RetrogeneDB ID: retro_pabe_1538

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17_random:15714196..15714541(+)
• Located in intron of: ENSPPYG00000008951

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS23
• Ensembl ID: ENSPPYG00000015608
• Aliases: None
• Description: ribosomal protein S23 [Source:HGNC Symbol;Acc:10410]

Sequence

>retro_pabe_1538
ATAGGCAAGTGTCATGGACTTCGTGCTGCTATGAAGCTCCACGCTCACTGATGAGACCAGAAGTGGCATGAAAAACAGTA
CAAGAAAGCCCATTTGGGCACAGCCCTGAAGGCCAACCCTTTTGAGGGTTGCATGAGAGGTGCTTCTCATGCAAAAGGAA
TTGTGCTGGAAAAAGGAGGGGTTGAAACCAAACAGCCAAATTCTGCCATCAGGAAGTGTGCCAGCATCCAGCTGATCAAG
AATAGCAAGAAAATCACAGCCTTTGTACCCAATGGTGGTTGCTTGAACTTTATTGAGAAAAACGATAAAGTTCTTGTTGC
TGGATTTGGTTAAAAAGGTCATTCT

Alignment

ORF - retro_pabe_1538 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.26 %
• Parental protein coverage: 77.62 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGKCRGLRTARKLRSHRRDQKWHDKQYKKAHLGTALKANPFGG----ASHAKGIVLEKVGVEAKQPNSAI
          .GKC.GLR.A.KL..H..DQKWH.KQYKKAHLGTALKANPF.G....ASHAKGIVLEK.GVE.KQPNSAI
Retrocopy IGKCHGLRAAMKLHAH**DQKWHEKQYKKAHLGTALKANPFEGCMRGASHAKGIVLEKGGVETKQPNSAI

Parental  RKCVRVQLIKNGKKITAFVPNDGCLNFIEENDEVLVAGFGRKGHA
          RKC...QLIKN.KKITAFVPN.GCLNFIE.ND.VLVAGFG.KGH.
Retrocopy RKCASIQLIKNSKKITAFVPNGGCLNFIEKNDKVLVAGFG*KGHS

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	66.07 RPM
SRP007412_cerebellum	0.00 RPM	93.75 RPM
SRP007412_heart	0.00 RPM	91.24 RPM
SRP007412_kidney	0.03 RPM	170.84 RPM
SRP007412_liver	0.00 RPM	127.18 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1538 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1538 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1538 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1778
Pan troglodytes	retro_ptro_1190
Gorilla gorilla	retro_ggor_2237
Macaca mulatta	retro_mmul_1239

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 63 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000011136	1 retrocopy	retro_acar_85,
Bos taurus	ENSBTAG00000013358	3 retrocopies	retro_btau_173, retro_btau_205, retro_btau_80,
Callithrix jacchus	ENSCJAG00000011247	2 retrocopies	retro_cjac_126, retro_cjac_256,
Dipodomys ordii	ENSDORG00000001813	2 retrocopies	retro_dord_187, retro_dord_93,
Macropus eugenii	ENSMEUG00000012931	1 retrocopy	retro_meug_811,
Macaca mulatta	ENSMMUG00000003578	4 retrocopies	retro_mmul_1239, retro_mmul_1974, retro_mmul_2305, retro_mmul_852,
Mus musculus	ENSMUSG00000049517	12 retrocopies	retro_mmus_2151, retro_mmus_2200, retro_mmus_2690, retro_mmus_2812, retro_mmus_3118, retro_mmus_3163, retro_mmus_3168, retro_mmus_323, retro_mmus_3619, retro_mmus_365, retro_mmus_836, retro_mmus_848,
Pongo abelii	ENSPPYG00000015608	7 retrocopies	retro_pabe_1538 , retro_pabe_1585, retro_pabe_19, retro_pabe_2515, retro_pabe_2567, retro_pabe_2716, retro_pabe_3129,
Pteropus vampyrus	ENSPVAG00000002083	4 retrocopies	retro_pvam_1483, retro_pvam_782, retro_pvam_80, retro_pvam_922,
Rattus norvegicus	ENSRNOG00000016580	12 retrocopies	retro_rnor_100, retro_rnor_1394, retro_rnor_149, retro_rnor_1691, retro_rnor_1941, retro_rnor_1959, retro_rnor_1982, retro_rnor_2119, retro_rnor_2182, retro_rnor_2492, retro_rnor_525, retro_rnor_559,
Sarcophilus harrisii	ENSSHAG00000008347	2 retrocopies	retro_shar_257, retro_shar_348,
Tursiops truncatus	ENSTTRG00000014491	6 retrocopies	retro_ttru_1253, retro_ttru_1555, retro_ttru_186, retro_ttru_458, retro_ttru_487, retro_ttru_578,
Vicugna pacos	ENSVPAG00000009427	7 retrocopies	retro_vpac_195, retro_vpac_239, retro_vpac_393, retro_vpac_543, retro_vpac_56, retro_vpac_598, retro_vpac_81,