RetrogeneDB ID: retro_pabe_2528

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:80444862..80445548(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBFD1
• Ensembl ID: ENSPPYG00000007191
• Aliases: None
• Description: ubiquitin family domain containing 1 [Source:HGNC Symbol;Acc:30565]

Sequence

>retro_pabe_2528
GCCCTAGCCCAGGCCCCTGGAGACCCCGTGTCCCAGGCTTCCGTCAGTAACAGCGAAGACACGGGCGGCAGCGCAGACAG
GGAGCTGGTGGACTTGAAGATCATCTGGAACAAGACCAAGCACGACGTGAAGTTCCACCTGGACAGCACAGGCTCCGAAC
TGAAACAGAAGATCCACTGATTACAGGTCTCCCGCCTGCCATACAGAAAGTCATGTATAAGGGACTCGTCCCTGAGGATA
AGACATTGAGAGAAATAAAAGTGACCAGTGGGGCCAAGATCATGGTGGTTGGCTCCACCATCAATGATGTTTTAGCAGTA
AACACACCCAAAGGTGCCGCGCAGCAGGATGCAAAGGCCGAAGACAACAAGAAGAAGCCTCTCTGCAGGCAGAAACAACA
CAGGAAAGTGTTGAATAAAGGAAAACCCGAAGATGTGATGCCATCTGTTAAGGGGGCCCAGGAGCACCTACCAAAGGTAC
CCCTGTCCAGCATGTACAATAAGTCCGGAGGAAAAGTGAGATTCACCTTGAAGTTAGAACAACACCAGCTGTGGATTGGC
ACTAAAGAGTGGACTGAGAAATTGCACATGGGCTCCATAAAAAATGTGGTCAGTGAACCTATGGAAGGACATGAAGACTA
CCACATGATGACGTTTCAGTTGGGCCCCACGAAAGCCTCTTACTAC

Alignment

ORF - retro_pabe_2528 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.26 %
• Parental protein coverage: 74.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  APAQPPGDPAAQASVSNGEDAGGGAGRELVDLKIIWNKTKHDVKFPLDSTGSELKQKIH-SITGLPPAMQ
          A.AQ.PGDP..QASVSN.ED.GG.A.RELVDLKIIWNKTKHDVKF.LDSTGSELKQKIH..ITGLPPA.Q
Retrocopy ALAQAPGDPVSQASVSNSEDTGGSADRELVDLKIIWNKTKHDVKFHLDSTGSELKQKIH<LITGLPPAIQ

Parental  KVMYKGLVPEDKTLREIKVTSGAKIMVVGSTINDVLAVNTPKDAAQQDAKAEENKKEPLCRQKQHRKVLD
          KVMYKGLVPEDKTLREIKVTSGAKIMVVGSTINDVLAVNTPK.AAQQDAKAE.NKK.PLCRQKQHRKVL.
Retrocopy KVMYKGLVPEDKTLREIKVTSGAKIMVVGSTINDVLAVNTPKGAAQQDAKAEDNKKKPLCRQKQHRKVLN

Parental  KGKPEDVMPSVKGAQERLPTVPLSGMYNKSGGKVRLTFKLEQDQLWIGTKERTEKLPMGSIKNVVSEPIE
          KGKPEDVMPSVKGAQE.LP.VPLS.MYNKSGGKVR.T.KLEQ.QLWIGTKE.TEKL.MGSIKNVVSEP.E
Retrocopy KGKPEDVMPSVKGAQEHLPKVPLSSMYNKSGGKVRFTLKLEQHQLWIGTKEWTEKLHMGSIKNVVSEPME

Parental  GHEDYHMMAFQLGPTEASYY
          GHEDYHMM.FQLGPT.ASYY
Retrocopy GHEDYHMMTFQLGPTKASYY

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	68.51 RPM
SRP007412_cerebellum	0.00 RPM	73.08 RPM
SRP007412_heart	0.00 RPM	28.45 RPM
SRP007412_kidney	0.00 RPM	44.02 RPM
SRP007412_liver	0.03 RPM	31.43 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2528 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2528 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2528 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000029331	2 retrocopies	retro_acar_106, retro_acar_204,
Canis familiaris	ENSCAFG00000017670	1 retrocopy	retro_cfam_1952,
Monodelphis domestica	ENSMODG00000006727	2 retrocopies	retro_mdom_1162, retro_mdom_1298,
Pongo abelii	ENSPPYG00000007191	1 retrocopy	retro_pabe_2528 ,