RetrogeneDB ID: retro_hsap_2467

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 20:30758106..30758585(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000224452
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RSL24D1
• Ensembl ID: ENSG00000137876
• Aliases: None
• Description: ribosomal L24 domain containing 1 [Source:HGNC Symbol;Acc:18479]

Sequence

>retro_hsap_2467
CAAGAGTGTTATTTCTGTTCGGGGCCCATCTACCCTGGCCATGGCATGATGTCTGTCCGCAATGATTGCAAGGTGTTCAG
ATTTTGTAAATCTAAATGTCATAAAAACTTTAAAAAGAAGCACAATCCTCACAAAGGTAGGTGGACCAAAGCATTCTGGA
AAACAGCTGGTAAAGGGCTTACAGTGGATAATTCATTTGAATTGGAAAAACATAGAAATGCACTTATCAAATATCAGTGA
GAGCTATGGAATAAAACTATTGATGCAATGAAGAGAGTTGAAGAGATCAAACAGAAATGCCAAGCTAAATTTATAATGAA
CAGACTGAAGAAACATAAAGGGCTACGTAGAGAAGTTCAGGATATCAAAGAAGTCAAGAAAAACATCCATCTTTCCGAGC
CCCTCTTGTAGGCAAAGGGAAGCAGCTGGAAGAGAAAATGGCACAGAGATTACAACAGGATGTGGACATGGAAGATGCT

Alignment

ORF - retro_hsap_2467 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.23 %
• Parental protein coverage: 97.55 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EKCYFCSGPIYPGHGMMFVRNDCKVFRFCKSKCHKNFKKKRNPRKVRWTKAFRKAAGKELTVDNSFEFEK
          ..CYFCSGPIYPGHGMM.VRNDCKVFRFCKSKCHKNFKKK.NP.K.RWTKAF.K.AGK.LTVDNSFE.EK
Retrocopy QECYFCSGPIYPGHGMMSVRNDCKVFRFCKSKCHKNFKKKHNPHKGRWTKAFWKTAGKGLTVDNSFELEK

Parental  RRNEPIKYQRELWNKTIDAMKRVEEIKQKRQAKFIMNRLKKNKELQK-VQDIKEVKQNIHL-IRAPLAGK
          .RN..IKYQ.ELWNKTIDAMKRVEEIKQK.QAKFIMNRLKK.K.L...VQDIKEVK.NIHL..RAPL.GK
Retrocopy HRNALIKYQ*ELWNKTIDAMKRVEEIKQKCQAKFIMNRLKKHKGLRREVQDIKEVKKNIHL<FRAPLVGK

Parental  GKQLEEKMVQQLQEDVDMEDA
          GKQLEEKM.Q.LQ.DVDMEDA
Retrocopy GKQLEEKMAQRLQQDVDMEDA

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	0.10 RPM	84.38 RPM
bodymap2_adrenal	0.16 RPM	100.71 RPM
bodymap2_brain	0.52 RPM	97.58 RPM
bodymap2_breast	0.19 RPM	89.90 RPM
bodymap2_colon	0.06 RPM	204.32 RPM
bodymap2_heart	0.52 RPM	49.05 RPM
bodymap2_kidney	0.33 RPM	74.84 RPM
bodymap2_liver	0.17 RPM	36.42 RPM
bodymap2_lung	0.30 RPM	159.14 RPM
bodymap2_lymph_node	0.02 RPM	91.24 RPM
bodymap2_ovary	0.75 RPM	199.23 RPM
bodymap2_prostate	0.24 RPM	236.44 RPM
bodymap2_skeletal_muscle	0.42 RPM	76.08 RPM
bodymap2_testis	0.26 RPM	147.26 RPM
bodymap2_thyroid	0.26 RPM	138.01 RPM
bodymap2_white_blood_cells	0.00 RPM	121.36 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2467 was not detected

EST

No EST(s) were mapped for retro_hsap_2467 retrocopy.

TSS

No TSS is located nearby retro_hsap_2467 retrocopy 5' end.

Lab

retro_hsap_2467 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2467 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1426
Gorilla gorilla	retro_ggor_1536
Pongo abelii	retro_pabe_1819
Macaca mulatta	retro_mmul_599

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Parental genes homology:

Parental genes homology involve 29 parental genes, and 171 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001342	1 retrocopy	retro_btau_1304,
Canis familiaris	ENSCAFG00000015904	1 retrocopy	retro_cfam_1744,
Choloepus hoffmanni	ENSCHOG00000011799	9 retrocopies	retro_chof_112, retro_chof_1237, retro_chof_1314, retro_chof_1357, retro_chof_1938, retro_chof_243, retro_chof_67, retro_chof_809, retro_chof_896,
Callithrix jacchus	ENSCJAG00000000795	2 retrocopies	retro_cjac_109, retro_cjac_7,
Dasypus novemcinctus	ENSDNOG00000010812	2 retrocopies	retro_dnov_858, retro_dnov_954,
Equus caballus	ENSECAG00000018861	1 retrocopy	retro_ecab_30,
Erinaceus europaeus	ENSEEUG00000006755	1 retrocopy	retro_eeur_50,
Felis catus	ENSFCAG00000019272	1 retrocopy	retro_fcat_851,
Homo sapiens	ENSG00000137876	17 retrocopies	retro_hsap_1049, retro_hsap_1125, retro_hsap_1355, retro_hsap_1635, retro_hsap_1829, retro_hsap_1887, retro_hsap_1941, retro_hsap_1963, retro_hsap_2268, retro_hsap_2467 , retro_hsap_3378, retro_hsap_338, retro_hsap_3566, retro_hsap_3861, retro_hsap_4015, retro_hsap_4101, retro_hsap_894,
Gorilla gorilla	ENSGGOG00000005195	15 retrocopies	retro_ggor_1055, retro_ggor_1081, retro_ggor_1151, retro_ggor_1194, retro_ggor_1235, retro_ggor_1412, retro_ggor_1536, retro_ggor_1688, retro_ggor_2286, retro_ggor_2406, retro_ggor_2600, retro_ggor_2697, retro_ggor_2754, retro_ggor_359, retro_ggor_879,
Microcebus murinus	ENSMICG00000002621	3 retrocopies	retro_mmur_1378, retro_mmur_306, retro_mmur_952,
Myotis lucifugus	ENSMLUG00000011976	4 retrocopies	retro_mluc_1415, retro_mluc_1512, retro_mluc_2173, retro_mluc_2320,
Macaca mulatta	ENSMMUG00000020693	16 retrocopies	retro_mmul_1030, retro_mmul_1107, retro_mmul_1257, retro_mmul_1363, retro_mmul_1406, retro_mmul_1560, retro_mmul_1824, retro_mmul_1907, retro_mmul_2105, retro_mmul_2364, retro_mmul_322, retro_mmul_424, retro_mmul_582, retro_mmul_599, retro_mmul_817, retro_mmul_872,
Monodelphis domestica	ENSMODG00000007966	1 retrocopy	retro_mdom_825,
Mustela putorius furo	ENSMPUG00000002228	1 retrocopy	retro_mputfur_514,
Mus musculus	ENSMUSG00000032215	1 retrocopy	retro_mmus_1695,
Nomascus leucogenys	ENSNLEG00000006578	16 retrocopies	retro_nleu_1289, retro_nleu_1321, retro_nleu_1392, retro_nleu_1468, retro_nleu_1779, retro_nleu_1809, retro_nleu_185, retro_nleu_2309, retro_nleu_2449, retro_nleu_2606, retro_nleu_2874, retro_nleu_2974, retro_nleu_386, retro_nleu_570, retro_nleu_919, retro_nleu_967,
Oryctolagus cuniculus	ENSOCUG00000007447	2 retrocopies	retro_ocun_1108, retro_ocun_1899,
Otolemur garnettii	ENSOGAG00000010400	15 retrocopies	retro_ogar_1135, retro_ogar_1320, retro_ogar_1433, retro_ogar_1539, retro_ogar_1876, retro_ogar_1947, retro_ogar_2088, retro_ogar_2171, retro_ogar_2579, retro_ogar_3029, retro_ogar_3154, retro_ogar_3174, retro_ogar_3239, retro_ogar_3445, retro_ogar_619,
Ochotona princeps	ENSOPRG00000013115	4 retrocopies	retro_opri_1047, retro_opri_1226, retro_opri_66, retro_opri_777,
Pongo abelii	ENSPPYG00000006495	19 retrocopies	retro_pabe_1123, retro_pabe_1350, retro_pabe_1499, retro_pabe_1568, retro_pabe_1602, retro_pabe_1614, retro_pabe_1623, retro_pabe_1726, retro_pabe_1819, retro_pabe_1873, retro_pabe_1949, retro_pabe_2774, retro_pabe_2939, retro_pabe_3046, retro_pabe_3297, retro_pabe_3359, retro_pabe_771, retro_pabe_875, retro_pabe_930,
Pan troglodytes	ENSPTRG00000007094	16 retrocopies	retro_ptro_1103, retro_ptro_1164, retro_ptro_1268, retro_ptro_1296, retro_ptro_1311, retro_ptro_1426, retro_ptro_1607, retro_ptro_2422, retro_ptro_2631, retro_ptro_270, retro_ptro_2725, retro_ptro_2783, retro_ptro_617, retro_ptro_679, retro_ptro_715, retro_ptro_929,
Pteropus vampyrus	ENSPVAG00000004093	3 retrocopies	retro_pvam_331, retro_pvam_619, retro_pvam_671,
Rattus norvegicus	ENSRNOG00000007630	2 retrocopies	retro_rnor_1945, retro_rnor_506,
Sarcophilus harrisii	ENSSHAG00000011494	1 retrocopy	retro_shar_465,
Sus scrofa	ENSSSCG00000024983	1 retrocopy	retro_sscr_916,
Ictidomys tridecemlineatus	ENSSTOG00000009408	6 retrocopies	retro_itri_100, retro_itri_1246, retro_itri_1388, retro_itri_1605, retro_itri_1699, retro_itri_1767,
Tupaia belangeri	ENSTBEG00000010750	9 retrocopies	retro_tbel_1552, retro_tbel_2292, retro_tbel_3033, retro_tbel_4025, retro_tbel_4076, retro_tbel_4138, retro_tbel_4462, retro_tbel_4711, retro_tbel_720,
Tarsius syrichta	ENSTSYG00000001271	1 retrocopy	retro_tsyr_677,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.11 RPM
CEU_NA11843	0.14 RPM
CEU_NA11930	0.03 RPM
CEU_NA12004	0.08 RPM
CEU_NA12400	0.11 RPM
CEU_NA12751	0.24 RPM
CEU_NA12760	0.13 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.11 RPM
CEU_NA12873	0.10 RPM
FIN_HG00183	0.11 RPM
FIN_HG00277	0.11 RPM
FIN_HG00315	0.11 RPM
FIN_HG00321	0.15 RPM
FIN_HG00328	0.09 RPM
FIN_HG00338	0.15 RPM
FIN_HG00349	0.11 RPM
FIN_HG00375	0.10 RPM
FIN_HG00377	0.13 RPM
FIN_HG00378	0.06 RPM
GBR_HG00099	0.09 RPM
GBR_HG00111	0.19 RPM
GBR_HG00114	0.11 RPM
GBR_HG00119	0.12 RPM
GBR_HG00131	0.11 RPM
GBR_HG00133	0.07 RPM
GBR_HG00134	0.07 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.14 RPM
GBR_HG00143	0.06 RPM
TSI_NA20512	0.20 RPM
TSI_NA20513	0.27 RPM
TSI_NA20518	0.11 RPM
TSI_NA20532	0.17 RPM
TSI_NA20538	0.05 RPM
TSI_NA20756	0.17 RPM
TSI_NA20765	0.17 RPM
TSI_NA20771	0.06 RPM
TSI_NA20786	0.13 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.14 RPM
YRI_NA18907	0.07 RPM
YRI_NA18916	0.08 RPM
YRI_NA19093	0.21 RPM
YRI_NA19099	0.08 RPM
YRI_NA19114	0.05 RPM
YRI_NA19118	0.17 RPM
YRI_NA19213	0.14 RPM
YRI_NA19214	0.05 RPM
YRI_NA19223	0.04 RPM

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Indel association:

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