RetrogeneDB ID: retro_hsap_3257

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 5:154777502..154778365(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000271477
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: OBFC1
• Ensembl ID: ENSG00000107960
• Aliases: None
• Description: oligonucleotide/oligosaccharide-binding fold containing 1 [Source:HGNC Symbol;Acc:26200]

Sequence

>retro_hsap_3257
ACTGGAGTTATAAACTGCATCTGCTAGAAAATATTGAGCAATATCAAGTTTTCATCCGCTGCTCCAAATGCAGCAAGAGA
ACTGAGCTTTACCTCAATACTCAAGAAGCTGCAAGACACCATTGAGCAGAGAACAAAAATTGAAACTGGGGACATGTTCT
GAATCAGAGGCTATGTCTACATGTGCAGAGAAGAGTGACAAATTTATGCCACTGCTTATTATAAAGTGGACGATCCAGTG
TGGAACATTCAAATTGCAAGGGTGTTTGAGCTGCCCATTAATCTACAGGAAAGTTTAGACCAAGCCTTTCCATTGCCCAG
ACTTAGAGAAAGAAGAAGCACTAAGCAATCCAGGTGTCCTGGCCTTCACTAGTCTCATGTGTTTGCTGAGTGAAAAAGCC
AAAGAATTCCCCATAAAGAACAGAGTGCAGAACTTTGACCAGCAGGAGTTGGAAATGGTGGAGCCTTTGCTGTCCCTTGC
TAACCAGCCTGTTACTGACAGTGCCTGCTCTGAACAAGGAAATTTTAAGAAGGATATCACTTTCAAGGCAATTTATAGCA
TATTTTAAAATGCTATTCAACAGCTGCAGGAAAAAGGACTCGTTTTCCAGAAAGATGGTGGTTTTGATAACCTATGCTGT
GTAACCAGAAAAGACAAAGACCTGTATAGGAAAATCCACTGGATAATTCAGGAAGACTACCAGAAACCAAATCACCCGAA
GAAGGGCTGCCACTTCCTGCACATCTTGGCCTGTGCTCACCCTGAGCATCTGCCCGGTTCTAGTTAGGGCTATGTTGCAG
CAAGTTCTGGAGCTCCTGGAGGACCAGAGTGACCTCATCAGCACAATGGAGCACCACTACTCC

Alignment

ORF - retro_hsap_3257 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.66 %
• Parental protein coverage: 77.72 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TGVINCICWKKL-NTESVSAAPSAARELSLTSQLKKLQETIEQKTKIEIGDTIRVRGSIRTYREEREIHA
          TGVINCIC.K.L.N....SAAP.AARELS.TS.LKKLQ.TIEQ.TKIE.GD....RG.....REE..I.A
Retrocopy TGVINCIC*KILSNIKFSSAAPNAARELSFTSILKKLQDTIEQRTKIETGDMF*IRGYVYMCREE*QIYA

Parental  TTYYKVDDPVWNIQIARMLELPT-IYRKVYDQPFHSSALEKEEALSNPGALDLPSLTSLLSEKAKEFLME
          T.YYKVDDPVWNIQIAR..ELP..IYRKV...PFH...LEKEEALSNPG.L...SL..LLSEKAKEF...
Retrocopy TAYYKVDDPVWNIQIARVFELPI>IYRKV*TKPFHCPDLEKEEALSNPGVLAFTSLMCLLSEKAKEFPIK

Parental  NRVQSFYQQELEMVESLLSLANQPVIHSASSDQVNFKKDTTSKAIHSIFKNAIQLLQEKGLVFQKDDGFD
          NRVQ.F.QQELEMVE.LLSLANQPV..SA.S.Q.NFKKD.T.KAI.SIF.NAIQ.LQEKGLVFQKD.GFD
Retrocopy NRVQNFDQQELEMVEPLLSLANQPVTDSACSEQGNFKKDITFKAIYSIF*NAIQQLQEKGLVFQKDGGFD

Parental  NLYYVTREDKDLHRKIHRIIQQDCQKPNHMEKGCHFLHILACAR-LSIRPGLSEAVLQQVLELLEDQSDI
          NL..VTR.DKDL.RKIH.IIQ.D.QKPNH..KGCHFLHILACA..LSI.P.L..A.LQQVLELLEDQSD.
Retrocopy NLCCVTRKDKDLYRKIHWIIQEDYQKPNHPKKGCHFLHILACAH>LSICPVLVRAMLQQVLELLEDQSDL

Parental  VSTMEHYYT
          .STMEH.Y.
Retrocopy ISTMEHHYS

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	17.11 RPM
bodymap2_adrenal	0.00 RPM	19.24 RPM
bodymap2_brain	0.00 RPM	9.52 RPM
bodymap2_breast	0.00 RPM	14.77 RPM
bodymap2_colon	0.00 RPM	10.05 RPM
bodymap2_heart	0.00 RPM	16.97 RPM
bodymap2_kidney	0.00 RPM	15.92 RPM
bodymap2_liver	0.00 RPM	7.39 RPM
bodymap2_lung	0.00 RPM	36.57 RPM
bodymap2_lymph_node	0.00 RPM	15.79 RPM
bodymap2_ovary	0.00 RPM	10.31 RPM
bodymap2_prostate	0.00 RPM	19.92 RPM
bodymap2_skeletal_muscle	0.00 RPM	12.40 RPM
bodymap2_testis	0.00 RPM	22.02 RPM
bodymap2_thyroid	0.00 RPM	12.71 RPM
bodymap2_white_blood_cells	0.00 RPM	26.17 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3257 was not detected

EST

No EST(s) were mapped for retro_hsap_3257 retrocopy.

TSS

No TSS is located nearby retro_hsap_3257 retrocopy 5' end.

Lab

retro_hsap_3257 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3257 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2203
Gorilla gorilla	retro_ggor_2219
Pongo abelii	retro_pabe_2701
Macaca mulatta	retro_mmul_2050
Callithrix jacchus	retro_cjac_1791

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018342	1 retrocopy	retro_cjac_1791,
Homo sapiens	ENSG00000107960	1 retrocopy	retro_hsap_3257 ,
Gorilla gorilla	ENSGGOG00000008979	1 retrocopy	retro_ggor_2219,
Macaca mulatta	ENSMMUG00000015323	1 retrocopy	retro_mmul_2050,
Nomascus leucogenys	ENSNLEG00000015282	1 retrocopy	retro_nleu_2689,
Pongo abelii	ENSPPYG00000002628	1 retrocopy	retro_pabe_2701,
Pan troglodytes	ENSPTRG00000002919	1 retrocopy	retro_ptro_2203,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.00 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).