RetrogeneDB ID: retro_hsap_1328

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 14:39680995..39681456(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000258671
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TMEM92
• Ensembl ID: ENSG00000167105
• Aliases: None
• Description: transmembrane protein 92 [Source:HGNC Symbol;Acc:26579]

Sequence

>retro_hsap_1328
GTCCCCGGCCTCATGCCCGCCTTGCTGCTCAGCCTGCTGGCTGGCCCCCAAAATGTTGCAGCTAAATGTGGTCTCTCCTT
CGCCTGCCCCAAAGGATTCAAATGCTGTGGCGACAGCTGCTGCCAGGAGAACGAGTTCTTCCCTGGCCCCTTGAGGATCT
TCGTCATCATCTTCCTGGTCATCCTGCCTCTCTTGTGCATCTGTGGCCTGGCTAAGCGCTTCTGTCCCAACTGCAGAGAC
CTGGACCCAGACGCCCTGAAGGATTGCCAGGGGCCCCGGGAACTGCCCTCCATCATCCCCCTAGAGAGGGTCAGAGCATC
CCTCTCTACTCCCCCACCCCCCTACAGTGAGTGATTCTGAAGCCTACTCGGGGCCAGAGTCCCACAGAGCCACCCCCTCC
CTACAGCTTCAGGCCTGAAAAATATACTGGGGATCAGAGGGCCATTGACAGCCCAGCCTTC

Alignment

ORF - retro_hsap_1328 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.71 %
• Parental protein coverage: 96.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VPGLAPTLLFSLLAGPQKIAAKCGLILACPKGFKCCGDSCCQENELFPGPVRIFVIIFLVILSVFCICGL
          VPGL.P.LL.SLLAGPQ..AAKCGL..ACPKGFKCCGDSCCQENE.FPGP.RIFVIIFLVIL...CICGL
Retrocopy VPGLMPALLLSLLAGPQNVAAKCGLSFACPKGFKCCGDSCCQENEFFPGPLRIFVIIFLVILPLLCICGL

Parental  AKCFCRNCREPEPDSPVDCRGPLELPSIIPPERVRVSLSAPPPPYSE-VILKPSLGPTPTEPPPPYSFRP
          AK.FC.NCR...PD...DC.GP.ELPSIIP.ERVR.SLS.PPPPYSE.VILKP..G..PTEPPPPYSFRP
Retrocopy AKRFCPNCRDLDPDALKDCQGPRELPSIIPLERVRASLSTPPPPYSE<VILKPTRGQSPTEPPPPYSFRP

Parental  EEYTGDQRGIDNPAF
          E.YTGDQR.ID.PAF
Retrocopy EKYTGDQRAIDSPAF

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	0.12 RPM
bodymap2_adrenal	0.00 RPM	0.00 RPM
bodymap2_brain	0.00 RPM	0.19 RPM
bodymap2_breast	0.00 RPM	0.00 RPM
bodymap2_colon	0.00 RPM	1.06 RPM
bodymap2_heart	0.00 RPM	0.00 RPM
bodymap2_kidney	0.00 RPM	0.10 RPM
bodymap2_liver	0.00 RPM	0.04 RPM
bodymap2_lung	0.00 RPM	3.59 RPM
bodymap2_lymph_node	0.00 RPM	0.02 RPM
bodymap2_ovary	0.00 RPM	2.12 RPM
bodymap2_prostate	0.00 RPM	0.59 RPM
bodymap2_skeletal_muscle	0.00 RPM	0.40 RPM
bodymap2_testis	0.00 RPM	0.60 RPM
bodymap2_thyroid	0.00 RPM	0.09 RPM
bodymap2_white_blood_cells	0.00 RPM	0.00 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_1328 was not detected

EST

No EST(s) were mapped for retro_hsap_1328 retrocopy.

TSS

No TSS is located nearby retro_hsap_1328 retrocopy 5' end.

Lab

retro_hsap_1328 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1328 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000167105	1 retrocopy	retro_hsap_1328 ,
Macaca mulatta	ENSMMUG00000001469	1 retrocopy	retro_mmul_2170,
Nomascus leucogenys	ENSNLEG00000009007	1 retrocopy	retro_nleu_1405,
Rattus norvegicus	ENSRNOG00000042868	3 retrocopies	retro_rnor_2441, retro_rnor_2442, retro_rnor_2443,