RetrogeneDB ID: retro_tbel_1411

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_4626:230396..231014(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMC5
• Ensembl ID: ENSTBEG00000010546
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, ATPase, 5 [Source:HGNC Symbol;Acc:9552]

Sequence

>retro_tbel_1411
ATGAGCATGGAAAAGGCCCTGCAGGAGACCTATGCCGATACTGGGGTGTTGGACAACCAAATCCAGGAGATTAAGGAATC
TGTGCAACTTCTTCTCATCCATCCTGAATATGAAGAAGGAAGGGTATAAAGTCCCCTAAGGGGGTCATTCTCTGTGGTCC
CCCGGCACAGGTAAAACTTTAGTAGCCAAAGCAGTTGCAAACCAAACTTCAGCCACTTTCTTGAGAGTGGTTGACTCTGA
ACTTAATCAGAAGCACCTGGGTGATGGGCCTAAACTTGTACGGGCACTGTTTCGAGTTGCTGAAGGTCATGCACCATCCA
TCATATTTATTGATGAAATCGGTGCCATTGGGACAAAAAGATAGGACTCAAATTCTGGTGATGAAAGAGAAATTCAGCGA
GCAATGTTGGAACTGTCGAACCAGCTGGATGGATTTGATTCAAGGGGAGATGTGAAAGTTATCATGGCCACAAACTGGAC
AGGAACTGGATCCAGCGCTTATTAGACCAGGCCGCATTGAACAGGAAGATTGTGTTCTCCTTGCCCGATGAAAAGACCAA
CAGGTGCAGATTTCAGATTCCCACAAGCAGGATGACACTGGCTGATGGTGTAACTCTG

Alignment

ORF - retro_tbel_1411 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.95 %
• Parental protein coverage: 52.55 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MMVEKVPDSTYEMIGGLDKQIKEIKEVIELPVKHPELFEAL-GIAQPKGVLLYGP-PGTGKTLLARAVAH
          M..EK....TY...G.LD.QI.EIKE...L...HPE..E...GI..PKGV.L.GP.PGTGKTL.A.AVA.
Retrocopy MSMEKALQETYADTGVLDNQIQEIKESVQLLLIHPEYEEGR<GIKSPKGVILCGP<PGTGKTLVAKAVAN

Parental  HTDCTFIRVSGSELVQKFIGEGARMVRELFVMAREHAPSIIFMDEIDSIGSSRLEGGSGGDSEVQRTMLE
          .T..TF.RV..SEL.QK..G.G...VR.LF..A..HAPSIIF.DEI..IG..R....SG...E.QR.MLE
Retrocopy QTSATFLRVVDSELNQKHLGDGPKLVRALFRVAEGHAPSIIFIDEIGAIGTKR*DSNSGDEREIQRAMLE

Parental  LLNQLDGFEATKNIKVIMATNRIDILDSA-LLRPGRIDRKIEFPPPNEEA-RDILKIHSRKMNLTRGINL
          L.NQLDGF......KVIMATN......SA.LL......RKI.F..P.E...R....I....M.L..G..L
Retrocopy LSNQLDGFDSRGDVKVIMATNWTGTGSSA<LLDQAALNRKIVFSLPDEKTNRCRFQIPTSRMTLADGVTL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_1411 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1411 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,