RetrogeneDB ID: retro_ggor_2902

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:44732865..44734451(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: RBM39
• Ensembl ID: ENSGGOG00000003950
• Aliases: None
• Description: None

Sequence

>retro_ggor_2902
ATGGCAGACGATATTAATATTGAAGCAATGCTTGAGGCTCCTTACAAGTAGGATGAGAACAAGTTGAGCAGGGCCAACGG
CCATGAAGAACGTAGCAAAAAAAGGAAAAAAAGCAAGAGCAGAAGTCGTAGTCGTGAACGAAAGAGAAGCAAAAGTAAGG
AACGGAAGCAAAGTACAGATCGAGAAAGGAAAAAGAGCAAAAGCCGTGAAAGGAAGCGAAGTCGAAGCAGAGAGGCGACG
GAGCCGCTCGAGAAGTCGAGATCGAAGATTTAGAGGCCGCTACAGAAGTCCTTACCGCGGACCAAAATTTAACAGTGCCA
TCTGAGGAAAGACTGGATTGCCTTATAGTATCAAATTAAGCATAGGACGTTCCCGAAGCAAAAGTCCACTCAGAAAAGAC
AAGAGCCCTGTGAGGGAACCTATTGATAATCTAACTCCTGAGGAAAGAGATGCAAGGACAGTCTTCTGTCTGCAGCTGGC
GGCAGGAATTCGACCAAAGGATTTGGAAGAGTTTTTCTCTACAGTAGGAAAGGCTCGAGGCGTGAGGATGATTTCCGATA
GAAATTCAAGACGTTCCAAAGGAATTGCTTACGTGGAGTTCGTCGGTGTTAGTTCAGTGCCTCTAGCAATAGGATTAACT
GGCCAACGAGTTTTAGGAGTGCCAATCATAGTACAGGCATCACAGGCAGAAAAAAACAGAGCTGCAGCCATGGCAAACAA
TATACAAAAGGGAAGTGCTGGACCTAAGAGGCTTTATGTGGACTCATTACACTTTTAACATAACTGAAGATACGCTTCGT
GGGATCTTTGAGCCTTTCGGAAGGATTGAAAGTATCCAGCTGACGATAGACAGTGAAACTGGTCGATCCAAGGGATACGG
ATTTATTACATTTTCTGATTCAGAATGTGCCAAAAAGTCTTTGGAACAATTTAACGGATTTGAACTAGCAGGGAGGCCAA
TGAAAGTTGGTCATGTTACTGAACGTGCTGATGCTTCGAGTACTAGTTCATTTTTGGACAGTGATGAACTGGAAAGGACT
AGAATTGATTTGGGAACAACTGGTCGTCTTCAGTTAGTGGCAAGACTTGCAGAGGATACAGGTTTGCAGATTCCACCAGC
AGCACAGCAAGCTCTACAAATGAGTGGCTCTTTGGCATTTGGTGCTGTGGCAGAATTTTCTTTTGTTATGGATTTGCAAA
CAAGACTTTCCCAGCAGACTGAAGCTTCAGCTTTAGCTGCAGCTGCTTCTGTTCAGCCACTTGCAACACAGTGTTTCCAA
CTCTCTAACATGTTTAACCCTCAAACAGAAGAAGTTGGATGGGATACAGAGATTAAGAACGATATGATTGAAGAATGTAA
TAAACATGGAGGAATTATTCATATTTATGTTGACAAAAATTCAGCTCAGGGCAATGTCTATGTGAAGTGCCCATCAATTG
CTGCAGCTATTACTGCTGTCAATGCATTGCATGGCAGGTGGTTTGCTGGTAAAATGATAACAGCAGCATATGTACCTCTT
CCAACTTACCACAACCTGTTTCCTGATTCTATGACAGCAACACAACTACTGGTTCCAAGCAGACGA

Alignment

ORF - retro_ggor_2902 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.93 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MADDIDIEAMLEAPYKKDENKLSSANGHEERSKKRKKSKSRSRSHERKRSKSKERKRSRDRER-KKSKSR
          MADDI.IEAMLEAPYK.DENKLS.ANGHEERS......KSRSRS.ERKRSKSKERK.S.DRER.K..K..
Retrocopy MADDINIEAMLEAPYK*DENKLSRANGHEERSXXXXXXKSRSRSRERKRSKSKERKQSTDRER>KRAKAV

Parental  ERKRSRSKERRRSRSRSRDRRFRGRYRSPYSGPKFNSAIRGKIGLPHSIKLSRRRSRSKSPFRKDKSPVR
          ........ERRRSRSRSRDRRFRGRYRSPY.GPKFNSAI.GK.GLP.SIKLS..RSRSKSP.RKDKSPVR
Retrocopy KGSEVEA-ERRRSRSRSRDRRFRGRYRSPYRGPKFNSAI*GKTGLPYSIKLSIGRSRSKSPLRKDKSPVR

Parental  EPIDNLTPEERDARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPL
          EPIDNLTPEERDARTVFC.QLAA.IRP.DLEEFFSTVGK.R.VRMISDRNSRRSKGIAYVEFV.VSSVPL
Retrocopy EPIDNLTPEERDARTVFCLQLAAGIRPKDLEEFFSTVGKARGVRMISDRNSRRSKGIAYVEFVGVSSVPL

Parental  AIGLTGQRVLGVPIIVQASQAEKNRAAAMANNLQKGSAGPMRLYVGSLHF-NITEDMLRGIFEPFGRIES
          AIGLTGQRVLGVPIIVQASQAEKNRAAAMANN.QKGSAGP.RLYV.SLHF.NITED.LRGIFEPFGRIES
Retrocopy AIGLTGQRVLGVPIIVQASQAEKNRAAAMANNIQKGSAGPKRLYVDSLHF>NITEDTLRGIFEPFGRIES

Parental  IQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERTDASSASSFLDSDELERTG
          IQL..DSETGRSKGYGFITFSDSECAKK.LEQ.NGFELAGRPMKVGHVTER.DASS.SSFLDSDELERT.
Retrocopy IQLTIDSETGRSKGYGFITFSDSECAKKSLEQFNGFELAGRPMKVGHVTERADASSTSSFLDSDELERTR

Parental  IDLGTTGRLQLMARLAEGTGLQIPPAAQQALQMSGSLAFGAVAEFSFVIDLQTRLSQQTEASALAAAASV
          IDLGTTGRLQL.ARLAE.TGLQIPPAAQQALQMSGSLAFGAVAEFSFV.DLQTRLSQQTEASALAAAASV
Retrocopy IDLGTTGRLQLVARLAEDTGLQIPPAAQQALQMSGSLAFGAVAEFSFVMDLQTRLSQQTEASALAAAASV

Parental  QPLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAV
          QPLATQCFQLSNMFNPQTEE.VGWDTEIK.D.IEECNKHGG.IHIYVDKNSAQGNVYVKCPSIAAAI.AV
Retrocopy QPLATQCFQLSNMFNPQTEE-VGWDTEIKNDMIEECNKHGGIIHIYVDKNSAQGNVYVKCPSIAAAITAV

Parental  NALHGRWFAVGKMITAAYVPLPTYHNLFPDSMTATQLLVPSRR
          NALHGRWFA.GKMITAAYVPLPTYHNLFPDSMTATQLLVPSRR
Retrocopy NALHGRWFA-GKMITAAYVPLPTYHNLFPDSMTATQLLVPSRR

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	2.78 RPM	96.92 RPM
SRP007412_cerebellum	3.98 RPM	122.06 RPM
SRP007412_heart	1.25 RPM	32.74 RPM
SRP007412_kidney	6.17 RPM	143.97 RPM
SRP007412_liver	5.91 RPM	121.13 RPM
SRP007412_testis	4.97 RPM	161.93 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_2902 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2902 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4679
Pan troglodytes	retro_ptro_3108
Pongo abelii	retro_pabe_3634

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000003950	1 retrocopy	retro_ggor_2902 ,
Myotis lucifugus	ENSMLUG00000003000	1 retrocopy	retro_mluc_1152,
Macaca mulatta	ENSMMUG00000031284	1 retrocopy	retro_mmul_2491,
Nomascus leucogenys	ENSNLEG00000010350	1 retrocopy	retro_nleu_2170,
Otolemur garnettii	ENSOGAG00000011227	1 retrocopy	retro_ogar_267,
Ochotona princeps	ENSOPRG00000002183	2 retrocopies	retro_opri_55, retro_opri_913,