RetrogeneDB ID: retro_hsap_711

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 10:93566938..93567196(-)
• Located in intron of: ENSG00000107854

Retrocopy information

• Ensembl ID: ENSG00000180581
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SRP9
• Ensembl ID: ENSG00000143742
• Aliases: SRP9, ALURBP
• Description: signal recognition particle 9kDa [Source:HGNC Symbol;Acc:11304]

Sequence

>retro_hsap_711
ATGCCGCAGTACCAGACCTGGGAGGAGTTCAGCCGCGCTGCCGAGAAGCTTTACCTCGCTGACCCTATGAAGGCACGTGT
GGTTCTCAAATATAGGCATTCTGATGGGAACTTGTGTGTTAAAGTAACAGATGATTTAGTTTGTTTGGTGTATAAAACAG
ACCAAGCTCAAGATGTAAAGAAGATTGAGAAATTCCACAGTCAACTAATGCGACTTATGGTAGCCAAGGAAGCCCGCAAT
GTTACCATGGAAACTGAG

Alignment

ORF - retro_hsap_711 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPQYQTWEEFSRAAEKLYLADPMKARVVLKYRHSDGNLCVKVTDDLVCLVYKTDQAQDVKKIEKFHSQLM
          MPQYQTWEEFSRAAEKLYLADPMKARVVLKYRHSDGNLCVKVTDDLVCLVYKTDQAQDVKKIEKFHSQLM
Retrocopy MPQYQTWEEFSRAAEKLYLADPMKARVVLKYRHSDGNLCVKVTDDLVCLVYKTDQAQDVKKIEKFHSQLM

Parental  RLMVAKEARNVTMETE
          RLMVAKEARNVTMETE
Retrocopy RLMVAKEARNVTMETE

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	0.02 RPM	84.10 RPM
bodymap2_adrenal	0.29 RPM	130.66 RPM
bodymap2_brain	0.23 RPM	203.98 RPM
bodymap2_breast	0.12 RPM	122.43 RPM
bodymap2_colon	0.00 RPM	148.81 RPM
bodymap2_heart	0.06 RPM	93.51 RPM
bodymap2_kidney	0.27 RPM	196.44 RPM
bodymap2_liver	0.00 RPM	110.33 RPM
bodymap2_lung	0.07 RPM	135.78 RPM
bodymap2_lymph_node	0.18 RPM	124.06 RPM
bodymap2_ovary	0.06 RPM	196.28 RPM
bodymap2_prostate	0.19 RPM	134.85 RPM
bodymap2_skeletal_muscle	0.13 RPM	64.62 RPM
bodymap2_testis	0.00 RPM	133.44 RPM
bodymap2_thyroid	0.08 RPM	171.68 RPM
bodymap2_white_blood_cells	0.08 RPM	136.32 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_711 was not detected

EST

No EST(s) were mapped for retro_hsap_711 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_8176	648 libraries	843 libraries	324 libraries	12 libraries	2 libraries

The graphical summary, for retro_hsap_711 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_711 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_711 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014744	2 retrocopies	retro_amel_1168, retro_amel_898,
Echinops telfairi	ENSETEG00000012291	1 retrocopy	retro_etel_272,
Homo sapiens	ENSG00000143742	1 retrocopy	retro_hsap_711 ,
Otolemur garnettii	ENSOGAG00000001752	1 retrocopy	retro_ogar_230,
Ochotona princeps	ENSOPRG00000012133	2 retrocopies	retro_opri_1135, retro_opri_324,