RetrogeneDB ID: retro_pabe_1899

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 22:25076346..25077070(-)
• Located in intron of: ENSPPYG00000011701

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_1899
CTTGATCCATTTTCTAAGAAAGATTGGTATGATGTGAAAGCACCTGCTATGTTCAGTATAATAACTATGGGAAAGACACT
CATCACCAGGACTCAAGGAATCAAAATTGCATCTGATGGCCTCAAGGGGCATGTGTTTGAAGTGAGTTTGTCTGATGTGC
AGAATGATGAAGTTGCATTTAGAAAATTCAAGCTGATACTGAAGATGTTCAGGGCAAAAATGCCTGACTAATTTCCACGG
CATAGATCTTACCTGTGACAAAATGTGTTCCATGGTTAAAAAATAGCAGACCATGATTAAAGTTCACATTGATGTCAAGA
CTACCAATGATTATTTACTTTGTCTGTTTTGTGTTGATTTTACTAAAAAATGCAACAATTATATACGGAAGACTTCTTAC
AATTAACACTAACAGGTCTGCCAAATCCAGAAGAAGATGATGGAAATCATGACCCAAGAGGTGCAGACAAATGACTTTAA
AGAAGTGGTCAATAAATTGATTCCAGACAGCACTGGAAAAGACACAGAAAAGGCTTGCCTATCTATTTATCCTCTCCATG
GTGTCTTCATTAGGAAAGTAAAAATAAAGAAGCCCAAGTTTGAATTGGGAAAACTCATGTAGCTTCATGGTGAAGGTAGT
AGTTTTGAAAAAGCTACTAAGGATGAGAAAGGTGCTAAAATTGAATGAGCTGATGGATATGAACCATCGGTCCACGAATC
TGTT

Alignment

ORF - retro_pabe_1899 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.82 %
• Parental protein coverage: 92.05 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASDGLKGRVFEVSLADLQNDEVAFRKFKLI-TED
          .DPFSKKDWYDVKAPAMF.I...GKTL.TRTQG.KIASDGLKG.VFEVSL.D.QNDEVAFRKFKLI.TED
Retrocopy LDPFSKKDWYDVKAPAMFSIITMGKTLITRTQGIKIASDGLKGHVFEVSLSDVQNDEVAFRKFKLI<TED

Parental  VQGKN-CLTNFHGMDLTRDKMCSMVKKWQTMIEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQ
          VQGKN.CLTNFHG.DLT.DKMCSMVKK.QTMI..H.DVKTT..YLL.LFCV.FTKK.NN.IRKTSY..H.
Retrocopy VQGKN<CLTNFHGIDLTCDKMCSMVKK*QTMIKVHIDVKTTNDYLLCLFCVDFTKKCNNYIRKTSYN*H*

Parental  QVRQIRKKMMEIMTREVQTNDLKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLM
          QV.QI.KKMMEIMT.EVQTND.KEVVNKLIPDS.GKD.EKAC.SIYPLH.VF.RKVK..KKPKFELGKLM
Retrocopy QVCQIQKKMMEIMTQEVQTNDFKEVVNKLIPDSTGKDTEKACLSIYPLHGVFIRKVK-IKKPKFELGKLM

Parental  ELHGEGSSSGKATGDETGAKVERADGYEPPVQESV
          .LHGEGSS..KAT.DE.GAK.E.ADGYEP.V.ESV
Retrocopy *LHGEGSSFEKATKDEKGAKIE*ADGYEPSVHESV

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	0.00 RPM	99.96 RPM
SRP007412_heart	0.00 RPM	95.16 RPM
SRP007412_kidney	0.00 RPM	145.71 RPM
SRP007412_liver	0.00 RPM	124.70 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1899 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1899 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1899 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2578

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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,