMNI.LWKANASEK.GVLTS.EKAAKDYN.KLKEKFQH.PHIK
Retrocopy VYHTKRMQHVICVKWTSDSKYIMCGSDEMNICLWKANASEKFGVLTS*EKAAKDYN*KLKEKFQHHPHIK

Parental  RIARHRHLPKSIYSQIQEQRIMKEARRRKEVNRIKHSKPGSVPIVSEKKKHVVAVVK
          .IA.H.HLPKSIYSQIQEQRIMKEARRRKEVNRIK.SKPGSVPIVSEKKKHV.AVVK
Retrocopy CIACH*HLPKSIYSQIQEQRIMKEARRRKEVNRIKRSKPGSVPIVSEKKKHVGAVVK

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	0.10 RPM	8.63 RPM
SRP007412_cerebellum	0.04 RPM	8.94 RPM
SRP007412_heart	0.06 RPM	3.41 RPM
SRP007412_kidney	0.16 RPM	37.25 RPM
SRP007412_liver	0.11 RPM	11.95 RPM
SRP007412_testis	0.31 RPM	73.97 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_1150 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1150 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1498
Pan troglodytes	retro_ptro_1017
Pongo abelii	retro_pabe_1249

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001595	3 retrocopies	retro_amel_1453, retro_amel_1723, retro_amel_399,
Canis familiaris	ENSCAFG00000000663	3 retrocopies	retro_cfam_1309, retro_cfam_1533, retro_cfam_305,
Callithrix jacchus	ENSCJAG00000016181	2 retrocopies	retro_cjac_3083, retro_cjac_612,
Felis catus	ENSFCAG00000027256	1 retrocopy	retro_fcat_1840,
Homo sapiens	ENSG00000164934	1 retrocopy	retro_hsap_1498,
Gorilla gorilla	ENSGGOG00000015124	1 retrocopy	retro_ggor_1150 ,
Myotis lucifugus	ENSMLUG00000007375	1 retrocopy	retro_mluc_2048,
Nomascus leucogenys	ENSNLEG00000003791	1 retrocopy	retro_nleu_1718,
Otolemur garnettii	ENSOGAG00000002277	1 retrocopy	retro_ogar_305,
Pongo abelii	ENSPPYG00000018809	2 retrocopies	retro_pabe_1249, retro_pabe_3211,
Pan troglodytes	ENSPTRG00000020493	1 retrocopy	retro_ptro_1017,
Sarcophilus harrisii	ENSSHAG00000006588	1 retrocopy	retro_shar_507,