RetrogeneDB ID: retro_hsap_1015

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 12:63359104..63359749(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000139239
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL14
• Ensembl ID: ENSG00000188846
• Aliases: RPL14, CAG-ISL-7, CTG-B33, L14, RL14, hRL14
• Description: ribosomal protein L14 [Source:HGNC Symbol;Acc:10305]

Sequence

>retro_hsap_1015
ATGGTGTTCAGGCGCTTCGTGGAGGTTGGCCGGGTGGCCTATGTCTCCTTTGGACCTCATGCCGGAAAATTGGTCGCGAT
TGTAGATGTTATTGATCAGAACAGGGCTTTGGTCGATGGACCTTGCACTCAAGTGAGGAGACAGGCCATGCCTTTCAAGT
GCATGCAGCTCACTGATTTCATCCTCAAGTTTCCGCACAGTGCCCGCCAAAAGTATGTCCAACAAGCCTGGCAGAAGGCA
GACATCAATACAAAATGGGCAGCCACACGATGGGCCAAGAAGATTGAAGCCAGAGAAAGGAAAGCCAAGATGACAGATTT
TGATCGTTTTAAAGTTATGAAGGCAAAGAAAACGAGGAACAGAATAATCAAGAATGAAGTTAAGAAGCTTCAAAAGGCAG
CTCTCCTGAAAGCTTCTCCCAAAAAAGCACCTGGTACTAAGGGTACTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTAAA
GTTCCAGCAAAAAAGATGACGGCCGCGAGTAAAAAGGCTTCAGCCCAGAAGGTTCCTGCCCAGAAAGCCACAGGCCAGAA
AGCAGCACCTGCTCCAAAAGCTCAGAAGGGTCAAAAAGCTCCAGCCCAGAAAGCACCTGCTCCAAAGGCATCTGGCAAGA
AAGCA

Alignment

ORF - retro_hsap_1015 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.56 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVFRRFVEVGRVAYVSFGPHAGKLVAIVDVIDQNRALVDGPCTQVRRQAMPFKCMQLTDFILKFPHSAHQ
          MVFRRFVEVGRVAYVSFGPHAGKLVAIVDVIDQNRALVDGPCTQVRRQAMPFKCMQLTDFILKFPHSA.Q
Retrocopy MVFRRFVEVGRVAYVSFGPHAGKLVAIVDVIDQNRALVDGPCTQVRRQAMPFKCMQLTDFILKFPHSARQ

Parental  KYVRQAWQKADINTKWAATRWAKKIEARERKAKMTDFDRFKVMKAKKMRNRIIKNEVKKLQKAALLKASP
          KYV.QAWQKADINTKWAATRWAKKIEARERKAKMTDFDRFKVMKAKK.RNRIIKNEVKKLQKAALLKASP
Retrocopy KYVQQAWQKADINTKWAATRWAKKIEARERKAKMTDFDRFKVMKAKKTRNRIIKNEVKKLQKAALLKASP

Parental  KKAPGTKGTAAAAAAAAAAKVPAKKITAASKKAPAQKVPAQKATGQKAAPAPKAQKGQKAPAQKAPAPKA
          KKAPGTKG...........KVPAKK.TAASKKA.AQKVPAQKATGQKAAPAPKAQKGQKAPAQKAPAPKA
Retrocopy KKAPGTKGXXXXXXXXXXXKVPAKKMTAASKKASAQKVPAQKATGQKAAPAPKAQKGQKAPAQKAPAPKA

Parental  SGKKA
          SGKKA
Retrocopy SGKKA

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	1.77 RPM	299.14 RPM
bodymap2_adrenal	2.76 RPM	319.71 RPM
bodymap2_brain	1.24 RPM	97.58 RPM
bodymap2_breast	1.63 RPM	176.29 RPM
bodymap2_colon	1.16 RPM	355.99 RPM
bodymap2_heart	0.44 RPM	110.66 RPM
bodymap2_kidney	0.77 RPM	152.44 RPM
bodymap2_liver	0.46 RPM	121.02 RPM
bodymap2_lung	1.23 RPM	333.16 RPM
bodymap2_lymph_node	1.53 RPM	354.64 RPM
bodymap2_ovary	2.74 RPM	392.07 RPM
bodymap2_prostate	4.33 RPM	571.10 RPM
bodymap2_skeletal_muscle	2.82 RPM	267.83 RPM
bodymap2_testis	1.11 RPM	185.40 RPM
bodymap2_thyroid	1.32 RPM	182.08 RPM
bodymap2_white_blood_cells	1.81 RPM	460.64 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1015 was not detected

EST

No EST(s) were mapped for retro_hsap_1015 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_27808	91 libraries	35 libraries	454 libraries	529 libraries	720 libraries

The graphical summary, for retro_hsap_1015 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_1015 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1015 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 87 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001709	4 retrocopies	retro_amel_1876, retro_amel_1933, retro_amel_296, retro_amel_660,
Canis familiaris	ENSCAFG00000005138	1 retrocopy	retro_cfam_31,
Callithrix jacchus	ENSCJAG00000017884	9 retrocopies	retro_cjac_1249, retro_cjac_1393, retro_cjac_1835, retro_cjac_2138, retro_cjac_2139, retro_cjac_2332, retro_cjac_2797, retro_cjac_3240, retro_cjac_630,
Cavia porcellus	ENSCPOG00000000711	1 retrocopy	retro_cpor_529,
Equus caballus	ENSECAG00000026813	2 retrocopies	retro_ecab_377, retro_ecab_743,
Echinops telfairi	ENSETEG00000012894	6 retrocopies	retro_etel_2117, retro_etel_2155, retro_etel_251, retro_etel_315, retro_etel_356, retro_etel_387,
Felis catus	ENSFCAG00000015655	4 retrocopies	retro_fcat_1000, retro_fcat_1457, retro_fcat_587, retro_fcat_671,
Homo sapiens	ENSG00000188846	6 retrocopies	retro_hsap_1015 , retro_hsap_1047, retro_hsap_2796, retro_hsap_3104, retro_hsap_3352, retro_hsap_4777,
Gorilla gorilla	ENSGGOG00000025958	3 retrocopies	retro_ggor_122, retro_ggor_1945, retro_ggor_2272,
Latimeria chalumnae	ENSLACG00000015639	1 retrocopy	retro_lcha_29,
Microcebus murinus	ENSMICG00000009217	4 retrocopies	retro_mmur_1218, retro_mmur_1352, retro_mmur_279, retro_mmur_3,
Myotis lucifugus	ENSMLUG00000014429	4 retrocopies	retro_mluc_1294, retro_mluc_2263, retro_mluc_420, retro_mluc_563,
Monodelphis domestica	ENSMODG00000015262	2 retrocopies	retro_mdom_1499, retro_mdom_1939,
Mustela putorius furo	ENSMPUG00000017961	1 retrocopy	retro_mputfur_90,
Mus musculus	ENSMUSG00000025794	3 retrocopies	retro_mmus_2904, retro_mmus_2929, retro_mmus_3011,
Nomascus leucogenys	ENSNLEG00000005682	2 retrocopies	retro_nleu_763, retro_nleu_918,
Oryctolagus cuniculus	ENSOCUG00000010309	3 retrocopies	retro_ocun_410, retro_ocun_464, retro_ocun_656,
Pan troglodytes	ENSPTRG00000011963	4 retrocopies	retro_ptro_1893, retro_ptro_2100, retro_ptro_2135, retro_ptro_713,
Pteropus vampyrus	ENSPVAG00000013914	7 retrocopies	retro_pvam_1108, retro_pvam_1413, retro_pvam_246, retro_pvam_446, retro_pvam_683, retro_pvam_903, retro_pvam_904,
Rattus norvegicus	ENSRNOG00000019007	4 retrocopies	retro_rnor_2268, retro_rnor_2620, retro_rnor_415, retro_rnor_591,
Sorex araneus	ENSSARG00000003974	2 retrocopies	retro_sara_349, retro_sara_504,
Sarcophilus harrisii	ENSSHAG00000001591	5 retrocopies	retro_shar_397, retro_shar_539, retro_shar_696, retro_shar_737, retro_shar_788,
Sus scrofa	ENSSSCG00000011272	2 retrocopies	retro_sscr_521, retro_sscr_63,
Tarsius syrichta	ENSTSYG00000002161	5 retrocopies	retro_tsyr_1036, retro_tsyr_1404, retro_tsyr_176, retro_tsyr_361, retro_tsyr_956,
Tursiops truncatus	ENSTTRG00000006708	1 retrocopy	retro_ttru_113,
Xenopus tropicalis	ENSXETG00000022018	1 retrocopy	retro_xtro_3,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	4.58 RPM
CEU_NA11843	5.83 RPM
CEU_NA11930	9.62 RPM
CEU_NA12004	3.00 RPM
CEU_NA12400	5.75 RPM
CEU_NA12751	2.87 RPM
CEU_NA12760	9.30 RPM
CEU_NA12827	5.09 RPM
CEU_NA12872	4.14 RPM
CEU_NA12873	4.05 RPM
FIN_HG00183	6.45 RPM
FIN_HG00277	3.73 RPM
FIN_HG00315	3.73 RPM
FIN_HG00321	4.35 RPM
FIN_HG00328	3.05 RPM
FIN_HG00338	3.43 RPM
FIN_HG00349	8.56 RPM
FIN_HG00375	4.18 RPM
FIN_HG00377	4.14 RPM
FIN_HG00378	3.38 RPM
GBR_HG00099	5.29 RPM
GBR_HG00111	3.16 RPM
GBR_HG00114	3.63 RPM
GBR_HG00119	3.81 RPM
GBR_HG00131	2.96 RPM
GBR_HG00133	3.98 RPM
GBR_HG00134	2.95 RPM
GBR_HG00137	4.21 RPM
GBR_HG00142	3.78 RPM
GBR_HG00143	2.71 RPM
TSI_NA20512	3.08 RPM
TSI_NA20513	2.78 RPM
TSI_NA20518	10.60 RPM
TSI_NA20532	3.44 RPM
TSI_NA20538	4.70 RPM
TSI_NA20756	7.62 RPM
TSI_NA20765	2.40 RPM
TSI_NA20771	6.81 RPM
TSI_NA20786	2.85 RPM
TSI_NA20798	3.15 RPM
YRI_NA18870	8.09 RPM
YRI_NA18907	2.91 RPM
YRI_NA18916	3.01 RPM
YRI_NA19093	2.73 RPM
YRI_NA19099	5.03 RPM
YRI_NA19114	4.01 RPM
YRI_NA19118	4.12 RPM
YRI_NA19213	2.63 RPM
YRI_NA19214	2.41 RPM
YRI_NA19223	2.27 RPM

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Indel association:

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