RetrogeneDB ID: retro_hsap_811

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 11:93268634..93268951(+)
• Located in intron of: ENSG00000166002

Retrocopy information

• Ensembl ID: ENSG00000234106
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SRP14
• Ensembl ID: ENSG00000140319
• Aliases: SRP14, ALURBP
• Description: signal recognition particle 14kDa (homologous Alu RNA binding protein) [Source:HGNC Symbol;Acc:11299]

Sequence

>retro_hsap_811
ATGGTGTTGTTGGAGAGCGAGCAGCTCCTGACGGAGCTGACCAGACTTTTCCAGAAGTGCTGGACATCAGGCAGCATCAT
ATCACCTTGAAGAAGTATGACAGTCGAACCAAATCCATTCCAAAGAAAGGTACTGTGGAGGGCTTTGAGCCTGCAGACAA
CAAGTGTCTGTTAAGAGCTACCGATGGGAAAAAGAAGATCAGCACAGTGGTGAGCTCCGAGGAAGTGAATAAGTTTCAGA
TGGCTTATTCAAACCTCCTGAGAGCTAACATGGATGGGCTGAAGAAGAGAGACAAAAAGAACAAAACTAAGAAGACC

Alignment

ORF - retro_hsap_811 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.52 %
• Parental protein coverage: 77.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVLLESEQFLTELTRLFQKCRTSGSV-YITLKKYDGRTKPIPKKGTVEGFEPADNKCLLRATDGKKKIST
          MVLLESEQ.LTELTRLFQKC.TSGS...ITLKKYD.RTK.IPKKGTVEGFEPADNKCLLRATDGKKKIST
Retrocopy MVLLESEQLLTELTRLFQKCWTSGSI<HITLKKYDSRTKSIPKKGTVEGFEPADNKCLLRATDGKKKIST

Parental  VVSSKEVNKFQMAYSNLLRANMDGLKKRDKKNKTKKT
          VVSS.EVNKFQMAYSNLLRANMDGLKKRDKKNKTKKT
Retrocopy VVSSEEVNKFQMAYSNLLRANMDGLKKRDKKNKTKKT

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	0.12 RPM	135.77 RPM
bodymap2_adrenal	0.00 RPM	159.52 RPM
bodymap2_brain	0.14 RPM	166.35 RPM
bodymap2_breast	0.14 RPM	158.43 RPM
bodymap2_colon	0.00 RPM	178.45 RPM
bodymap2_heart	0.00 RPM	113.94 RPM
bodymap2_kidney	0.14 RPM	182.61 RPM
bodymap2_liver	0.02 RPM	81.56 RPM
bodymap2_lung	0.02 RPM	160.28 RPM
bodymap2_lymph_node	0.00 RPM	148.51 RPM
bodymap2_ovary	0.12 RPM	182.46 RPM
bodymap2_prostate	0.02 RPM	224.16 RPM
bodymap2_skeletal_muscle	0.04 RPM	70.06 RPM
bodymap2_testis	0.00 RPM	182.71 RPM
bodymap2_thyroid	0.02 RPM	225.96 RPM
bodymap2_white_blood_cells	0.04 RPM	135.90 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_811 was not detected

EST

No EST(s) were mapped for retro_hsap_811 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_19601	324 libraries	542 libraries	207 libraries	220 libraries	536 libraries
TSS #2	TSS_19602	692 libraries	451 libraries	571 libraries	91 libraries	24 libraries
TSS #3	TSS_19603	94 libraries	45 libraries	412 libraries	369 libraries	909 libraries

The graphical summary, for retro_hsap_811 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_811 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_811 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_564
Gorilla gorilla	retro_ggor_665

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000029889	2 retrocopies	retro_cfam_210, retro_cfam_40,
Choloepus hoffmanni	ENSCHOG00000005321	2 retrocopies	retro_chof_212, retro_chof_2659,
Callithrix jacchus	ENSCJAG00000020912	3 retrocopies	retro_cjac_1642, retro_cjac_171, retro_cjac_3057,
Cavia porcellus	ENSCPOG00000008994	2 retrocopies	retro_cpor_1071, retro_cpor_462,
Dasypus novemcinctus	ENSDNOG00000011147	3 retrocopies	retro_dnov_1303, retro_dnov_2164, retro_dnov_2599,
Echinops telfairi	ENSETEG00000011870	1 retrocopy	retro_etel_1094,
Homo sapiens	ENSG00000140319	3 retrocopies	retro_hsap_1765, retro_hsap_811 , retro_hsap_949,
Gorilla gorilla	ENSGGOG00000009921	1 retrocopy	retro_ggor_665,
Myotis lucifugus	ENSMLUG00000010531	5 retrocopies	retro_mluc_1489, retro_mluc_2284, retro_mluc_2545, retro_mluc_375, retro_mluc_384,
Macaca mulatta	ENSMMUG00000016061	4 retrocopies	retro_mmul_1228, retro_mmul_1740, retro_mmul_573, retro_mmul_780,
Monodelphis domestica	ENSMODG00000029204	1 retrocopy	retro_mdom_1806,
Mustela putorius furo	ENSMPUG00000008324	1 retrocopy	retro_mputfur_376,
Nomascus leucogenys	ENSNLEG00000002457	2 retrocopies	retro_nleu_246, retro_nleu_2831,
Otolemur garnettii	ENSOGAG00000029070	2 retrocopies	retro_ogar_2839, retro_ogar_40,
Pongo abelii	ENSPPYG00000006342	3 retrocopies	retro_pabe_1534, retro_pabe_262, retro_pabe_811,
Pan troglodytes	ENSPTRG00000006911	3 retrocopies	retro_ptro_1181, retro_ptro_564, retro_ptro_656,
Tupaia belangeri	ENSTBEG00000016637	1 retrocopy	retro_tbel_196,
Tarsius syrichta	ENSTSYG00000009467	4 retrocopies	retro_tsyr_1283, retro_tsyr_1985, retro_tsyr_60, retro_tsyr_73,
Tursiops truncatus	ENSTTRG00000000036	5 retrocopies	retro_ttru_1185, retro_ttru_1288, retro_ttru_594, retro_ttru_74, retro_ttru_782,
Vicugna pacos	ENSVPAG00000010282	1 retrocopy	retro_vpac_20,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.47 RPM
CEU_NA11843	1.11 RPM
CEU_NA11930	0.55 RPM
CEU_NA12004	0.08 RPM
CEU_NA12400	0.81 RPM
CEU_NA12751	0.05 RPM
CEU_NA12760	0.22 RPM
CEU_NA12827	0.19 RPM
CEU_NA12872	0.03 RPM
CEU_NA12873	0.16 RPM
FIN_HG00183	0.38 RPM
FIN_HG00277	0.59 RPM
FIN_HG00315	0.08 RPM
FIN_HG00321	0.12 RPM
FIN_HG00328	0.17 RPM
FIN_HG00338	0.04 RPM
FIN_HG00349	0.14 RPM
FIN_HG00375	0.05 RPM
FIN_HG00377	0.10 RPM
FIN_HG00378	0.02 RPM
GBR_HG00099	0.09 RPM
GBR_HG00111	0.06 RPM
GBR_HG00114	0.26 RPM
GBR_HG00119	0.14 RPM
GBR_HG00131	0.09 RPM
GBR_HG00133	0.07 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.19 RPM
GBR_HG00142	0.17 RPM
GBR_HG00143	0.06 RPM
TSI_NA20512	0.08 RPM
TSI_NA20513	0.34 RPM
TSI_NA20518	0.06 RPM
TSI_NA20532	0.54 RPM
TSI_NA20538	0.05 RPM
TSI_NA20756	0.23 RPM
TSI_NA20765	0.27 RPM
TSI_NA20771	0.23 RPM
TSI_NA20786	0.16 RPM
TSI_NA20798	0.03 RPM
YRI_NA18870	0.34 RPM
YRI_NA18907	0.17 RPM
YRI_NA18916	0.19 RPM
YRI_NA19093	0.10 RPM
YRI_NA19099	0.16 RPM
YRI_NA19114	0.16 RPM
YRI_NA19118	0.08 RPM
YRI_NA19213	0.33 RPM
YRI_NA19214	0.07 RPM
YRI_NA19223	0.16 RPM

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Indel association:

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