RetrogeneDB ID: retro_pabe_3660

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:72658987..72659302(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BUD31
• Ensembl ID: ENSPPYG00000017376
• Aliases: None
• Description: BUD31 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:29629]

Sequence

>retro_pabe_3660
GGAAAGTGGAAAGTGGAATCTCTGTTGCCCATCTTCAGGATCTACCACCAGAAAATCCACCATATCGTTGACTTTGTTTA
TAAGTGGAAAGTCATAACCAGAGCACTCTATGAATATTGTATTAAAGAAGGCTATGCAGGAAAAAACTTAATCACAATAT
GGAAAAAGCAAGGCTATGAGAACTTGTGCTGGTTGCTGTGCCTTCAGACACGGAACACCAATTTTGGGACAAACTGCAAT
TGCTCCGTTCCTAAAACAAAGATAGAAGTGGGCTGCATCATTGAGTGCATGCACTGTGGCTGCCAGGGCTGCTCT

Alignment

ORF - retro_pabe_3660 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.29 %
• Parental protein coverage: 72.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GKRKVESLWPIFRIHHQKTRYIFDLFYKRKAISRELYEYCIKEGYADKNLIAKWKKQGYENLCCLRCIQT
          GK.KVESL.PIFRI.HQK...I.D..YK.K.I.R.LYEYCIKEGYA.KNLI..WKKQGYENLC.L.C.QT
Retrocopy GKWKVESLLPIFRIYHQKIHHIVDFVYKWKVITRALYEYCIKEGYAGKNLITIWKKQGYENLCWLLCLQT

Parental  RDTNFGTNCICRVPKSKLEVGRIIECTHCGCRGCS
          R.TNFGTNC.C.VPK.K.EVG.IIEC.HCGC.GCS
Retrocopy RNTNFGTNCNCSVPKTKIEVGCIIECMHCGCQGCS

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	5.69 RPM
SRP007412_cerebellum	0.00 RPM	6.57 RPM
SRP007412_heart	0.00 RPM	2.68 RPM
SRP007412_kidney	0.00 RPM	5.20 RPM
SRP007412_liver	0.00 RPM	5.66 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3660 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3660 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3660 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4712
Gorilla gorilla	retro_ggor_2928

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006269	2 retrocopies	retro_amel_1325, retro_amel_997,
Bos taurus	ENSBTAG00000020439	1 retrocopy	retro_btau_1066,
Choloepus hoffmanni	ENSCHOG00000004055	1 retrocopy	retro_chof_1013,
Dipodomys ordii	ENSDORG00000000739	1 retrocopy	retro_dord_58,
Equus caballus	ENSECAG00000024151	2 retrocopies	retro_ecab_254, retro_ecab_672,
Ficedula albicollis	ENSFALG00000013804	1 retrocopy	retro_falb_27,
Homo sapiens	ENSG00000106245	1 retrocopy	retro_hsap_4712,
Gorilla gorilla	ENSGGOG00000015119	1 retrocopy	retro_ggor_2928,
Loxodonta africana	ENSLAFG00000012201	1 retrocopy	retro_lafr_24,
Macropus eugenii	ENSMEUG00000006920	1 retrocopy	retro_meug_446,
Microcebus murinus	ENSMICG00000017426	2 retrocopies	retro_mmur_470, retro_mmur_622,
Nomascus leucogenys	ENSNLEG00000011020	1 retrocopy	retro_nleu_2053,
Pongo abelii	ENSPPYG00000017376	2 retrocopies	retro_pabe_3313, retro_pabe_3660 ,
Pan troglodytes	ENSPTRG00000019451	1 retrocopy	retro_ptro_2735,
Pteropus vampyrus	ENSPVAG00000007527	1 retrocopy	retro_pvam_474,
Rattus norvegicus	ENSRNOG00000000989	1 retrocopy	retro_rnor_1852,
Tupaia belangeri	ENSTBEG00000010640	2 retrocopies	retro_tbel_2683, retro_tbel_4119,
Tursiops truncatus	ENSTTRG00000003005	1 retrocopy	retro_ttru_815,