RetrogeneDB ID: retro_pabe_1310

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:70888320..70888752(-)
• Located in intron of: ENSPPYG00000006624

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS15
• Ensembl ID: ENSPPYG00000001537
• Aliases: None
• Description: mitochondrial ribosomal protein S15 [Source:HGNC Symbol;Acc:14504]

Sequence

>retro_pabe_1310
AGTCTCCTCCTCCAGGCTGCAGCAGATACACCATCCAGAAACCAGTCTGGCCTAGACAGGACCATGACCTTCCCCTTTCC
ATGCTGCTCAAAGACCACCAGACCATCCCTGAAATTGAGAAGGGCAATGATACAGTGAAAAGACCCTTGTCTTTGGAAAT
GACCAACCAAAAGGAGAAGCTAAATATCAAGTAAGAACATCTGATGAACAAAGTCGTGGCAAACCCTAAGGATACCAGCT
TCCCGGAGGCTCGAATTATTCCCTTGACCAAAGCCCACAATTATGAAGAACATGGCAGAAAAACTGAAAGAACAAAACCC
ACAAATACTATCTGGTGATGGGCACTGTCCAGAGGAAAAAGATGCTCAAAAACCTTCGTTAGACCAATATGATGTCTCTG
AGAGGACACACTGGGGATTGAGCACACCTTTT

Alignment

ORF - retro_pabe_1310 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.39 %
• Parental protein coverage: 57.48 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SLLLQAARG-YVIRKPAQPRQDDDPPPSTLLKDYQNVPGIEKVDDVVKRILSLEMANKKETLKAKREQFM
          SLLLQAA...Y.I.KP..PRQD.D.P.S.LLKD.Q..P.IEK..D.VKR.LSLEM.N.KE.L..K.E..M
Retrocopy SLLLQAAAD<YTIQKPVWPRQDHDLPLSMLLKDHQTIPEIEKGNDTVKRPLSLEMTNQKEKLNIK*EHLM

Parental  KKIVANPEDTRSLEARIIALSVKIRSYEEH-LEKHRKDKAHKRYLLMSIDQRKKMLKNLRNTN-YDVFEK
          .K.VANP.DT...EARII.L..K...YEEH...K..K.K.HK.YL.M...QRKKMLKNLR.TN.YDV.E.
Retrocopy NKVVANPKDTSFPEARIIPLT-KAHNYEEH<WQKN*KNKTHKYYLVMGTVQRKKMLKNLR*TN<YDVSER

Parental  ICRGLGIEY
          ...GL....
Retrocopy THWGLSTPF

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	34.06 RPM
SRP007412_cerebellum	0.12 RPM	26.39 RPM
SRP007412_heart	0.03 RPM	33.44 RPM
SRP007412_kidney	0.07 RPM	48.76 RPM
SRP007412_liver	0.03 RPM	43.45 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1310 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1310 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1310 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1594
Pan troglodytes	retro_ptro_1071
Callithrix jacchus	retro_cjac_761

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001463	1 retrocopy	retro_amel_1564,
Canis familiaris	ENSCAFG00000030390	1 retrocopy	retro_cfam_1939,
Callithrix jacchus	ENSCJAG00000001852	3 retrocopies	retro_cjac_3095, retro_cjac_761, retro_cjac_859,
Cavia porcellus	ENSCPOG00000010877	1 retrocopy	retro_cpor_430,
Dipodomys ordii	ENSDORG00000007581	1 retrocopy	retro_dord_118,
Felis catus	ENSFCAG00000005265	1 retrocopy	retro_fcat_915,
Homo sapiens	ENSG00000116898	1 retrocopy	retro_hsap_1594,
Myotis lucifugus	ENSMLUG00000006475	1 retrocopy	retro_mluc_1945,
Monodelphis domestica	ENSMODG00000017813	1 retrocopy	retro_mdom_1094,
Mus musculus	ENSMUSG00000028861	1 retrocopy	retro_mmus_3447,
Nomascus leucogenys	ENSNLEG00000011467	1 retrocopy	retro_nleu_615,
Otolemur garnettii	ENSOGAG00000002656	2 retrocopies	retro_ogar_1327, retro_ogar_16,
Pongo abelii	ENSPPYG00000001537	1 retrocopy	retro_pabe_1310 ,
Pan troglodytes	ENSPTRG00000000541	1 retrocopy	retro_ptro_1071,
Sus scrofa	ENSSSCG00000026393	1 retrocopy	retro_sscr_1190,
Ictidomys tridecemlineatus	ENSSTOG00000000608	1 retrocopy	retro_itri_454,
Tupaia belangeri	ENSTBEG00000000958	4 retrocopies	retro_tbel_1633, retro_tbel_4438, retro_tbel_845, retro_tbel_882,
Tarsius syrichta	ENSTSYG00000008948	2 retrocopies	retro_tsyr_1612, retro_tsyr_372,
Tursiops truncatus	ENSTTRG00000002345	1 retrocopy	retro_ttru_1500,