RetrogeneDB ID: retro_pabe_1606

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 18:76237671..76238376(-)
• Located in intron of: ENSPPYG00000009214

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMC5
• Ensembl ID: ENSPPYG00000008533
• Aliases: None
• Description: 26S protease regulatory subunit 8 [Source:RefSeq peptide;Acc:NP_001127417]

Sequence

>retro_pabe_1606
GATGGACCAGAGCAGATGGAGCTGGAAGAGGGGAAGACAGGCAACAGACTCTGCCAGTATTATCTGTCTGAGACTGAAGA
ACTCCAGTCAGTTGTGAATGATAAGAGCCAGGACCTCCAGAGGCTGCAGGCACAAAGGAATGAACTAAATGCAAAAGTTC
ACCTATTGCAGGAGGAGCTACAGCTTCTGCAGGAACAGGGCTCCTGTATGAGGGAAGTAGTCCGGGCCATGGGTAAGAAG
AAAGTGTTAGTCAAGGTGTATCCCAAGGGCAGGTTTGTCTTAGATGTGGACAGAAAGAGCGACATCAATGACATGAGACC
TAATTGCCAGGGGGCGCTAAGAAATGATAGCTACACACTGCACAATATCATACCCAGCAAAGTAGACCCACTGGTGTCAC
CAGTGATGGTGGAGAAGGTGCCAACCTTGATTTAAGAGATGATAGGTGGACTGGACAAGCAGATTAAGGACATCACAGAA
GTGATCGAGCCGCCTGTTAAGCATCCCAAGCTCTTTGAAGCACTGGGTATCACACAACCCAGGGTGGTACTGCTGTACGG
ACCTCTAGGCACTGGGAAGACACTGTTTGCCTCGGCCATGGCTCACCATACAGACTGTACCTTTGTTCATATCCCTGGCT
CTGAATTGGTATAGAAGTTCATCAGGAAAGGGCCAAGAATGGTGAGGGAGCTGTTTGTCATGGCA

Alignment

ORF - retro_pabe_1606 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.6 %
• Parental protein coverage: 57.88 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DGPEQMELEEGKAGSGLRQYYLSKIEELQLIVNDKSQNLRRLQAQRNELNAKVRLLREELQLLQEQGSYV
          DGPEQMELEEGK.G..L.QYYLS..EELQ..VNDKSQ.L.RLQAQRNELNAKV.LL.EELQLLQEQGS..
Retrocopy DGPEQMELEEGKTGNRLCQYYLSETEELQSVVNDKSQDLQRLQAQRNELNAKVHLLQEELQLLQEQGSCM

Parental  GEVVRAMDKKKVLVKVHPEGKFVVDVDKNIDINDVTPNCRVALRNDSYTLHKILPNKVDPLVSLMMVEKV
          .EVVRAM.KKKVLVKV.P.G.FV.DVD...DIND..PNC..ALRNDSYTLH.I.P.KVDPLVS..MVEKV
Retrocopy REVVRAMGKKKVLVKVYPKGRFVLDVDRKSDINDMRPNCQGALRNDSYTLHNIIPSKVDPLVSPVMVEKV

Parental  PDSTYEMIGGLDKQIKEIKEVIELPVKHPELFEALGIAQPKGVLLYGPPGTGKTLLARAVAHHTDCTFIR
          P....EMIGGLDKQIK.I.EVIE.PVKHP.LFEALGI.QP..VLLYGP.GTGKTL.A.A.AHHTDCTF..
Retrocopy PTLI*EMIGGLDKQIKDITEVIEPPVKHPKLFEALGITQPRVVLLYGPLGTGKTLFASAMAHHTDCTFVH

Parental  VSGSELVQKFIGEGARMVRELFVMA
          ..GSELV.KFI..G.RMVRELFVMA
Retrocopy IPGSELV*KFIRKGPRMVRELFVMA

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	0.11 RPM	184.17 RPM
SRP007412_cerebellum	0.85 RPM	168.30 RPM
SRP007412_heart	0.09 RPM	64.51 RPM
SRP007412_kidney	0.40 RPM	161.59 RPM
SRP007412_liver	0.28 RPM	69.13 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1606 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1606 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1606 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1303

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000002393	1 retrocopy	retro_dnov_1508,
Homo sapiens	ENSG00000087191	1 retrocopy	retro_hsap_1949,
Gorilla gorilla	ENSGGOG00000006803	1 retrocopy	retro_ggor_1418,
Macaca mulatta	ENSMMUG00000016769	1 retrocopy	retro_mmul_1354,
Monodelphis domestica	ENSMODG00000009873	2 retrocopies	retro_mdom_1411, retro_mdom_1583,
Nomascus leucogenys	ENSNLEG00000004150	1 retrocopy	retro_nleu_1480,
Oryctolagus cuniculus	ENSOCUG00000004329	1 retrocopy	retro_ocun_78,
Otolemur garnettii	ENSOGAG00000008296	1 retrocopy	retro_ogar_911,
Procavia capensis	ENSPCAG00000002653	1 retrocopy	retro_pcap_352,
Pongo abelii	ENSPPYG00000008533	1 retrocopy	retro_pabe_1606 ,
Pan troglodytes	ENSPTRG00000009525	1 retrocopy	retro_ptro_1303,
Ictidomys tridecemlineatus	ENSSTOG00000008945	1 retrocopy	retro_itri_1046,
Tupaia belangeri	ENSTBEG00000010546	3 retrocopies	retro_tbel_1411, retro_tbel_2422, retro_tbel_3450,
Tursiops truncatus	ENSTTRG00000006984	1 retrocopy	retro_ttru_1532,