RetrogeneDB ID: retro_pcap_352

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_46972:4201..5082(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMC5
• Ensembl ID: ENSPCAG00000002653
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, ATPase, 5 [Source:HGNC Symbol;Acc:9552]

Sequence

>retro_pcap_352
GTAGACAAGGATCTGCTGGAGCCAGGCTGCTCCGTCCTGCTCAACCACAAGGTGCACGCAGTGATAGGGCTGTTGATGGA
TGACACTGATCCCCTGGTCACAGTGATGAAGGTGGAAAAGGCCCCCCAGGAGACCTATGCTGACATTGGGGGACTGGACA
ACCAAATTCAGGAAATTAAGGAATCTGTGGAGCTTCCTCTCACTCATCCTGAATATTATGAAGAGATGGGTATAAAACCT
CCTAAGGGGGTCATTCTGTATGGTCCACCTGGCACAGGTAAAACGTTATTAGCCAAAGCAGTAGCAAACCAAACCTCAGC
CACTTTCTTGAGAGTGGTGGGCTCCGAATTGATTCAGAAATACCTGGGAGATGAGCCCAAACTTGTGCGGGAATTGTTTC
ATGTTGAGGAGGAACATGCCCCGTCGATTGTGTTCATACATGAGATCGATGTCATTGGGATTAAAAGATGCGACTCAAAT
TCTGGTGGTGCGAGAGAAATTCAGCGGACGATGTTGGAGCTGTTGAACCAGTTGGATGGGTTTGATTTAAGAGGAGATGT
TAAAGTTATCATGGCCACAAACTGAATAGAAACATTAGACCCACACTCATCAGACCAGGCCGCACTGACCGCAAGATCAA
GCTCCCCCTGCCCGATGAGAAGACCAAGAAGCGCATCTTTCAGAGCCACACCAGCAGGATGACGCTGGTCGATGATGTGA
CTTTAGACAACTTAATCATGGCTAAAGATGACCTCTCTGGGGCTGACATCAAGGCAATCTGTACAGAAGCTGGGCTCATG
GACTTGAGAGAACGTAGGATGAAAGTCACAAATGAAGATTTCAAAAAGTCAAAAGAAAACGTCCTGTATAAGAAACAGGA
A

Alignment

ORF - retro_pcap_352 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.86 %
• Parental protein coverage: 72.41 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IDINDVTPNCRVALRNDSYTLHKILPNKVDPLVSLMMVEKVPDSTYEMIGGLDKQIKEIKEVIELPVKHP
          .D.....P.C.V.L..........L....DPLV..M.VEK.P..TY..IGGLD.QI.EIKE..ELP..HP
Retrocopy VDKDLLEPGCSVLLNHKVHAVIGLLMDDTDPLVTVMKVEKAPQETYADIGGLDNQIQEIKESVELPLTHP

Parental  ELFEALGIAQPKGVLLYGPPGTGKTLLARAVAHHTDCTFIRVSGSELVQKFIGEGARMVRELFVMAREHA
          E..E..GI..PKGV.LYGPPGTGKTLLA.AVA..T..TF.RV.GSEL.QK..G.....VRELF....EHA
Retrocopy EYYEEMGIKPPKGVILYGPPGTGKTLLAKAVANQTSATFLRVVGSELIQKYLGDEPKLVRELFHVEEEHA

Parental  PSIIFMDEIDSIGSSRLEGGSGGDSEVQRTMLELLNQLDGFEATKNIKVIMATNRIDILD-SALLRPGRI
          PSI.F..EID.IG..R....SGG..E.QRTMLELLNQLDGF......KVIMATN.I..LD...L.RPGR.
Retrocopy PSIVFIHEIDVIGIKRCDSNSGGAREIQRTMLELLNQLDGFDLRGDVKVIMATN*IETLD<PTLIRPGRT

Parental  DRKIEFPPPNEEARLDILKIHSRKRNLTRGINLRKIAELMPGASGAEVKGVCTEAGMYALRERRVHVTQE
          DRKI..P.P.E.....I...H.....L.....L..........SGA..K..CTEAG...LRERR..VT.E
Retrocopy DRKIKLPLPDEKTKKRIFQSHTSRMTLVDDVTLDNLIMAKDDLSGADIKAICTEAGLMDLRERRMKVTNE

Parental  DFEMAVAKVMQKDSE
          DF......V..K..E
Retrocopy DFKKSKENVLYKKQE

Legend:

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

Expression

RNA-Seq

Procavia capensis was not studied using RNA-Seq expression data.

ChIP-Seq

Procavia capensis was not studied using ChIP-Seq data.

EST

Procavia capensis was not studied using EST data.

TSS

Procavia capensis was not studied using FANTOM5 data.

Lab

retro_pcap_352 was not experimentally validated.

Homology

Retrocopy orthology:

Procavia capensis 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,