RetrogeneDB ID: retro_hsap_2831

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 3:113950247..113951726(-)
• Located in intron of: ENSG00000241490

Retrocopy information

• Ensembl ID: ENSG00000240487
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FAM214B
• Ensembl ID: ENSG00000005238
• Aliases: FAM214B, KIAA1539, P1.11659_5, bA182N22.6
• Description: family with sequence similarity 214, member B [Source:HGNC Symbol;Acc:25666]

Sequence

>retro_hsap_2831
ACATCCCCCAGGCTCTACCAGGTATTTATCTTTTCCCCTCCAGCTGGTGCCTCTGAGCTTCACAGGGCCCAGAAGCGACC
AGCCCCACCCACTAAGGGTCCTCAGGAGCTGGAGAGGGGCCCTGGGCTGGGGGCCAGAGAGGGACTACCCCCTGAAGAAC
CATCTTCTGTAGGGCTATTGGGCCCAGGGGGACTGGGGCTGGGAGTAGGTGTGTCCAGCCACCATTTCTCCCACCGTGGC
CTCTGTGTTGTGGAACAGGGAAGTAGTGCCACCTCTTCTTGGACTTCAGGGGCCTGGAGTCCCTCCTGGCCCCGATCATA
TGCTTCCTGAAATACTTTACACACCAGAGACTAGGCTTTCCCAGACCCAGGGGGACAGGGGTCCCTAGGGGAGTCCCCAG
GGCCAGCCCTCTGGGCCAGCTACACACGCTGGACACTGATTTGCAGTTTTGCACAAATAAGGGGTAAGAGCCCAGTGGCT
AGGGTGGGCAAGAGGGGGAGCCTCTGGCCTAGGGAGTCCCCTGGCATTGACAGTGGGCACAGTCCCAAGCACACACCCCC
AGCCCTGGACCTCCAGGCCCCTGCCCCACCAAGCAAAGGCTGCTTCTGCTGGAGAAGCCCCAAATGTCAGTTCTAAGGAA
GAGGGTCCAGCCCTTTGGACGTGCCAGGGAACCCTGGGCCACCCTACTGCTACCAACAGTTCTGATGCTCAAACCACACC
CATCTGGAGCCACCTGCTGCCTGGGCCCAAGGAGCCTGTTTTGGACCCAACAGACTGCAGTCCCATGGGGCGGAGGCTGA
CAGGTGCCCATCACCTGAAGCTGAGCCCACTTTGAAGCCTCTGGAAGGGGCCAGGCCTGCTGAGCCCCCGTAGTGCCTCC
CCTGTTCCTACCCCTGCTATCAGCTGTACCCTGCTGGGCAACTTTGAGGAATCATTGCTGCAAGGACGCTTTGCACCATC
TGGCCACATTGAGGGCTTCACAGCAGAGACTGGAGCTAGTGGGTCCTACTGCCCCCACCATGTCACACTGCCTGTCACTG
TCACCTTCTTTGAGGTTTCTGAGCAAAATGCCCCCACCCACTTCCTGGGCTTTGTGGATCTGAACCTCCTGGGGAGGAAG
AGTTACAGCGTGCCCAAAGTGGGCACCACACAAGTAACATTTAACCCCAACCAGACTGTGGTGAAGATGTTCCTGGTGAC
CTTTGACTTCTTGGACATGGCTGCTGCCACATGCCCTTATTGTGCCATTGCCTCTTTTTGGTGCCTGTGGGTGAGGAGAA
AAATGCTAACCCCACCTACTGCCTCCTCTGCTACTCGCTGCACCTTGGGTTCTGGAGCTCCCGCTCAGGCCTCTTAAGCC
TGAATGGAGATCTCTGCCAGCTTTTTTCCTGCTAGAGCCTGGAGCTGGACGCAGGGCTCCCCTGCGAACTTCAGGCTGTG
ACTGGGGCCCCTCTTAACCCACGTTATTCACTTTTGCCC

Alignment

ORF - retro_hsap_2831 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.36 %
• Parental protein coverage: 92.19 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TSPGVYQVSIFSPPAGTSEPHRALKRQAPSTEGPRELKRGPGLGAREGLPPEEPSTVGLLGPEGPGLGLG
          TSP..YQV.IFSPPAG.SE.HRA.KR.AP.T.GP.EL.RGPGLGAREGLPPEEPS.VGLLGP.G.GLG.G
Retrocopy TSPRLYQVFIFSPPAGASELHRAQKRPAPPTKGPQELERGPGLGAREGLPPEEPSSVGLLGPGGLGLGVG

Parental  VASQHFSHRGLCVVEQRSSVTSSWTSGAWSPPCPPSNASCNTLHTRDWASPDPGGQGSLGESPGPAPPGQ
          V.S.HFSHRGLCVVEQ.SS.TSSWTSGAWSP..P.S.AS.NTLHTRD.A.PDPGGQGSLGESPGPA....
Retrocopy VSSHHFSHRGLCVVEQGSSATSSWTSGAWSPSWPRSYAS*NTLHTRD*AFPDPGGQGSLGESPGPALWAS

Parental  LHTLDTDLHSLAQIGGKSPVAGVGNGGSLWPRESPGTANGHSPEHTPPG-PGPPGPCPTKRRLL-PAGEA
          ..T..T...S.AQI.GKSPVA.VG..GSLWPRESPG...GHSP.HTPP..PGPPGPCPTK.RLL..AGEA
Retrocopy -YTRWTLICSFAQIRGKSPVARVGKRGSLWPRESPGIDSGHSPKHTPPA<PGPPGPCPTKQRLL<SAGEA

Parental  PDVSSEEEGPAPRRRRGSLGHPTAANSSDAKATPFWSHLLPGPKEPVLDPTDCGPMGRRLKGARRLKLSP
          P.VSS.EEGPA.....G.LGHPTA.NSSDA..TP.WSHLLPGPKEPVLDPTDC.PMGRRL.GA..LKLSP
Retrocopy PNVSSKEEGPALWTCQGTLGHPTATNSSDAQTTPIWSHLLPGPKEPVLDPTDCSPMGRRLTGAHHLKLSP

Parental  LRSLRKGPGLLSPPSASPVPTPAVSRTLLGNFEESLLRGRFAPSGHIEGFTAEIGASGSYCPQHVTLPVT
          L.SL.KGPGLLSP.SASPVPTPA.S.TLLGNFEESLL.GRFAPSGHIEGFTAE.GASGSYCP.HVTLPVT
Retrocopy L*SLWKGPGLLSPRSASPVPTPAISCTLLGNFEESLLQGRFAPSGHIEGFTAETGASGSYCPHHVTLPVT

Parental  VTFFDVSEQNAPAPFLGIVDLNPLGRKGYSVPKVGTVQVTLFNPNQTVVKMFLVTFDFSDMPAA-HMTFL
          VTFF.VSEQNAP..FLG.VDLN.LGRK.YSVPKVGT.QVT.FNPNQTVVKMFLVTFDF.DM.AA.HM..L
Retrocopy VTFFEVSEQNAPTHFLGFVDLNLLGRKSYSVPKVGTTQVT-FNPNQTVVKMFLVTFDFLDMAAA<HMPLL

Parental  RHRLFLVPVGEEGNANPTHRLLCYLLHLRFRSSRSGRLSLHGDIRLLFSRRSLELDTGLPYELQAVTEAP
          .H.LFLVPVGEE.NANPT..LLCY.LHL.F.SSRSG.LSL.GD...LFS..SLELD.GLP.ELQAVT.AP
Retrocopy CHCLFLVPVGEEKNANPTYCLLCYSLHLGFWSSRSGLLSLNGDLCQLFSC*SLELDAGLPCELQAVTGAP

Parental  HNPRYSPLP
          .NPRYS.LP
Retrocopy LNPRYSLLP

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	10.89 RPM
bodymap2_adrenal	0.12 RPM	9.93 RPM
bodymap2_brain	0.00 RPM	19.92 RPM
bodymap2_breast	0.00 RPM	14.01 RPM
bodymap2_colon	0.00 RPM	11.78 RPM
bodymap2_heart	0.00 RPM	13.51 RPM
bodymap2_kidney	0.00 RPM	17.48 RPM
bodymap2_liver	0.00 RPM	4.98 RPM
bodymap2_lung	0.00 RPM	20.76 RPM
bodymap2_lymph_node	0.02 RPM	13.71 RPM
bodymap2_ovary	0.00 RPM	6.03 RPM
bodymap2_prostate	0.00 RPM	12.96 RPM
bodymap2_skeletal_muscle	0.00 RPM	8.26 RPM
bodymap2_testis	0.00 RPM	11.07 RPM
bodymap2_thyroid	0.00 RPM	8.06 RPM
bodymap2_white_blood_cells	0.12 RPM	44.44 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_2831 was not detected

EST

1 EST(s) were mapped to retro_hsap_2831 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AA128618	113950203	113950622	97.6	405	8	393

TSS

No TSS is located nearby retro_hsap_2831 retrocopy 5' end.

Lab

retro_hsap_2831 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2831 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1919
Gorilla gorilla	retro_ggor_1966
Pongo abelii	retro_pabe_2200
Macaca mulatta	retro_mmul_1504

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009210	1 retrocopy	retro_cjac_1357,
Homo sapiens	ENSG00000005238	1 retrocopy	retro_hsap_2831 ,
Gorilla gorilla	ENSGGOG00000003218	1 retrocopy	retro_ggor_1966,
Microcebus murinus	ENSMICG00000005528	1 retrocopy	retro_mmur_1580,
Macaca mulatta	ENSMMUG00000011862	1 retrocopy	retro_mmul_1504,
Nomascus leucogenys	ENSNLEG00000004530	1 retrocopy	retro_nleu_1207,
Pongo abelii	ENSPPYG00000019101	1 retrocopy	retro_pabe_2200,
Pan troglodytes	ENSPTRG00000020904	1 retrocopy	retro_ptro_1919,