RetrogeneDB ID: retro_hsap_3995

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 8:104671642..104672536(+)
• Located in intron of: ENSG00000176406

Retrocopy information

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

Parental gene information

• Parental gene symbol: TARBP2
• Ensembl ID: ENSG00000139546
• Aliases: TARBP2, LOQS, TRBP, TRBP1, TRBP2
• Description: TAR (HIV-1) RNA binding protein 2 [Source:HGNC Symbol;Acc:11569]

Sequence

>retro_hsap_3995
TCTGTTGGCAACACCAGCTGCACTGCTCAGGGCCCCAGGAAGAAGGTAGTCAAGCACAAGGCAGCTGAGGTGGCCCTCAG
ACACCTCAAAGTGGAGAGCATGTTGGAGCCGGCCCCGGAGGACAGCAGTTCTTTTTCTCCCCTAGACTCTTCACTGCCTG
AGGACTTTCCAGTTTTTACTGCTGCAGCAGCTGCTACCCCAGTTTCATCTGTTTTCCTAACCAGGAGCACCCCCATGGAA
AAGCAGCCCCCGCTCCTCCCTTCAGCAGTCGGAGTGCATCCCTGTTGGTGCTCTTCAGAAACTGGTGGTGCAGAAAGGCT
GGTGGTTGCCAGAGCACACAGTGACCTAGGAGTCCAGGCCAGATCAACACGAAGAATTGACCTGACGAGTGGAGCGTTTC
ACTGAGATTGGCAGTGGCACTTCCAAAAAATCAACAAGTTGTAATGCAGTGACCAAAATGCTGCTTCGAGTGCACACGGT
GTCTGTGGATGCCTGGGATGGCAATGAGGCAGAGCCTGATGATGACTACTTCTCCATTGATGTGGGCTCCCGCCTGGATG
GTCTTCAGAACCGGGGCCCAGGCCGCACCTGAGATTTTCTACCAAATTCATTGGAGAGAAGATCCTGTCCTTCTGCAATT
GCTCCCTGGGCTCCATAGGTGCCCTGGGCCCTGCCTGCTGCCGTGTCCTCAGTGAGCTCTCTGAAGAGCAGGTCTTCCAC
GTCAATTACCTGGATGTTGAGGAGCTGAGCCTGAGTAGACTCTGCCAGTGTCTGGTGGAACTGTCCTTCCAGCTGGCCAC
TGCATATCATGGCTCTGCAACCACCAGGGAGGCAGCCCGTGGTGAGGCTGCTTGCCGTGCCCTGCAGTACCACAAGATCA
TGGCGGGCAGCAAG

Alignment

ORF - retro_hsap_3995 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.15 %
• Parental protein coverage: 81.97 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TVGDTSCTGQGPSKKAAKHKAAEVALKHLKGGSMLEPALEDSSSFSPLDSSLPEDIPVFTAAAAATPVPS
          .VG.TSCT.QGP.KK..KHKAAEVAL.HLK..SMLEPA.EDSSSFSPLDSSLPED.PVFTAAAAATPV.S
Retrocopy SVGNTSCTAQGPRKKVVKHKAAEVALRHLKVESMLEPAPEDSSSFSPLDSSLPEDFPVFTAAAAATPVSS

Parental  VVLTRSPPMELQPPVSP-QQSECNPVGALQELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRVERFIEIG
          V.LTRS.PME.QPP..P.QQSEC.PVGALQ.LVVQKGW.LPE.TVT.ES.P....E...T.RVERF.EIG
Retrocopy VFLTRSTPMEKQPPLLP>QQSECIPVGALQKLVVQKGWWLPEHTVT*ESRPDQHEE--LT*RVERFTEIG

Parental  SGTSKKLAKRNAAAKMLLRVHTVPLDARDGNEVEPDDDHFSIGVGSRLDGLRNRGPGCTWDSLRNS-VGE
          SGTSKK....NA..KMLLRVHTV..DA.DGNE.EPDDD.FSI.VGSRLDGL.NRGPG.T.D.L.NS..GE
Retrocopy SGTSKKSTSCNAVTKMLLRVHTVSVDAWDGNEAEPDDDYFSIDVGSRLDGLQNRGPGRT*DFLPNS<IGE

Parental  KILSLRSCSLGSLGALGPACCRVLSELSEEQAFHVSYLDIEELSLSGLCQCLVELSTQPATVCHGSATTR
          KILS...CSLGS.GALGPACCRVLSELSEEQ.FHV.YLD.EELSLS.LCQCLVELS.Q.AT..HGSATTR
Retrocopy KILSFCNCSLGSIGALGPACCRVLSELSEEQVFHVNYLDVEELSLSRLCQCLVELSFQLATAYHGSATTR

Parental  EAARGEAARRALQYLKIMAGSK
          EAARGEAA.RALQY.KIMAGSK
Retrocopy EAARGEAACRALQYHKIMAGSK

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	3.70 RPM
bodymap2_adrenal	0.00 RPM	12.26 RPM
bodymap2_brain	0.02 RPM	3.70 RPM
bodymap2_breast	0.00 RPM	7.30 RPM
bodymap2_colon	0.00 RPM	4.72 RPM
bodymap2_heart	0.00 RPM	2.62 RPM
bodymap2_kidney	0.00 RPM	13.83 RPM
bodymap2_liver	0.00 RPM	8.77 RPM
bodymap2_lung	0.00 RPM	4.34 RPM
bodymap2_lymph_node	0.00 RPM	14.87 RPM
bodymap2_ovary	0.00 RPM	9.39 RPM
bodymap2_prostate	0.00 RPM	11.05 RPM
bodymap2_skeletal_muscle	0.00 RPM	2.18 RPM
bodymap2_testis	0.00 RPM	12.44 RPM
bodymap2_thyroid	0.00 RPM	11.28 RPM
bodymap2_white_blood_cells	0.00 RPM	7.66 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3995 was not detected

EST

No EST(s) were mapped for retro_hsap_3995 retrocopy.

TSS

No TSS is located nearby retro_hsap_3995 retrocopy 5' end.

Lab

retro_hsap_3995 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3995 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2712
Gorilla gorilla	retro_ggor_2682
Pongo abelii	retro_pabe_3281

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018668	1 retrocopy	retro_cjac_1526,
Homo sapiens	ENSG00000139546	1 retrocopy	retro_hsap_3995 ,
	ENSG00000180228	0 retrocopies
Gorilla gorilla	ENSGGOG00000012637	1 retrocopy	retro_ggor_2682,
Mus musculus	ENSMUSG00000023051	1 retrocopy	retro_mmus_2820,
Nomascus leucogenys	ENSNLEG00000017690	1 retrocopy	retro_nleu_545,
Pongo abelii	ENSPPYG00000004583	1 retrocopy	retro_pabe_3281,
Pan troglodytes	ENSPTRG00000005020	1 retrocopy	retro_ptro_2712,

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	0.03 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	0.03 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	0.07 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.06 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

---

Indel association:

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