RetrogeneDB ID: retro_pabe_3271

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:84166737..84167088(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2H
• Ensembl ID: ENSPPYG00000017997
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2H [Source:HGNC Symbol;Acc:12484]

Sequence

>retro_pabe_3271
TCAGAGGGATTGGTGAATAAAATTTTCCATCCCAACATTGATGACGTGTCAGGAACTGCGTGTCTAGATGTAATTAATCA
AACTTGGACAGCTCTCTATGATCTTACCAATATATTTGAGTCCTTCCTGCCCCAGTTGTTGGCCTATCCTAACCCCATAG
ATCCTCTCAATGGTGAAGATGCAGCCATGTACCTCCAAAGACCAGAAGAATACAAGCAGAAAATTAGAGAGTAAATCCAG
AAATATGCCACGGAGCAGGCGCTGAAAGAGCAGGAAGAGGGTACCAGTGACAGCTCATTGGAGAGCTCTATATCTGACTT
TTCCGAAGATGAGGCCCAGGATATGGAGTTG

Alignment

ORF - retro_pabe_3271 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.18 %
• Parental protein coverage: 63.93 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SIGFMNKIFHPNIDEASGTVCLDVINQTWTALYDLTNIFESFLPQLLAYPNPIDPLNGDAAAMYLHRPEE
          S.G..NKIFHPNID..SGT.CLDVINQTWTALYDLTNIFESFLPQLLAYPNPIDPLNG..AAMYL.RPEE
Retrocopy SEGLVNKIFHPNIDDVSGTACLDVINQTWTALYDLTNIFESFLPQLLAYPNPIDPLNGEDAAMYLQRPEE

Parental  YKQKIKEYIQKYATEEALKEQEEGTGDSSSESSMSDFSEDEAQDMEL
          YKQKI.E.IQKYATE.ALKEQEEGT.DSS.ESS.SDFSEDEAQDMEL
Retrocopy YKQKIRE*IQKYATEQALKEQEEGTSDSSLESSISDFSEDEAQDMEL

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	0.06 RPM	143.53 RPM
SRP007412_cerebellum	0.00 RPM	138.14 RPM
SRP007412_heart	0.00 RPM	75.32 RPM
SRP007412_kidney	0.00 RPM	100.73 RPM
SRP007412_liver	0.00 RPM	61.30 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3271 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3271 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3271 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3977

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003605	2 retrocopies	retro_chof_1862, retro_chof_1932,
Callithrix jacchus	ENSCJAG00000010520	1 retrocopy	retro_cjac_1081,
Homo sapiens	ENSG00000186591	1 retrocopy	retro_hsap_3977,
Nomascus leucogenys	ENSNLEG00000012685	1 retrocopy	retro_nleu_2037,
Pongo abelii	ENSPPYG00000017997	1 retrocopy	retro_pabe_3271 ,
Rattus norvegicus	ENSRNOG00000048205	2 retrocopies	retro_rnor_2188, retro_rnor_2266,