RetrogeneDB ID: retro_hsap_3583

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 6:42924085..42924466(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000181524
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL24
• Ensembl ID: ENSG00000114391
• Aliases: RPL24, HEL-S-310, L24
• Description: ribosomal protein L24 [Source:HGNC Symbol;Acc:10325]

Sequence

>retro_hsap_3583
ATGAAGGTCGAGCTGTGCAGTTTTAGCGGGTACAAGATCTACCCCGGACACGGGAGGCGCTACGCCAGGACCGACGGGAA
GGTTTTCCAGTTTCTTAATGCGAAATGCGAGTTGGCGTTCCTTTCCAAGAGGAATCCTCGGCAGATAAACTGGACTGTCC
TCTACAGAAGGAAGCACAAAAAGGGGCAGTCGGAAGAAATTCAAAAGAAAAGAACCCGCCGAGCAGTCAAATTCCAGAGG
GCCATTACTGGTGCATCTCTTGCTGATATAACGGCCAAGAGGAATCAGAAACCTGAAGTTAGAAAGACTCGACGAGAACA
AGCTATCAGGGCTGCTAAGGAAGCAAAAAAGGCTAAGCAAGCATCTAAAAAGACTGCAATG

Alignment

ORF - retro_hsap_3583 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.85 %
• Parental protein coverage: 84.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKVELCSFSGYKIYPGHGRRYARTDGKVFQFLNAKCESAFLSKRNPRQINWTVLYRRKHKKGQSEEIQKK
          MKVELCSFSGYKIYPGHGRRYARTDGKVFQFLNAKCE.AFLSKRNPRQINWTVLYRRKHKKGQSEEIQKK
Retrocopy MKVELCSFSGYKIYPGHGRRYARTDGKVFQFLNAKCELAFLSKRNPRQINWTVLYRRKHKKGQSEEIQKK

Parental  RTRRAVKFQRAITGASLADIMAKRNQKPEVRKAQREQAIRAAKEAKKAKQASKKTAM
          RTRRAVKFQRAITGASLADI.AKRNQKPEVRK..REQAIRAAKEAKKAKQASKKTAM
Retrocopy RTRRAVKFQRAITGASLADITAKRNQKPEVRKTRREQAIRAAKEAKKAKQASKKTAM

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	0.22 RPM	341.30 RPM
bodymap2_adrenal	0.33 RPM	408.71 RPM
bodymap2_brain	0.28 RPM	165.67 RPM
bodymap2_breast	0.21 RPM	275.51 RPM
bodymap2_colon	0.41 RPM	476.15 RPM
bodymap2_heart	0.26 RPM	145.77 RPM
bodymap2_kidney	0.15 RPM	194.71 RPM
bodymap2_liver	0.09 RPM	148.52 RPM
bodymap2_lung	0.32 RPM	506.66 RPM
bodymap2_lymph_node	0.29 RPM	378.56 RPM
bodymap2_ovary	0.46 RPM	616.67 RPM
bodymap2_prostate	0.94 RPM	602.13 RPM
bodymap2_skeletal_muscle	0.89 RPM	255.01 RPM
bodymap2_testis	0.36 RPM	306.44 RPM
bodymap2_thyroid	0.13 RPM	410.22 RPM
bodymap2_white_blood_cells	0.53 RPM	390.61 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3583 was not detected

EST

No EST(s) were mapped for retro_hsap_3583 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_165937	992 libraries	643 libraries	188 libraries	3 libraries	3 libraries
TSS #2	TSS_165938	9 libraries	0 libraries	5 libraries	2 libraries	1813 libraries

The graphical summary, for retro_hsap_3583 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

• Experiment type: PCR amplification
• Forward primer: TTCTGTGGAGCTGTCGCCA (19 nt long)
• Reverse primer: GCTTGTTCTCGTCGAGTCTT (20 nt long)
• Anneling temperature: 54 °C
• (Expected) product size: 341
• Electrophoresis gel image:
• Additional comment: Red arrow indicates PCR product of retrogene in pooled cDNA from 16 human tissues (Clontech). Red number of lane indicates particular retrogene; L - GeneRuler 100 bp DNA Ladder (Thermo Fisher Scientific); N - No template control (water instead of cDNA)

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3583 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2417

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 162 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013461	1 retrocopy	retro_btau_1143,
Callithrix jacchus	ENSCJAG00000000496	3 retrocopies	retro_cjac_2544, retro_cjac_2941, retro_cjac_327,
Cavia porcellus	ENSCPOG00000019941	5 retrocopies	retro_cpor_1020, retro_cpor_461, retro_cpor_474, retro_cpor_904, retro_cpor_947,
Dasypus novemcinctus	ENSDNOG00000003194	9 retrocopies	retro_dnov_1209, retro_dnov_1259, retro_dnov_1449, retro_dnov_1643, retro_dnov_2191, retro_dnov_2407, retro_dnov_2537, retro_dnov_523, retro_dnov_657,
Erinaceus europaeus	ENSEEUG00000009320	3 retrocopies	retro_eeur_505, retro_eeur_534, retro_eeur_621,
Felis catus	ENSFCAG00000003327	1 retrocopy	retro_fcat_31,
Homo sapiens	ENSG00000114391	8 retrocopies	retro_hsap_1437, retro_hsap_1752, retro_hsap_2418, retro_hsap_2614, retro_hsap_2743, retro_hsap_281, retro_hsap_3583 , retro_hsap_4179,
Gorilla gorilla	ENSGGOG00000011609	8 retrocopies	retro_ggor_1106, retro_ggor_1504, retro_ggor_1831, retro_ggor_1909, retro_ggor_2252, retro_ggor_2417, retro_ggor_2803, retro_ggor_324,
Macropus eugenii	ENSMEUG00000009177	7 retrocopies	retro_meug_1769, retro_meug_371, retro_meug_385, retro_meug_449, retro_meug_730, retro_meug_759, retro_meug_963,
Myotis lucifugus	ENSMLUG00000017005	4 retrocopies	retro_mluc_1990, retro_mluc_2185, retro_mluc_35, retro_mluc_393,
Macaca mulatta	ENSMMUG00000015059	9 retrocopies	retro_mmul_1234, retro_mmul_1711, retro_mmul_1803, retro_mmul_2263, retro_mmul_2521, retro_mmul_37, retro_mmul_560, retro_mmul_609, retro_mmul_823,
Monodelphis domestica	ENSMODG00000001916	3 retrocopies	retro_mdom_675, retro_mdom_854, retro_mdom_974,
Nomascus leucogenys	ENSNLEG00000003276	6 retrocopies	retro_nleu_1413, retro_nleu_1790, retro_nleu_1894, retro_nleu_2031, retro_nleu_2815, retro_nleu_2937,
Oryctolagus cuniculus	ENSOCUG00000000791	8 retrocopies	retro_ocun_1401, retro_ocun_190, retro_ocun_303, retro_ocun_323, retro_ocun_420, retro_ocun_480, retro_ocun_526, retro_ocun_531,
Ochotona princeps	ENSOPRG00000004255	6 retrocopies	retro_opri_1100, retro_opri_1109, retro_opri_1131, retro_opri_900, retro_opri_918, retro_opri_95,
Procavia capensis	ENSPCAG00000005918	1 retrocopy	retro_pcap_192,
Pongo abelii	ENSPPYG00000013588	6 retrocopies	retro_pabe_1191, retro_pabe_1450, retro_pabe_1782, retro_pabe_2277, retro_pabe_2343, retro_pabe_3419,
Pan troglodytes	ENSPTRG00000015176	2 retrocopies	retro_ptro_1214, retro_ptro_85,
Pteropus vampyrus	ENSPVAG00000009889	3 retrocopies	retro_pvam_1317, retro_pvam_743, retro_pvam_831,
Rattus norvegicus	ENSRNOG00000001611	25 retrocopies	retro_rnor_1244, retro_rnor_1245, retro_rnor_1247, retro_rnor_1248, retro_rnor_1250, retro_rnor_1251, retro_rnor_1252, retro_rnor_1253, retro_rnor_1452, retro_rnor_1643, retro_rnor_1699, retro_rnor_1850, retro_rnor_1851, retro_rnor_1985, retro_rnor_2026, retro_rnor_2134, retro_rnor_2148, retro_rnor_2205, retro_rnor_2214, retro_rnor_2294, retro_rnor_2709, retro_rnor_435, retro_rnor_751, retro_rnor_964, retro_rnor_993,
Sorex araneus	ENSSARG00000007615	6 retrocopies	retro_sara_198, retro_sara_204, retro_sara_330, retro_sara_535, retro_sara_574, retro_sara_711,
Sarcophilus harrisii	ENSSHAG00000008226	2 retrocopies	retro_shar_171, retro_shar_264,
Ictidomys tridecemlineatus	ENSSTOG00000014654	2 retrocopies	retro_itri_442, retro_itri_69,
Tupaia belangeri	ENSTBEG00000012044	30 retrocopies	retro_tbel_1349, retro_tbel_1429, retro_tbel_1676, retro_tbel_2076, retro_tbel_2248, retro_tbel_2553, retro_tbel_2836, retro_tbel_2853, retro_tbel_2931, retro_tbel_3363, retro_tbel_3507, retro_tbel_3544, retro_tbel_3552, retro_tbel_3557, retro_tbel_3634, retro_tbel_3636, retro_tbel_3664, retro_tbel_4105, retro_tbel_4114, retro_tbel_4139, retro_tbel_4236, retro_tbel_4237, retro_tbel_431, retro_tbel_4677, retro_tbel_569, retro_tbel_607, retro_tbel_678, retro_tbel_700, retro_tbel_73, retro_tbel_779,
Tarsius syrichta	ENSTSYG00000002314	4 retrocopies	retro_tsyr_266, retro_tsyr_285, retro_tsyr_401, retro_tsyr_460,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	1.01 RPM
CEU_NA11843	1.14 RPM
CEU_NA11930	3.00 RPM
CEU_NA12004	0.95 RPM
CEU_NA12400	1.05 RPM
CEU_NA12751	0.66 RPM
CEU_NA12760	1.62 RPM
CEU_NA12827	1.32 RPM
CEU_NA12872	0.52 RPM
CEU_NA12873	0.70 RPM
FIN_HG00183	1.51 RPM
FIN_HG00277	0.92 RPM
FIN_HG00315	0.94 RPM
FIN_HG00321	0.76 RPM
FIN_HG00328	0.64 RPM
FIN_HG00338	1.13 RPM
FIN_HG00349	1.68 RPM
FIN_HG00375	0.86 RPM
FIN_HG00377	0.68 RPM
FIN_HG00378	0.74 RPM
GBR_HG00099	0.93 RPM
GBR_HG00111	0.84 RPM
GBR_HG00114	0.58 RPM
GBR_HG00119	0.74 RPM
GBR_HG00131	0.66 RPM
GBR_HG00133	1.04 RPM
GBR_HG00134	0.46 RPM
GBR_HG00137	0.69 RPM
GBR_HG00142	1.03 RPM
GBR_HG00143	0.86 RPM
TSI_NA20512	0.65 RPM
TSI_NA20513	0.44 RPM
TSI_NA20518	1.78 RPM
TSI_NA20532	0.75 RPM
TSI_NA20538	0.97 RPM
TSI_NA20756	1.45 RPM
TSI_NA20765	0.62 RPM
TSI_NA20771	1.42 RPM
TSI_NA20786	0.50 RPM
TSI_NA20798	0.41 RPM
YRI_NA18870	1.46 RPM
YRI_NA18907	0.42 RPM
YRI_NA18916	0.78 RPM
YRI_NA19093	0.57 RPM
YRI_NA19099	0.91 RPM
YRI_NA19114	0.87 RPM
YRI_NA19118	0.87 RPM
YRI_NA19213	0.60 RPM
YRI_NA19214	0.42 RPM
YRI_NA19223	0.58 RPM

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Indel association:

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