RetrogeneDB ID: retro_hsap_4679

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: X:43888578..43890164(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000214019
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RBM39
• Ensembl ID: ENSG00000131051
• Aliases: RBM39, CAPER, CAPERalpha, FSAP59, HCC1, RNPC2
• Description: RNA binding motif protein 39 [Source:HGNC Symbol;Acc:15923]

Sequence

>retro_hsap_4679
ATGGCAGACGATATTAATATTGAAGCAATGCTTGAGGCTCCTTACAAGTAGGATGAGAACAAGTTGAGCAGGGCCAACGG
CCATGAAGAACGTAGCAAAAAAAGGAAAAAAAGCAAGAGCAGAAGTCGTAGTCGTGAACGAAAGAGAAGCAAAAGTAAGG
AACGGAAGCAAAGTACAGATCGAGAAAGGAAAAAGAGCAAAAGCCGTGAAAGGAAGCGAAGTCGAAGCAGAGAGGCGACG
GAGCCGCTCAAGAAGTCGAGATTGAAGATTTAGAGGCCGCTACAGAAGTCCTTACTGCGGACCAAAATTTAACAGTGCCA
TCTGAGGAAAGACTGGATTGCCTTATAGTATCAAATTAAGCATAGGACGTTCCCGAAGCAAAAGTCCACTCAGAAAAGAC
AAGAGCCCTGTGAGGGAACCTATTGATAATCTAACTCCTGAGGAAAGAGATGCAAGGACAGTCTTCTGTATGCAGCTGGC
GGCAGGAATTCGACCAAAGGATTTGGAAGAGTTTTTCTCTACAGTAGGAAAGGCTCGAGGCGTGAGGATGATTTCCGATA
GAAATTCAAGACATTCCAAAGGAATTGCTTACGTGGAGTTCGTGGGTGTTAGTTCAGTGCCTCTAACAATAGGATTAACT
GGCCAACGAGTTTTAGGAGTGCCAATCATAGTACAGGCATCACAGGCAGAAAAAAACAGAGCTGCAGCCATGGCAAACAA
TGTACAAAAGGGAAGTGCTGGACCTAAGAGGCTTTAGGTGGACTCATTACACTTTTAACATAACTGAAGATACGCTTCGT
GGGTTCTTTGAGCCTTTCGGAAGGATTGAAAGTATCCAGCTGACGATAGACAGTGAAACTGGTCGATCCAAGGGATATGG
ATTTATTACATTTTCTGATTCAGAATGTGCCAAAAAGTCTTTGGAACAATTTAATGGATTTGAACTAGCAGGGAGGCCAA
TGAAAGTTGGTCATGTTATTGAACGTGCTGATGCTTCGAGTACTAGTTCATTTTTGGACAGTGATGAACTGGAAAGGACT
AGAATTGATTTGGGAACAACTGGTCGTCTTCAGTTAGTGGCAAGACTTGCAGAGGATACAGGTTTGCAGATTCCACCAGC
AGCACAGCAAGCTCTACAAATGAGTGGCTCTTTGGCATTTGGTGCTGTGGCAGAATTTTCTTTTGTTATGGATTTGCAAA
CAAGACTTTCCCAGCAGACTGAAGCTTCAGCTTTAGCTGCAGCTGCTTCTGTTCAGCCACTTGCAACACAGTGTTTCCAA
CTCTCTAACATGTTTAACCCTCAAACAGAAGAAGTTGGATGGGATACAGAGATTAAGGACGATGTGATTGAGGAATGTAA
TAAACATGGAGGAATTATTCATATTTATGTTGACAAAAATTCAGCTCAGGGCAATGTCTATGTGAAGTGCTCATCAATTG
CTGCAGCTATTGCTGCTGTCAATGCATTGCATGGCAGGTGGTTTGCTGGTAAAATGATAACAGCAGCATATGTACCTCTT
CCAACTTACCACAACCTGTTTCCTGATTCTATGACAGCAACACAACTACTGGTTCCAAGTAGACGA

Alignment

ORF - retro_hsap_4679 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.53 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 4
• 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
          ........ERRRSRSRSRD.RFRGRYRSPY.GPKFNSAI.GK.GLP.SIKLS..RSRSKSP.RKDKSPVR
Retrocopy KGSEVEA-ERRRSRSRSRD*RFRGRYRSPYCGPKFNSAI*GKTGLPYSIKLSIGRSRSKSPLRKDKSPVR

Parental  EPIDNLTPEERDARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPL
          EPIDNLTPEERDARTVFCMQLAA.IRP.DLEEFFSTVGK.R.VRMISDRNSR.SKGIAYVEFV.VSSVPL
Retrocopy EPIDNLTPEERDARTVFCMQLAAGIRPKDLEEFFSTVGKARGVRMISDRNSRHSKGIAYVEFVGVSSVPL

Parental  AIGLTGQRVLGVPIIVQASQAEKNRAAAMANNLQKGSAGPMRLYVGSLHF-NITEDMLRGIFEPFGRIES
          .IGLTGQRVLGVPIIVQASQAEKNRAAAMANN.QKGSAGP.RL.V.SLHF.NITED.LRG.FEPFGRIES
Retrocopy TIGLTGQRVLGVPIIVQASQAEKNRAAAMANNVQKGSAGPKRL*VDSLHF>NITEDTLRGFFEPFGRIES

Parental  IQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERTDASSASSFLDSDELERTG
          IQL..DSETGRSKGYGFITFSDSECAKK.LEQ.NGFELAGRPMKVGHV.ER.DASS.SSFLDSDELERT.
Retrocopy IQLTIDSETGRSKGYGFITFSDSECAKKSLEQFNGFELAGRPMKVGHVIERADASSTSSFLDSDELERTR

Parental  IDLGTTGRLQLMARLAEGTGLQIPPAAQQALQMSGSLAFGAVAEFSFVIDLQTRLSQQTEASALAAAASV
          IDLGTTGRLQL.ARLAE.TGLQIPPAAQQALQMSGSLAFGAVAEFSFV.DLQTRLSQQTEASALAAAASV
Retrocopy IDLGTTGRLQLVARLAEDTGLQIPPAAQQALQMSGSLAFGAVAEFSFVMDLQTRLSQQTEASALAAAASV

Parental  QPLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAV
          QPLATQCFQLSNMFNPQTEE.VGWDTEIKDDVIEECNKHGG.IHIYVDKNSAQGNVYVKC.SIAAAIAAV
Retrocopy QPLATQCFQLSNMFNPQTEE-VGWDTEIKDDVIEECNKHGGIIHIYVDKNSAQGNVYVKCSSIAAAIAAV

Parental  NALHGRWFAGKMITAAYVPLPTYHNLFPDSMTATQLLVPSRR
          NALHGRWFAGKMITAAYVPLPTYHNLFPDSMTATQLLVPSRR
Retrocopy NALHGRWFAGKMITAAYVPLPTYHNLFPDSMTATQLLVPSRR

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
bodymap2_adipose	0.00 RPM	102.17 RPM
bodymap2_adrenal	0.02 RPM	273.70 RPM
bodymap2_brain	0.00 RPM	123.27 RPM
bodymap2_breast	0.00 RPM	150.92 RPM
bodymap2_colon	0.08 RPM	213.89 RPM
bodymap2_heart	0.00 RPM	87.21 RPM
bodymap2_kidney	0.02 RPM	235.63 RPM
bodymap2_liver	0.00 RPM	79.81 RPM
bodymap2_lung	0.00 RPM	223.44 RPM
bodymap2_lymph_node	0.02 RPM	305.72 RPM
bodymap2_ovary	0.04 RPM	273.17 RPM
bodymap2_prostate	0.02 RPM	262.94 RPM
bodymap2_skeletal_muscle	0.00 RPM	65.97 RPM
bodymap2_testis	0.11 RPM	170.73 RPM
bodymap2_thyroid	0.02 RPM	292.17 RPM
bodymap2_white_blood_cells	0.08 RPM	160.06 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_4679 was not detected

EST

No EST(s) were mapped for retro_hsap_4679 retrocopy.

TSS

No TSS is located nearby retro_hsap_4679 retrocopy 5' end.

Lab

retro_hsap_4679 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4679 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_3108
Gorilla gorilla	retro_ggor_2902
Pongo abelii	retro_pabe_3634

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017535	1 retrocopy	retro_cjac_2199,
Homo sapiens	ENSG00000131051	1 retrocopy	retro_hsap_4679 ,
Macaca mulatta	ENSMMUG00000031284	1 retrocopy	retro_mmul_2491,
Mus musculus	ENSMUSG00000027620	3 retrocopies	retro_mmus_1512, retro_mmus_2792, retro_mmus_2793,
Otolemur garnettii	ENSOGAG00000011227	1 retrocopy	retro_ogar_267,
Ochotona princeps	ENSOPRG00000002183	2 retrocopies	retro_opri_55, retro_opri_913,
Pongo abelii	ENSPPYG00000010963	1 retrocopy	retro_pabe_3634,