RetrogeneDB ID: retro_pabe_3046

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:22338517..22339006(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: RSL24D1
• Ensembl ID: ENSPPYG00000006495
• Aliases: RSL24D1, C15orf15
• Description: Probable ribosome biogenesis protein RLP24 [Source:UniProtKB/Swiss-Prot;Acc:Q5RF04]

Sequence

>retro_pabe_3046
ATGCACTTCGAGATATGTTATTTCTGTTTGGGGCCCACCTACCCTGGCCGTGGCATGATGTTCATCCGCAATGATTGCAA
GGTGTTCAGATTTCGTAAATCTAAATGTCATAAAAACTTTAAAAAGAAGTGCAATCCTCACAAAGTTAGGTGGACCAAAG
CATTCCGTCCAGAAAGCAGCTGGTAAAGAGCTTATAGTGGATAGTTCATTTGAATTTGAAAAACGTAGAAATGAACCTAT
CAAATACCAGCAAGAGCTATGGAATAAAACTATTGATGCAATAAAGTGAGTTGAAGAGATGATCAAACAGAAACACCAAG
CTAAATTTATAATGAACAGATTGAAGAAAAAGAAAGAGCTACAGAAAGTTCAGGATATCAAAGAAGTCAAGCAAAACATC
CATCTTATCCGAGCCTTGCAGGCAAAGGGAAGCAGCTGGAAGAGAAAACGGTACAGCAGTTACAAGAGGATGTGGACATG
GAAGATGCT

Alignment

ORF - retro_pabe_3046 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.11 %
• Parental protein coverage: 99.39 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MRIEKCYFCSGPIYPGHGMMFVRNDCKVFRFCKSKCH-KNFKKRRNPRKVRWTK-AFRKAAGKELTVDNS
          M..E.CYFC.GP.YPG.GMMF.RNDCKVFRF.KSKCH.K..K......K....K....KAAGKEL.VD.S
Retrocopy MHFEICYFCLGPTYPGRGMMFIRNDCKVFRFRKSKCH>KTLKRSAILTKLGGPKHSVQKAAGKELIVDSS

Parental  FEFEKRRNEPIKYQRELWNKTIDAMKRVEE-IKQKRQAKFIMNRLKKNKELQKVQDIKEVKQNIHLIRAP
          FEFEKRRNEPIKYQ.ELWNKTIDA.K.VEE.IKQK.QAKFIMNRLKK.KELQKVQDIKEVKQNIHLIRA.
Retrocopy FEFEKRRNEPIKYQQELWNKTIDAIK*VEEMIKQKHQAKFIMNRLKKKKELQKVQDIKEVKQNIHLIRA-

Parental  LAGK-GKQLEEKMVQQLQEDVDMEDA
          L..K.GKQLEEK.VQQLQEDVDMEDA
Retrocopy LQAK<GKQLEEKTVQQLQEDVDMEDA

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
SRP007412_brain_prefrontal_cortex	0.06 RPM	19.96 RPM
SRP007412_cerebellum	0.00 RPM	25.78 RPM
SRP007412_heart	0.00 RPM	15.68 RPM
SRP007412_kidney	0.00 RPM	17.70 RPM
SRP007412_liver	0.00 RPM	13.92 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3046 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3046 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3046 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3861
Pan troglodytes	retro_ptro_2631
Gorilla gorilla	retro_ggor_2600

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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,