RetrogeneDB ID: retro_pabe_2578

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:176192804..176193596(-)
• Located in intron of: ENSPPYG00000015190

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS3A
• Ensembl ID: ENSPPYG00000025869
• Aliases: None
• Description: 40S ribosomal protein S3a [Source:RefSeq peptide;Acc:NP_001126750]

Sequence

>retro_pabe_2578
ATGGCGGTTGGCAAGAACAAGCACCTTACGAAAGGCGGCAAAAAGGGAGCCAAGAAGAAAGTGGTTGATCCATTTTCTAA
GAAAGATTGGTATGATGTGAAAGCACTCGCTATGTTCAATATAAGAAATATTGGAAAGACGCTCGTCACCAGGACCCAAG
GAACCAAAATTGCATCTGATGGTCTCAAGGGTCGTGTATTTGAAGTGAGTCTTGCTGATTTGCAGAATGGTGAAGTTGCA
TTTAGAAAATTCAAGCTGATTACTGAAGATGTTCAGGATAAAAACTGCCTGACTAACTTCTATGGCATGGATCTTACCCG
TGACAAAATGTGTTCCATGGTCAAAAAATGGCAGACAATGATTGAAGCTCATGTTGATGTCAAGACTACCGATGGTTATT
TGCTTCGTCTGTTCTGTGTTGGTTTTACTAAAAAACGCAACAATCAGATACGGAAGACCTCTTATGCTCAGCACCAACAG
GTCTGCCAAATCCGGAAGAAGATGATGGAAATCATGACCCGAGAGGTGCAGACCAATGACTTGAAAGAAGTGGTCAATAA
ATTGATTCCAGACAGCACTGGAAAAGACATAGAAAAGGCTTGCCAATCTATTTATCCTCTCCATGATGTCTTCGTTAGGA
AAGTAAAAATGCTGAAGAAGCCCAAGTTTGAATTGGGAAAGCTCATGGAGCTTCATGGTGAAGGCAGTAGTTCTGGAAAA
GCCACTGGGTACGAGACAGGTGCTAAAGTTGAACGAGCTGATGGATATGAACCACCAGTCCAAGAATCTGTT

Alignment

ORF - retro_pabe_2578 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.97 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASDGLKGRVFEVS
          MAVGKNK.LTKGGKKGAKKKVVDPFSKKDWYDVKA.AMFNIRNIGKTLVTRTQGTKIASDGLKGRVFEVS
Retrocopy MAVGKNKHLTKGGKKGAKKKVVDPFSKKDWYDVKALAMFNIRNIGKTLVTRTQGTKIASDGLKGRVFEVS

Parental  LADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTMIEAHVDVKTTDGYLLRLFCV
          LADLQN.EVAFRKFKLITEDVQ.KNCLTNF.GMDLTRDKMCSMVKKWQTMIEAHVDVKTTDGYLLRLFCV
Retrocopy LADLQNGEVAFRKFKLITEDVQDKNCLTNFYGMDLTRDKMCSMVKKWQTMIEAHVDVKTTDGYLLRLFCV

Parental  GFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTNDLKEVVNKLIPDSIGKDIEKACQSIYPLHDV
          GFTKKRNNQIRKTSYAQHQQV.QIRKKMMEIMTREVQTNDLKEVVNKLIPDS.GKDIEKACQSIYPLHDV
Retrocopy GFTKKRNNQIRKTSYAQHQQVCQIRKKMMEIMTREVQTNDLKEVVNKLIPDSTGKDIEKACQSIYPLHDV

Parental  FVRKVKMLKKPKFELGKLMELHGEGSSSGKATGDETGAKVERADGYEPPVQESV
          FVRKVKMLKKPKFELGKLMELHGEGSSSGKATG.ETGAKVERADGYEPPVQESV
Retrocopy FVRKVKMLKKPKFELGKLMELHGEGSSSGKATGYETGAKVERADGYEPPVQESV

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	0.00 RPM	71.93 RPM
SRP007412_cerebellum	0.12 RPM	99.96 RPM
SRP007412_heart	0.30 RPM	95.16 RPM
SRP007412_kidney	0.17 RPM	145.71 RPM
SRP007412_liver	0.09 RPM	124.70 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2578 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2578 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2578 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 101 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000015569	9 retrocopies	retro_cpor_1154, retro_cpor_1229, retro_cpor_210, retro_cpor_383, retro_cpor_460, retro_cpor_555, retro_cpor_609, retro_cpor_646, retro_cpor_789,
Equus caballus	ENSECAG00000009573	6 retrocopies	retro_ecab_168, retro_ecab_222, retro_ecab_256, retro_ecab_597, retro_ecab_626, retro_ecab_885,
Felis catus	ENSFCAG00000031288	5 retrocopies	retro_fcat_1110, retro_fcat_134, retro_fcat_1878, retro_fcat_780, retro_fcat_858,
Loxodonta africana	ENSLAFG00000017660	3 retrocopies	retro_lafr_10, retro_lafr_38, retro_lafr_385,
Macaca mulatta	ENSMMUG00000021821	1 retrocopy	retro_mmul_2297,
Monodelphis domestica	ENSMODG00000000969	6 retrocopies	retro_mdom_1040, retro_mdom_1229, retro_mdom_1396, retro_mdom_1480, retro_mdom_627, retro_mdom_694,
Mustela putorius furo	ENSMPUG00000007139	8 retrocopies	retro_mputfur_1293, retro_mputfur_1363, retro_mputfur_278, retro_mputfur_316, retro_mputfur_504, retro_mputfur_695, retro_mputfur_764, retro_mputfur_847,
Mus musculus	ENSMUSG00000028081	2 retrocopies	retro_mmus_218, retro_mmus_254,
Procavia capensis	ENSPCAG00000015040	6 retrocopies	retro_pcap_211, retro_pcap_286, retro_pcap_355, retro_pcap_420, retro_pcap_456, retro_pcap_57,
Pongo abelii	ENSPPYG00000025869	27 retrocopies	retro_pabe_1339, retro_pabe_1572, retro_pabe_1636, retro_pabe_1895, retro_pabe_1899, retro_pabe_2117, retro_pabe_2570, retro_pabe_2578 , retro_pabe_2661, retro_pabe_2769, retro_pabe_2779, retro_pabe_2826, retro_pabe_2942, retro_pabe_3014, retro_pabe_3076, retro_pabe_3186, retro_pabe_3214, retro_pabe_3560, retro_pabe_369, retro_pabe_3692, retro_pabe_394, retro_pabe_473, retro_pabe_550, retro_pabe_602, retro_pabe_789, retro_pabe_912, retro_pabe_985,
Pteropus vampyrus	ENSPVAG00000015406	24 retrocopies	retro_pvam_1053, retro_pvam_1056, retro_pvam_1058, retro_pvam_1138, retro_pvam_1180, retro_pvam_1203, retro_pvam_1476, retro_pvam_149, retro_pvam_311, retro_pvam_330, retro_pvam_354, retro_pvam_36, retro_pvam_368, retro_pvam_376, retro_pvam_462, retro_pvam_486, retro_pvam_582, retro_pvam_73, retro_pvam_754, retro_pvam_799, retro_pvam_86, retro_pvam_893, retro_pvam_917, retro_pvam_996,
Rattus norvegicus	ENSRNOG00000011893	1 retrocopy	retro_rnor_198,
Sarcophilus harrisii	ENSSHAG00000015088	2 retrocopies	retro_shar_777, retro_shar_95,
Ictidomys tridecemlineatus	ENSSTOG00000024203	1 retrocopy	retro_itri_58,