RetrogeneDB ID: retro_pabe_2153

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:108388505..108389134(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMB3
• Ensembl ID: ENSPPYG00000008505
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 3 [Source:HGNC Symbol;Acc:9540]

Sequence

>retro_pabe_2153
ATGCCTATTATGTCCTATAACGGAGGAGCCATCGTGGCCATGAAGGGGAAGAACTGTGCGGCCATCGCTGCAGACAGGCA
CTTTGGGATCCAGGCCCAGATGGTGACCACGGACTTCCAGGAGATCTTTCCCATGGGTGGTTGGTTGTACATCGGTCTGG
CTGGGCTTGCCACTGATGTCCAGACAGTTACCCAGTGCCTCAAGTTCCGGCTGAACCTATATGCGTTGAAGGAAGGTCAG
CAGATCAAACCTTATACCTTCACGAGCATGGTGGCCAGCCTCTTGTATGAGAAACATTTTGGCCCCTGCTACACTGAGCC
AGTCATTGCTGGTTTGGACCTGAAGACCTTTAAGCTCTTCAGTTGCTCTCTAGACCTCATCGGCTGCCCCATGGTGACTG
ATGACTTTGTGGTCAGTGGCAGCTATGCCGAACAAATGTACAGAATGTGCAAGTCCCTCTGGGAACCCAACATGGATCCA
GAACACCTGTTTGAAACTATCTCCCAAGCCATGCTGAATGCTGTGGACTAGGATGCAGGGTGAGGCATGGGAGTCATCAT
CCACATCACCAAGAAGGACAAAATCACCACGAGGACACTGAAGGCCCAAATGGACTAACCCTGTTCCCA

Alignment

ORF - retro_pabe_2153 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.89 %
• Parental protein coverage: 96.33 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSIMSYNGGAVMAMKGKNCVAIAADRRFGIQAQMVTTDFQKIFPMGDRLYIGLAGLATDVQTVAQRLKFR
          M.IMSYNGGA..AMKGKNC.AIAADR.FGIQAQMVTTDFQ.IFPMG..LYIGLAGLATDVQTV.Q.LKFR
Retrocopy MPIMSYNGGAIVAMKGKNCAAIAADRHFGIQAQMVTTDFQEIFPMGGWLYIGLAGLATDVQTVTQCLKFR

Parental  LNLYELKEGRQIKPYTLMSLVANLLYEKRFGPYYTEPVIAGLDPKTFKPFICSLDLIGCPMVTDDFVVSG
          LNLY.LKEG.QIKPYT..S.VA.LLYEK.FGP.YTEPVIAGLD.KTFK.F.CSLDLIGCPMVTDDFVVSG
Retrocopy LNLYALKEGQQIKPYTFTSMVASLLYEKHFGPCYTEPVIAGLDLKTFKLFSCSLDLIGCPMVTDDFVVSG

Parental  TCAEQMYGMCESLWEPNMDPEHLFETISQAMLNAVDRDAVSGMGVIVHIIEKDKITTRTLKARI-GLTLF
          ..AEQMY.MC.SLWEPNMDPEHLFETISQAMLNAVD.DA..GMGVI.HI..KDKITTRTLKA...GLTLF
Retrocopy SYAEQMYRMCKSLWEPNMDPEHLFETISQAMLNAVD*DAG*GMGVIIHITKKDKITTRTLKAQM<GLTLF

Parental  P
          P
Retrocopy P

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	0.28 RPM	21.40 RPM
SRP007412_cerebellum	0.73 RPM	19.58 RPM
SRP007412_heart	0.15 RPM	28.81 RPM
SRP007412_kidney	0.36 RPM	39.54 RPM
SRP007412_liver	0.64 RPM	46.97 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2153 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2153 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2153 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2387
Gorilla gorilla	retro_ggor_103
Callithrix jacchus	retro_cjac_2852

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016587	2 retrocopies	retro_cfam_135, retro_cfam_532,
Callithrix jacchus	ENSCJAG00000008246	1 retrocopy	retro_cjac_2852,
Equus caballus	ENSECAG00000000987	1 retrocopy	retro_ecab_476,
Erinaceus europaeus	ENSEEUG00000015275	1 retrocopy	retro_eeur_10,
Loxodonta africana	ENSLAFG00000002233	1 retrocopy	retro_lafr_70,
Macropus eugenii	ENSMEUG00000004131	2 retrocopies	retro_meug_1804, retro_meug_551,
Microcebus murinus	ENSMICG00000002997	1 retrocopy	retro_mmur_397,
Macaca mulatta	ENSMMUG00000012363	1 retrocopy	retro_mmul_868,
Monodelphis domestica	ENSMODG00000012614	2 retrocopies	retro_mdom_1722, retro_mdom_1812,
Mus musculus	ENSMUSG00000069744	8 retrocopies	retro_mmus_1449, retro_mmus_1551, retro_mmus_1790, retro_mmus_1938, retro_mmus_2110, retro_mmus_41, retro_mmus_46, retro_mmus_536,
Oryctolagus cuniculus	ENSOCUG00000002598	1 retrocopy	retro_ocun_561,
Pongo abelii	ENSPPYG00000008505	2 retrocopies	retro_pabe_2153 , retro_pabe_927,
Pteropus vampyrus	ENSPVAG00000002270	1 retrocopy	retro_pvam_822,
Rattus norvegicus	ENSRNOG00000012938	7 retrocopies	retro_rnor_1016, retro_rnor_2094, retro_rnor_2448, retro_rnor_2537, retro_rnor_2804, retro_rnor_743, retro_rnor_8,
Ictidomys tridecemlineatus	ENSSTOG00000014258	3 retrocopies	retro_itri_527, retro_itri_935, retro_itri_936,