RetrogeneDB ID: retro_pabe_3720

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:8592420..8592765(-)
• 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_3720
TCACTCTTCCTTTGTGGGACTGAGACACTGTGGTTTAATCTGGATCGACCTTGTATGGAAGAGACAGAGCTGCAGCAGCA
GGAACAGCAGCATCAGACCTGGCTCGAAAGCATCACAGAGAAAGACAACAATCTGGTTCCTATTGGCAAGCCAGCCTCAG
AGCACTATGATGAAGAGGAAGAGGAGGATGATGAAGACAATGAGGATAGTGAAGAGGACTTAGAGGATGATGAGGACATG
CGGGACATGGACAAGATGAATGACTACTATGAGTCACCTGATGACGGAGAGGTCAATGAGGTGGACGTGGAAGGCAACGA
ACAGGATCAGGACCAGTGGATGATC

Alignment

ORF - retro_pabe_3720 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.83 %
• Parental protein coverage: 95.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SLFPRVTETLWFNLDRPCVEETELQQQEQQHQAWLQSIAEKDNNLVPIGKPASEHYDDEEEEDDEDDEDS
          SLF...TETLWFNLDRPC.EETELQQQEQQHQ.WL.SI.EKDNNLVPIGKPASEHYD.EEEEDDED.EDS
Retrocopy SLFLCGTETLWFNLDRPCMEETELQQQEQQHQTWLESITEKDNNLVPIGKPASEHYDEEEEEDDEDNEDS

Parental  EEDSEDDEDMQDMDEMNDYNESPDDGEVNEVDMEGNEQDQDQWMI
          EED.EDDEDM.DMD.MNDY.ESPDDGEVNEVD.EGNEQDQDQWMI
Retrocopy EEDLEDDEDMRDMDKMNDYYESPDDGEVNEVDVEGNEQDQDQWMI

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	0.00 RPM	0.52 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3720 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3720 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3720 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4780
Gorilla gorilla	retro_ggor_2977
Macaca mulatta	retro_mmul_2551

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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,