RetrogeneDB ID: retro_pabe_1107

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 14:50005833..50006268(+)
• Located in intron of: ENSPPYG00000005787

Retrocopy information

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

Parental gene information

• Parental gene symbol: RHOQ
• Ensembl ID: ENSPPYG00000012439
• Aliases: None
• Description: ras homolog family member Q [Source:HGNC Symbol;Acc:17736]

Sequence

>retro_pabe_1107
CTATATAACACGGCCGGACAGGAAGACTATGACCGTCTGAGGCCTTTATCTTACCCAATGACCAACGTCTTCCTTTTATG
CTTCTCGGTGGTAAATCCAGCCTCATTTCAAAATGTGAAAGAGGAGTGAGTACCGGAACTTAAGGAATACGCACCAAATG
TACCCTTTTTATTAATAGGAATTCAGATTGATCTCCGAGATGACCCCAAAACTTTAGCAAGACTGAATGATATGAAAGAA
AAGCCTATATGTGTGGAACAAGGACAGAAACTAGCAAAAGAGATAGGAGCATGCTGCTATGTGGAATGTTCAGCTTTAAC
CCAGAAGGGATTGAAGACTGTTTTTGATGAGGCTATCATAGCCATTTTAACTCCAAAGAAACACACTGTAAAAAAAAGAA
TAGGATCAAGATGTATAAACTATTGTTTAATTACG

Alignment

ORF - retro_pabe_1107 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.1 %
• Parental protein coverage: 63.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LYDTAGQEDYDRLRPLSYPMTDVFLICFSVVNPASFQNVKEEWVPELKEYAPNVPFLLIGTQIDLRDDPK
          LY.TAGQEDYDRLRPLSYPMT.VFL.CFSVVNPASFQNVKEE.VPELKEYAPNVPFLLIG.QIDLRDDPK
Retrocopy LYNTAGQEDYDRLRPLSYPMTNVFLLCFSVVNPASFQNVKEE*VPELKEYAPNVPFLLIGIQIDLRDDPK

Parental  TLARLNDMKEKPICVEQGQKLAKEIGACCYVECSALTQKGLKTVFDEAIIAILTPKKHTVKKRIGSRCIN
          TLARLNDMKEKPICVEQGQKLAKEIGACCYVECSALTQKGLKTVFDEAIIAILTPKKHT....IGSRCIN
Retrocopy TLARLNDMKEKPICVEQGQKLAKEIGACCYVECSALTQKGLKTVFDEAIIAILTPKKHTXXXXIGSRCIN

Parental  CCLIT
          .CLIT
Retrocopy YCLIT

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	0.11 RPM	3.54 RPM
SRP007412_cerebellum	0.12 RPM	1.09 RPM
SRP007412_heart	0.09 RPM	25.29 RPM
SRP007412_kidney	0.03 RPM	3.55 RPM
SRP007412_liver	0.06 RPM	1.47 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1107 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1107 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1107 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1333
Pan troglodytes	retro_ptro_910

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000549	3 retrocopies	retro_chof_2030, retro_chof_457, retro_chof_914,
Callithrix jacchus	ENSCJAG00000000685	1 retrocopy	retro_cjac_2403,
Erinaceus europaeus	ENSEEUG00000015226	1 retrocopy	retro_eeur_129,
Homo sapiens	ENSG00000119729	3 retrocopies	retro_hsap_1333, retro_hsap_2158, retro_hsap_2316,
Loxodonta africana	ENSLAFG00000004327	1 retrocopy	retro_lafr_316,
Microcebus murinus	ENSMICG00000009124	1 retrocopy	retro_mmur_29,
Otolemur garnettii	ENSOGAG00000033272	1 retrocopy	retro_ogar_742,
Pongo abelii	ENSPPYG00000001755	6 retrocopies	retro_pabe_2240, retro_pabe_2461, retro_pabe_2801, retro_pabe_3215, retro_pabe_3239, retro_pabe_3295,
Pongo abelii	ENSPPYG00000008763	2 retrocopies	retro_pabe_1047, retro_pabe_2546,
Pongo abelii	ENSPPYG00000011791	3 retrocopies	retro_pabe_1591, retro_pabe_21, retro_pabe_3818,
Pongo abelii	ENSPPYG00000012439	2 retrocopies	retro_pabe_1107 , retro_pabe_2195,
Pteropus vampyrus	ENSPVAG00000013691	1 retrocopy	retro_pvam_611,
Rattus norvegicus	ENSRNOG00000015415	1 retrocopy	retro_rnor_473,
Sus scrofa	ENSSSCG00000008439	1 retrocopy	retro_sscr_102,
Tarsius syrichta	ENSTSYG00000002837	1 retrocopy	retro_tsyr_1609,