RetrogeneDB ID: retro_pabe_2388

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:177961462..177961777(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ANAPC15
• Ensembl ID: ENSPPYG00000003646
• Aliases: None
• Description: anaphase promoting complex subunit 15 [Source:HGNC Symbol;Acc:24531]

Sequence

>retro_pabe_2388
CCGGAAGTGACTGATATATTGTGATTTAAATCTATATTGAACCTGTGTAGAGGAGACAGAGCTGCAGCAGCAGGAACAGC
AGCATCAGGCCTGTAGCTTCACAGAGAAAGACAACAACCTGTTTCCTGAGCCAGGCTCAAAGCACTATGAGGATGAGGGG
GAGGAGTATGAAGATGAGGAGGATAGTAAAGAATGGAGGATGAGCACATGCAGGACATGGATGACATGAATGATTTCAAT
GAGTAACCTGGTGATGGAGACACCAATGATGTGGATGTGGGAGGCAACAAACAGGATCAGGACAAGTGGACAATC

Alignment

ORF - retro_pabe_2388 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.14 %
• Parental protein coverage: 92.56 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PRVTETLWF-NLDRPCVEETELQQQEQQHQAWLQSIAEKDNNLVPIGKPASEHYDDEEEEDDEDDEDSEE
          P.VT..L.F.NL...CVEETELQQQEQQHQA...S..EKDNNL.P...P.S.HY.D...E..E.......
Retrocopy PEVTDIL*F>NLY*TCVEETELQQQEQQHQAC--SFTEKDNNLFP--EPGSKHYED---EGEEYEDEEDS

Parental  DS-EDDEDMQDMDEMNDYNESPDDGEVNEVDMEGNEQDQDQWMI
          .....DE.MQDMD.MND.NE.P.DG..N.VD..GN.QDQD.W.I
Retrocopy KE<MEDEHMQDMDDMNDFNE*PGDGDTNDVDVGGNKQDQDKWTI

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	2.05 RPM
SRP007412_cerebellum	0.00 RPM	0.97 RPM
SRP007412_heart	0.00 RPM	0.96 RPM
SRP007412_kidney	0.00 RPM	2.12 RPM
SRP007412_liver	0.03 RPM	0.52 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2388 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2388 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2388 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1999
Bos taurus	retro_btau_269
Equus caballus	retro_ecab_470

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010843	1 retrocopy	retro_amel_298,
Bos taurus	ENSBTAG00000002999	2 retrocopies	retro_btau_252, retro_btau_269,
Canis familiaris	ENSCAFG00000005781	1 retrocopy	retro_cfam_1752,
Equus caballus	ENSECAG00000021041	1 retrocopy	retro_ecab_470,
Felis catus	ENSFCAG00000005321	1 retrocopy	retro_fcat_1350,
Homo sapiens	ENSG00000110200	1 retrocopy	retro_hsap_4780,
Myotis lucifugus	ENSMLUG00000014120	1 retrocopy	retro_mluc_238,
Macaca mulatta	ENSMMUG00000016270	1 retrocopy	retro_mmul_2551,
Mustela putorius furo	ENSMPUG00000010260	1 retrocopy	retro_mputfur_596,
Nomascus leucogenys	ENSNLEG00000017234	1 retrocopy	retro_nleu_1100,
Pongo abelii	ENSPPYG00000003646	2 retrocopies	retro_pabe_2388 , retro_pabe_3720,
Pteropus vampyrus	ENSPVAG00000015797	1 retrocopy	retro_pvam_404,
Sorex araneus	ENSSARG00000004171	2 retrocopies	retro_sara_444, retro_sara_686,
Tarsius syrichta	ENSTSYG00000014179	1 retrocopy	retro_tsyr_35,
Tursiops truncatus	ENSTTRG00000010773	1 retrocopy	retro_ttru_277,