RetrogeneDB ID: retro_hsap_3728

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 7:45853871..45854301(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AC118758.1
• Ensembl ID: ENSG00000263064
• Aliases: None
• Description: None

Sequence

>retro_hsap_3728
GGAACAGCTGGGCCTGCAGAGGCCGCCATGCGGGAGGCAGAGGCCAGGCCTCTCCAGACCCACTTGCAACCTCCCGGCGT
CCTCTCCGGGCCCAGCTCTTCCTCCCGGCTGCGTCTCTAGGCCCGACTCCGGCCTCCCAACAACCTCTTTGGACTCAGCT
CCTGCCCAGCTCCCAGTGGCCCTGGTAGGCCCACAACTTCCTGAAGCCAAGCTCCCCAGGCCCAGGTCAGGCCTCACGGT
GGCCTCGCCAGGCTCAGCTCCTGCCCTCCGATGGCATCTCCAGGTCCCAAACGGCCTCCGGTCGGTGGGCTCCTCTAGGC
CCAGCTTGGGCCTCCCGGCGGCCTCTGCAGGCCCAAATCGTCCTGAAGTCGGCCTCTCCAGGTCCAGCTCCAGCCTCCCG
GCAGCCTCTGCAGGCCTAAGTTGTCCTCAA

Alignment

ORF - retro_hsap_3728 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.62 %
• Parental protein coverage: 59.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GRAGPGEAAMREAEAGPPELGLCRP-PRASPGPAVPPSCVSRPDCCLPTTSLDSVPAQLLEALVGPQLPQ
          G.AGP.EAAMREAEA.P....L..P.P..SPGPA.PP.CVSRPD..LPTTSLDS.PAQL..ALVGPQLP.
Retrocopy GTAGPAEAAMREAEARPLQTHL-QP>PASSPGPALPPGCVSRPDSGLPTTSLDSAPAQLPVALVGPQLPE

Parental  AKLPRPSSGLTVASPGSAPALRWHLQAPNGLRSVGSSRPSLGLPAASADPSRPEVGLSRPSSGLPVASPG
          AKLPRP.SGLTVASPGSAPALRWHLQ.PNGLRSVGSSRPSLGLPAASA.P.RPEVGLSR.SS.LP.AS.G
Retrocopy AKLPRPRSGLTVASPGSAPALRWHLQVPNGLRSVGSSRPSLGLPAASAGPNRPEVGLSRSSSSLPAASAG

Parental  ATRPQ
          ...PQ
Retrocopy LSCPQ

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	0.26 RPM	0.00 RPM
bodymap2_adrenal	0.25 RPM	0.00 RPM
bodymap2_brain	0.05 RPM	0.00 RPM
bodymap2_breast	0.43 RPM	0.00 RPM
bodymap2_colon	0.04 RPM	0.00 RPM
bodymap2_heart	0.06 RPM	0.00 RPM
bodymap2_kidney	0.15 RPM	0.00 RPM
bodymap2_liver	0.02 RPM	0.00 RPM
bodymap2_lung	0.07 RPM	0.00 RPM
bodymap2_lymph_node	0.09 RPM	0.00 RPM
bodymap2_ovary	0.19 RPM	0.00 RPM
bodymap2_prostate	0.10 RPM	0.00 RPM
bodymap2_skeletal_muscle	0.00 RPM	0.00 RPM
bodymap2_testis	0.77 RPM	0.00 RPM
bodymap2_thyroid	0.21 RPM	0.00 RPM
bodymap2_white_blood_cells	0.00 RPM	0.00 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3728 was not detected

EST

No EST(s) were mapped for retro_hsap_3728 retrocopy.

TSS

No TSS is located nearby retro_hsap_3728 retrocopy 5' end.

Lab

retro_hsap_3728 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3728 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000263064	6 retrocopies	retro_hsap_315, retro_hsap_3728 , retro_hsap_3735, retro_hsap_3849, retro_hsap_3853, retro_hsap_4929,