RetrogeneDB ID: retro_hsap_3853

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 7:56877314..56877972(-)
• 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_3853
GGAACAGCTGGGCTTGCAGAGGCTGCCATGCGGGAGGCAGAGGCTGGGCCTCCTGAAGTCGGCCTCTCCAGACCCACTTG
CAGACTCCCGGCATCCTCTCTGGGCTCAGCTCTTCCTCCCGGCTGCGTCTCCAGGCCCGACTCCGGCCTCCCAACAACCT
CTTTGGACTCAGCTCCCGCCCAGCTCCCGGTGGCCCTGGTTGGCCCACAACTTCCTGAAGCCAAGCTCCCCAGCCCCAGC
TCAGGCCTCACGGTGGCCTCTCCAGGCTCAGCTCCTGCCCTCTGACAGCGTCTCCAGGCCCCGAACGGCCTCCAGTCGGT
GGATTCCTCTATGCCCAGCTTGGGCCTCCCGGCAGCCTCTGCTGGCCCAAATCGTCCTGAAGTCGCCCTCTCCAGGCCCA
GCTCCGGCCTCCCGGCAGCCTCTCCAGGCGCAACGCGTCGTCAACGAGGGCCCCTCCGGGGTCAGCTCCTGCCTCTCATC
AGCCTCTAGAGGCCAGTCTGGCGGCCTCTGCAGGCCCAGACTGCCCTTGAGTCAGGCTCTCCAGGGCCAGCTCCAGCCTC
CTGGCAGACTCTGCAGGCCCAAGTCGTCCTCAAGTCGGCCTGGAAGTGGGCCTGGAAGAGCTGCATTTTGGCCTCCCCGG
GCCCAGCTCCGTCCTCTC

Alignment

ORF - retro_hsap_3853 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.64 %
• Parental protein coverage: 87.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GRAGPGEAAMREAEAGPPELGLCRP----PRASPGPAVPPSCVSRPDCCLPTTSLDSVPAQLLEALVGPQ
          G.AG..EAAMREAEAGPPE.GL.RP....P..S.G.A.PP.CVSRPD..LPTTSLDS.PAQL..ALVGPQ
Retrocopy GTAGLAEAAMREAEAGPPEVGLSRPTCRLPASSLGSALPPGCVSRPDSGLPTTSLDSAPAQLPVALVGPQ

Parental  LPQAKLPRPSSGLTVASPGSAPALRWHLQAPNGLRSVGSSRPSLGLPAASADPSRPEVGLSRPSSGLPVA
          LP.AKLP.PSSGLTVASPGSAPAL...LQAPNGL.SV.SS.PSLGLPAASA.P.RPEV.LSRPSSGLP.A
Retrocopy LPEAKLPSPSSGLTVASPGSAPAL*QRLQAPNGLQSVDSSMPSLGLPAASAGPNRPEVALSRPSSGLPAA

Parental  SPGATRPQ-GPSR-ASSCLPSASRGPASASRLAASPGPAVPPGCVSRPSS-CLPASNLFWAQLMPLLASP
          SPGATR.Q.GP.R..SSCL.SASRG..........P......G....P...C.P.S........P..A..
Retrocopy SPGATRRQRGPLR>VSSCLSSASRGQSGGLCRPRLPLSQALQGQLQPPGRLCRPKSSSSRPGSGPGRAAF

Parental  GPAPACWRPL
          .P..A..RPL
Retrocopy WPPRAQLRPL

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	0.00 RPM
bodymap2_adrenal	0.00 RPM	0.00 RPM
bodymap2_brain	0.00 RPM	0.00 RPM
bodymap2_breast	0.00 RPM	0.00 RPM
bodymap2_colon	0.00 RPM	0.00 RPM
bodymap2_heart	0.00 RPM	0.00 RPM
bodymap2_kidney	0.00 RPM	0.00 RPM
bodymap2_liver	0.00 RPM	0.00 RPM
bodymap2_lung	0.00 RPM	0.00 RPM
bodymap2_lymph_node	0.00 RPM	0.00 RPM
bodymap2_ovary	0.00 RPM	0.00 RPM
bodymap2_prostate	0.00 RPM	0.00 RPM
bodymap2_skeletal_muscle	0.00 RPM	0.00 RPM
bodymap2_testis	1.28 RPM	0.00 RPM
bodymap2_thyroid	0.00 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_3853 was not detected

EST

No EST(s) were mapped for retro_hsap_3853 retrocopy.

TSS

No TSS is located nearby retro_hsap_3853 retrocopy 5' end.

Lab

retro_hsap_3853 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3853 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,